2022
Nolen, Haley B; Smith, Cheryl; Davis, TM; A., Poleatewich
Evaluation of disease severity and molecular relationships among Peronospora variabilis isolates on Chenopodium species in New Hampshire. Journal Article
In: Plant Disease, vol. 106, no. 2, pp. 564-571, 2022.
@article{27202,
title = {Evaluation of disease severity and molecular relationships among Peronospora variabilis isolates on Chenopodium species in New Hampshire.},
author = { Haley B Nolen and Cheryl Smith and TM Davis and Poleatewich A.},
year = {2022},
date = {2022-01-01},
journal = {Plant Disease},
volume = {106},
number = {2},
pages = {564-571},
abstract = {Quinoa is a potential new crop for New England; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle for cultivation. The objectives of this study were to evaluate differential resistance within the Chenopodium genus, identify novel sources of resistance for use in future genetic studies or breeding programs, and investigate phylogenetic relationships of P. variabilis isolates from different Chenopodium hosts. The long-term goal of this research is to develop a resistant variety of quinoa to be grown in New England. Field trials conducted at the University of New Hampshire evaluated downy mildew disease severity on 10 Chenopodium accessions representing four species. Disease severity for each treatment was compared and significant differences in disease severity were observed between accessions. C. berlandieri var. macrocalycium ecotypes collected from Rye Beach, New Hampshire and Appledore Island, Maine exhibited the lowest disease severity over the growing season. P. variabilis was isolated from each accession, and COX2 sequences were compared. Phylogenetic analyses suggest no effect of host species on P. variabilis sequence similarity; however, isolates are shown to cluster by geographic location. This research provides the first step in identifying potential New England native sources of resistance to downy mildew within the genus Chenopodium and provides preliminary information needed to further investigate resistance at the genomic level in Chenopodium spp.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Quinoa is a potential new crop for New England; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle for cultivation. The objectives of this study were to evaluate differential resistance within the Chenopodium genus, identify novel sources of resistance for use in future genetic studies or breeding programs, and investigate phylogenetic relationships of P. variabilis isolates from different Chenopodium hosts. The long-term goal of this research is to develop a resistant variety of quinoa to be grown in New England. Field trials conducted at the University of New Hampshire evaluated downy mildew disease severity on 10 Chenopodium accessions representing four species. Disease severity for each treatment was compared and significant differences in disease severity were observed between accessions. C. berlandieri var. macrocalycium ecotypes collected from Rye Beach, New Hampshire and Appledore Island, Maine exhibited the lowest disease severity over the growing season. P. variabilis was isolated from each accession, and COX2 sequences were compared. Phylogenetic analyses suggest no effect of host species on P. variabilis sequence similarity; however, isolates are shown to cluster by geographic location. This research provides the first step in identifying potential New England native sources of resistance to downy mildew within the genus Chenopodium and provides preliminary information needed to further investigate resistance at the genomic level in Chenopodium spp.
Frailey, Daniel C.; Zhang, Qian; Wood, Dave J.; Davis, Thomas M.
Defining the mutation sites in chickpea nodulation mutants PM233 and PM405 Journal Article
In: BMC Plant Biology, vol. 22, no. 66, pp. 1-12, 2022.
@article{25485,
title = {Defining the mutation sites in chickpea nodulation mutants PM233 and PM405},
author = { Daniel C. Frailey and Qian Zhang and Dave J. Wood and Thomas M. Davis},
year = {2022},
date = {2022-01-01},
journal = {BMC Plant Biology},
volume = {22},
number = {66},
pages = {1-12},
abstract = {Background: Like most legumes, chickpeas form specialized organs called root nodules. These nodules allow for a symbiotic relationship with rhizobium bacteria. The rhizobia provide fixed atmospheric nitrogen to the plant in a usable form. It is of both basic and practical interest to understand the host plant genetics of legume root nodulation. Chickpea lines PM233 and PM405, which harbor the mutationally identified nodulation genes rn1 and rn4, respectively, both display nodulation-deficient phenotypes. Previous investigators identified the rn1 mutation with the chickpea homolog of Medicago truncatula nodulation gene NSP2, but were unable to define the mutant rn1 allele. We used Illumina and Nanopore sequencing reads to attempt to identify and characterize candidate mutation sites responsible for the PM233 and PM405 phenotypes. Results: We aligned Illumina reads to the available desi chickpea reference genome, and did a de novo contig assembly of Nanopore reads. In mutant PM233, the Nanopore contigs allowed us to identify the breakpoints of a ~ 35 kb deleted region containing the CaNSP2 gene, the Medicago truncatula homolog of which is involved in nodulation. In mutant PM405, we performed variant calling in read alignments and identified 10 candidate mutations. Genotyping of a segregating progeny population narrowed that pool down to a single candidate gene which displayed homology to M. truncatula nodulation gene NIN. Conclusions: We have characterized the nodulation mutation sites in chickpea mutants PM233 and PM405. In mutant PM233, the rn1 mutation was shown to be due to deletion of the entire CaNSP2 nodulation gene, while in mutant PM405 the rn4 mutation was due to a single base deletion resulting in a frameshift mutation between the predicted RWP-RK and PB1 domains of the NIN nodulation gene. Critical to characterization of the rn1 allele was the generation of Nanopore contigs for mutant PM233 and its wild type parent ICC 640, without which the deletional boundaries could not be defined. Our results suggest that efforts of prior investigators were hampered by genomic misassemblies in the CaNSP2 region of both the desi and kabuli reference genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: Like most legumes, chickpeas form specialized organs called root nodules. These nodules allow for a symbiotic relationship with rhizobium bacteria. The rhizobia provide fixed atmospheric nitrogen to the plant in a usable form. It is of both basic and practical interest to understand the host plant genetics of legume root nodulation. Chickpea lines PM233 and PM405, which harbor the mutationally identified nodulation genes rn1 and rn4, respectively, both display nodulation-deficient phenotypes. Previous investigators identified the rn1 mutation with the chickpea homolog of Medicago truncatula nodulation gene NSP2, but were unable to define the mutant rn1 allele. We used Illumina and Nanopore sequencing reads to attempt to identify and characterize candidate mutation sites responsible for the PM233 and PM405 phenotypes. Results: We aligned Illumina reads to the available desi chickpea reference genome, and did a de novo contig assembly of Nanopore reads. In mutant PM233, the Nanopore contigs allowed us to identify the breakpoints of a ~ 35 kb deleted region containing the CaNSP2 gene, the Medicago truncatula homolog of which is involved in nodulation. In mutant PM405, we performed variant calling in read alignments and identified 10 candidate mutations. Genotyping of a segregating progeny population narrowed that pool down to a single candidate gene which displayed homology to M. truncatula nodulation gene NIN. Conclusions: We have characterized the nodulation mutation sites in chickpea mutants PM233 and PM405. In mutant PM233, the rn1 mutation was shown to be due to deletion of the entire CaNSP2 nodulation gene, while in mutant PM405 the rn4 mutation was due to a single base deletion resulting in a frameshift mutation between the predicted RWP-RK and PB1 domains of the NIN nodulation gene. Critical to characterization of the rn1 allele was the generation of Nanopore contigs for mutant PM233 and its wild type parent ICC 640, without which the deletional boundaries could not be defined. Our results suggest that efforts of prior investigators were hampered by genomic misassemblies in the CaNSP2 region of both the desi and kabuli reference genomes.
2021
Subedi, Madhav; Neff, Erin; Davis, Thomas M.
Developing Chenopodium ficifolium as a potential B genome diploid model system for genetic characterization and improvement of allotetraploid quinoa (Chenopodium quinoa) Journal Article
In: BMC Plant Biology, vol. 21, no. 1, pp. 490, 2021, (doi: 10.1186/s12870-021-03270-5).
@article{25367,
title = {Developing Chenopodium ficifolium as a potential B genome diploid model system for genetic characterization and improvement of allotetraploid quinoa (Chenopodium quinoa)},
author = { Madhav Subedi and Erin Neff and Thomas M. Davis},
year = {2021},
date = {2021-01-01},
journal = {BMC Plant Biology},
volume = {21},
number = {1},
pages = {490},
abstract = {Background: Quinoa (Chenopodium quinoa) is a high-value grain known for its excellent nutritional bal- ance. It is an allotetraploid species (AABB},
note = {doi: 10.1186/s12870-021-03270-5},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: Quinoa (Chenopodium quinoa) is a high-value grain known for its excellent nutritional bal- ance. It is an allotetraploid species (AABB
2020
Iezzoni, Amy F; McFerson, Jim; Luby, James; Gasic, Ksenija; Whitaker, Vance; Bassil, Nahla; Yue, Chengyan; Gallardo, Karina; McCracken, Vicki; Coe, Michael; Hardner, Craig; Zurn, Jason D.; Hokanson, Stan; Weg, Eric Van De; Jung, Sook; Main, Dorrie; da Silva Linge, Cassia; Vanderzande, Stijn; Davis, Thomas M.; Mahoney, Lise L.; Finn, Chad; Peace, Cameron
RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops Journal Article
In: Horticulture Research, vol. 7, no. 1, pp. 1-23, 2020, ISBN: 2052-7276.
@article{25369,
title = {RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops},
author = { Amy F Iezzoni and Jim McFerson and James Luby and Ksenija Gasic and Vance Whitaker and Nahla Bassil and Chengyan Yue and Karina Gallardo and Vicki McCracken and Michael Coe and Craig Hardner and Jason D. Zurn and Stan Hokanson and Eric Van De Weg and Sook Jung and Dorrie Main and Cassia da Silva Linge and Stijn Vanderzande and Thomas M. Davis and Lise L. Mahoney and Chad Finn and Cameron Peace},
url = {https://doi.org/10.1038/s41438-020-00398-7 www.nature.com/hortres},
isbn = {2052-7276},
year = {2020},
date = {2020-01-01},
journal = {Horticulture Research},
volume = {7},
number = {1},
pages = {1-23},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wettberg, Eric Von; Davis, Thomas M.; Smýkal, Petr
Wild Plants as Source of New Crops Journal Article
In: Frontiers in Plant Science, vol. 11, pp. 1426, 2020.
@article{21214,
title = {Wild Plants as Source of New Crops},
author = { Eric Von Wettberg and Thomas M. Davis and Petr Sm{ý}kal},
year = {2020},
date = {2020-01-01},
journal = {Frontiers in Plant Science},
volume = {11},
pages = {1426},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Davis, T. M.; Yang, Y.; Mahoney, L. L.; Frailey, D. C.
A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination Journal Article
In: Horticulture Research, vol. 7, no. 77, 2020.
@article{20146,
title = {A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination},
author = { T.M. Davis and Y. Yang and L.L. Mahoney and D. C. Frailey},
url = {https://www.nature.com/articles/s41438-020-0308-2},
year = {2020},
date = {2020-01-01},
journal = {Horticulture Research},
volume = {7},
number = {77},
abstract = {The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species, Fragaria virginiana, was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygous F. virginiana hybrid “LB48” as a paternal parent with diploid (2n = 2x = 14) Fragaria vesca “Hawaii 4”. The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an “A” subgenome associated with ancestral diploid Fragaria vesca, while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously published Fragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species, Fragaria virginiana, was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygous F. virginiana hybrid “LB48” as a paternal parent with diploid (2n = 2x = 14) Fragaria vesca “Hawaii 4”. The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an “A” subgenome associated with ancestral diploid Fragaria vesca, while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously published Fragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders.
2018
Letscher, RT; Villareal, TA
In: Biogeosciences Discussions, 2018.
@article{4806,
title = {Vertically migrating phytoplankton drive seasonal formation of subsurface negative preformed nitrate anomalies in the subtropical North Pacific and North Atlantic},
author = {RT Letscher and TA Villareal},
url = {https://www.biogeosciences-discuss.net/bg-2018-125/},
year = {2018},
date = {2018-01-01},
journal = {Biogeosciences Discussions},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lonborg, C; Alvarez-Salgado, XA; Letscher, RT; Hansell, DA
Large stimulation of recalcitrant dissolved organic carbon degradation by increasing ocean temperatures Journal Article
In: Frontiers in Marine Science, vol. 4, pp. 436, 2018.
@article{4805,
title = {Large stimulation of recalcitrant dissolved organic carbon degradation by increasing ocean temperatures},
author = {C Lonborg and XA Alvarez-Salgado and RT Letscher and DA Hansell},
url = {https://www.frontiersin.org/articles/10.3389/fmars.2017.00436/full},
year = {2018},
date = {2018-01-01},
journal = {Frontiers in Marine Science},
volume = {4},
pages = {436},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Neff, Erin; Sullivan, Janet R.; Davis, Thomas M.
Enhanced Documentation of Chenopodium foggii (Amaranthaceae) in Northern New England Journal Article
In: Rhodora, vol. 120, no. 983, pp. 257-259, 2018.
@article{6745,
title = {Enhanced Documentation of Chenopodium foggii (Amaranthaceae) in Northern New England},
author = { Erin Neff and Janet R. Sullivan and Thomas M. Davis},
url = {https://bioone.org/journals/rhodora/volume-120/issue-983/18-02/Enhanced-Documentation-of-Chenopodium-foggii-Amaranthaceae-in-Northern-New-England/10.3119/18-02.full},
year = {2018},
date = {2018-01-01},
journal = {Rhodora},
volume = {120},
number = {983},
pages = {257-259},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Smith, RG; Birthisel, SK; Bosworth, SC; Brown, B; Davis, TM; Gallandt, ER; Hazelrigg, A; Venturini, E; Warren, ND
Environmental correlates with germinable weed seed banks on organic farms across northern New England Journal Article
In: Weed Science, vol. 66, no. 1, pp. 78-93, 2018, (doi:10.1017/wsc.2017.40).
@article{1212,
title = {Environmental correlates with germinable weed seed banks on organic farms across northern New England},
author = { RG Smith and SK Birthisel and SC Bosworth and B Brown and TM Davis and ER Gallandt and A Hazelrigg and E Venturini and ND Warren},
url = {https://www-cambridge-org.libproxy.unh.edu/core/journals/weed-science/article/environmental-correlates-with-germinable-weed-seedbanks-on-organic-farms-across-northern-new-england/B6BF81F665AB34540243B446139C2D3E/core-reader},
year = {2018},
date = {2018-01-01},
journal = {Weed Science},
volume = {66},
number = {1},
pages = {78-93},
abstract = {The northern New England region includes the states of Vermont, New Hampshire, and Maine and encompasses a large degree of climate and edaphic variation across a relatively small spatial area, making it ideal for studying climate change impacts on agricultural weed communities. We sampled weed seed banks and measured soil physical and chemical characteristics on 77 organic farms across the region and analyzed the relationships between weed community parameters and select geographic, climatic, and edaphic variables using multivariate procedures. Temperature-related variables (latitude, longitude, mean maximum and minimum temperature) were the strongest and most consistent correlates with weed seed bank composition. Edaphic variables were, for the most part, relatively weaker and inconsistent correlates with weed seed banks. Our analyses also indicate that a number of agriculturally important weed species are associated with specific USDA plant hardiness zones, implying that future changes in climate factors that result in geographic shifts in these zone will likely be accompanied by changes in the composition of weed communities and therefore new management challenges for farmers. },
note = {doi:10.1017/wsc.2017.40},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The northern New England region includes the states of Vermont, New Hampshire, and Maine and encompasses a large degree of climate and edaphic variation across a relatively small spatial area, making it ideal for studying climate change impacts on agricultural weed communities. We sampled weed seed banks and measured soil physical and chemical characteristics on 77 organic farms across the region and analyzed the relationships between weed community parameters and select geographic, climatic, and edaphic variables using multivariate procedures. Temperature-related variables (latitude, longitude, mean maximum and minimum temperature) were the strongest and most consistent correlates with weed seed bank composition. Edaphic variables were, for the most part, relatively weaker and inconsistent correlates with weed seed banks. Our analyses also indicate that a number of agriculturally important weed species are associated with specific USDA plant hardiness zones, implying that future changes in climate factors that result in geographic shifts in these zone will likely be accompanied by changes in the composition of weed communities and therefore new management challenges for farmers.
2017
Opazo, María Cecilia; Lizana, Rodrigo; Stappung, Yazmina; Davis, Thomas M.; Herrera, Raúl; Moya-León, María Alejandra
XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues Journal Article
In: BMC Genomics, vol. 18, no. 1, pp. 852, 2017, ISBN: 1471-2164.
@article{3587,
title = {XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues},
author = { María Cecilia Opazo and Rodrigo Lizana and Yazmina Stappung and Thomas M. Davis and Ra{ú}l Herrera and María Alejandra Moya-León},
url = {https://doi.org/10.1186/s12864-017-4255-8},
doi = {10.1186/s12864-017-4255-8},
isbn = {1471-2164},
year = {2017},
date = {2017-11-01},
journal = {BMC Genomics},
volume = {18},
number = {1},
pages = {852},
abstract = {Fragaria vesca or ‘woodland strawberry’ has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes. Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell wall-associated enzyme, which is encoded by a multigene family. Its action modifies the structure of xyloglucans, a diverse group of polysaccharides that crosslink with cellulose microfibrills, affecting therefore the functional structure of the cell wall. The aim of this work is to identify the XTH-encoding genes present in F. vesca and to determine its transcription level in ripening fruit.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fragaria vesca or ‘woodland strawberry’ has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes. Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell wall-associated enzyme, which is encoded by a multigene family. Its action modifies the structure of xyloglucans, a diverse group of polysaccharides that crosslink with cellulose microfibrills, affecting therefore the functional structure of the cell wall. The aim of this work is to identify the XTH-encoding genes present in F. vesca and to determine its transcription level in ripening fruit.
Elliott, S.; Burrows, S.; Cameron-Smith, P.; Hoffman, F.; Hunke, E.; Jeffery, N.; Liu, Y.; Maltrud, M.; Ogunro, O.; Roekel, L. Van; Wang, S.; Brunke, M.; Deal, C.; Jin, M.; Letscher, R. T.; Meskhidze, N.; Russell, L.; Simpson, I.; Stokes, D.; Wingenter, O.
Does Marine Surface Tension have Global Biogeography? Addition for the OCEANFILMS Package Journal Article
In: Atmosphere, 2017.
@article{2519,
title = {Does Marine Surface Tension have Global Biogeography? Addition for the OCEANFILMS Package},
author = {S. Elliott and S. Burrows and P. Cameron-Smith and F. Hoffman and E. Hunke and N. Jeffery and Y. Liu and M. Maltrud and O. Ogunro and L. Van Roekel and S. Wang and M. Brunke and C. Deal and M. Jin and R. T. Letscher and N. Meskhidze and L. Russell and I. Simpson and D. Stokes and O. Wingenter},
url = {https://www.preprints.org/manuscript/201710.0167/v1},
year = {2017},
date = {2017-10-01},
journal = {Atmosphere},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Letscher, R. T.; Moore, J. K.
Modest net autotrophy in the oligotrophic ocean Journal Article
In: Global Biogeochemical Cycles, vol. 31, pp. 699-708, 2017.
@article{2518,
title = {Modest net autotrophy in the oligotrophic ocean},
author = {R. T. Letscher and J. K. Moore},
url = {http://onlinelibrary.wiley.com/doi/10.1002/2016GB005503/full},
year = {2017},
date = {2017-01-01},
journal = {Global Biogeochemical Cycles},
volume = {31},
pages = {699-708},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bourbonnais, A.; Letscher, R. T.; Bange, H. W.; Echevin, V.; Larkum, J.; Mohn, J.; Yoshida, N.; Altabet, M. A.
N2O production and consumption from stable isotopic and concentration data in the Peruvian coastal upwelling system Journal Article
In: Global Biogeochemical Cycles, vol. 31, pp. 678-698, 2017.
@article{2517,
title = {N2O production and consumption from stable isotopic and concentration data in the Peruvian coastal upwelling system},
author = {A. Bourbonnais and R. T. Letscher and H. W. Bange and V. Echevin and J. Larkum and J. Mohn and N. Yoshida and M. A. Altabet},
url = {http://onlinelibrary.wiley.com/doi/10.1002/2016GB005567/full},
year = {2017},
date = {2017-01-01},
journal = {Global Biogeochemical Cycles},
volume = {31},
pages = {678-698},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Yang, Yilong; Davis, Thomas M
A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis Journal Article
In: Genome Biology and Evolution, vol. 9, no. 12, pp. 3433-3448, 2017.
@article{doi:10.1093/gbe/evx214,
title = {A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis},
author = { Yilong Yang and Thomas M Davis},
url = {https://academic.oup.com/gbe/article/9/12/3433/4554418},
doi = {10.1093/gbe/evx214},
year = {2017},
date = {2017-01-01},
journal = {Genome Biology and Evolution},
volume = {9},
number = {12},
pages = {3433-3448},
abstract = {The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria(strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria(strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis.
Hummer, KE; Davis, TM
Seeking the northern boundary of the Cascade strawberry Journal Article
In: Acta Hortic, vol. 1156, pp. 111-116, 2017.
@article{1210,
title = {Seeking the northern boundary of the Cascade strawberry},
author = { KE Hummer and TM Davis},
url = {https://doi.org/10.17660/ActaHortic.2017.1156.15},
year = {2017},
date = {2017-01-01},
journal = {Acta Hortic},
volume = {1156},
pages = {111-116},
publisher = {International Society for Horticultural Science},
address = {Quebec City, Canada},
abstract = {Fragaria cascadensis K.E. Hummer, an endemic decaploid strawberry species, was described from the Oregon Cascade Mountains in the Pacific North-western United States. Its range occurs near Mt. Hood, the highest peak in the northern Oregon Cascades, in a band of higher elevation sites southwards to near Crater Lake in southern Oregon. The objective of this study was to examine in more detail, the distribution of this species at the northern end of its range. During summer and fall 2015, several excursions were taken in the vicinity of Mt. Hood to seek the wild distribution of Fragaria species. These excursions encircled the mountain by road and hiking. The most northerly observation of the occurrence of F. cascadensis was at Lolo Pass near the junction of the Pacific Crest Trail (PCT) and Route 18; the highest elevation occurrence was observed on Mt. Hood, 2 miles south of Timberline Lodge at 1589 m (5213RSQUO). Interestingly, the region to the east of the PCT and north of Hood, was populated with octoploid strawberries, Fragaria virginiana ssp. platypetala. This region included the Cooper Spur Recreational Area. The decaploid F. cascadensis was not observed in the north to northeast sector of the mountain. While the diploid F. vesca spp. bracteata (A. Heller) Staudt was present at the PCT at Cascade Locks near the Columbia River, no higher ploidy species were observed in that vicinity. Further research is ongoing regarding the distribution and phylogeny of the Cascade strawberry in Oregon.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fragaria cascadensis K.E. Hummer, an endemic decaploid strawberry species, was described from the Oregon Cascade Mountains in the Pacific North-western United States. Its range occurs near Mt. Hood, the highest peak in the northern Oregon Cascades, in a band of higher elevation sites southwards to near Crater Lake in southern Oregon. The objective of this study was to examine in more detail, the distribution of this species at the northern end of its range. During summer and fall 2015, several excursions were taken in the vicinity of Mt. Hood to seek the wild distribution of Fragaria species. These excursions encircled the mountain by road and hiking. The most northerly observation of the occurrence of F. cascadensis was at Lolo Pass near the junction of the Pacific Crest Trail (PCT) and Route 18; the highest elevation occurrence was observed on Mt. Hood, 2 miles south of Timberline Lodge at 1589 m (5213RSQUO). Interestingly, the region to the east of the PCT and north of Hood, was populated with octoploid strawberries, Fragaria virginiana ssp. platypetala. This region included the Cooper Spur Recreational Area. The decaploid F. cascadensis was not observed in the north to northeast sector of the mountain. While the diploid F. vesca spp. bracteata (A. Heller) Staudt was present at the PCT at Cascade Locks near the Columbia River, no higher ploidy species were observed in that vicinity. Further research is ongoing regarding the distribution and phylogeny of the Cascade strawberry in Oregon.
Mathey, MM; Mookerjee, Sonali; Mahoney, LL; Gündüz, K; Rosyara, Umesh; Hancock, James F; Stewart, Philip J; Whitaker, Vance M; Bassil, Nahla V; Davis, Thomas M
Genotype by environment interactions and combining ability for strawberry families grown in diverse environments Journal Article
In: Euphytica, vol. 213, no. 5, pp. 112, 2017, ISBN: 0014-2336, (https://doi.org/10.1007/s10681-017-1892-6).
@article{1169,
title = {Genotype by environment interactions and combining ability for strawberry families grown in diverse environments},
author = { MM Mathey and Sonali Mookerjee and LL Mahoney and K Gündüz and Umesh Rosyara and James F Hancock and Philip J Stewart and Vance M Whitaker and Nahla V Bassil and Thomas M Davis},
url = {https://link.springer.com/article/10.1007/s10681-017-1892-6},
isbn = {0014-2336},
year = {2017},
date = {2017-01-01},
journal = {Euphytica},
volume = {213},
number = {5},
pages = {112},
publisher = {Springer},
abstract = {Ten seedlings from 36 crosses representing eastern and western North American short day and remontant genotypes were evaluated in 2011 and 2012 in California, Michigan, New Hampshire and Oregon, for phenology, flower related traits, plant characteristics, fruit characteristics and fruit chemistry traits. There was significant variability among genotypes, locations and evaluation year for most of the characteristics; however, few genotype × location and genotype × year interactions were detected. General combining ability variance components were significant for all traits and greater than SCA variance components for peduncle length, total flowering weeks, flowering cycles, truss size, growing degree days for harvest data, remontancy, achene position, ease of capping, fruit weight, percent soluble solids, titratable acidity and soluble solids/titratable acidity. ‘Sarian’ was identified as the best contributing parent for remontancy. Narrow-sense heritability estimates were moderate to high (0.33–0.78) for total flowering weeks, flowering cycle, truss size, remontancy, number of runners, fruit weight, pH, and titratable acidity. Having a better understanding of these attributes will provide breeders guidance on the most effective breeding strategies for incorporating superior traits from this germplasm into their programs.},
note = {https://doi.org/10.1007/s10681-017-1892-6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ten seedlings from 36 crosses representing eastern and western North American short day and remontant genotypes were evaluated in 2011 and 2012 in California, Michigan, New Hampshire and Oregon, for phenology, flower related traits, plant characteristics, fruit characteristics and fruit chemistry traits. There was significant variability among genotypes, locations and evaluation year for most of the characteristics; however, few genotype × location and genotype × year interactions were detected. General combining ability variance components were significant for all traits and greater than SCA variance components for peduncle length, total flowering weeks, flowering cycles, truss size, growing degree days for harvest data, remontancy, achene position, ease of capping, fruit weight, percent soluble solids, titratable acidity and soluble solids/titratable acidity. ‘Sarian’ was identified as the best contributing parent for remontancy. Narrow-sense heritability estimates were moderate to high (0.33–0.78) for total flowering weeks, flowering cycle, truss size, remontancy, number of runners, fruit weight, pH, and titratable acidity. Having a better understanding of these attributes will provide breeders guidance on the most effective breeding strategies for incorporating superior traits from this germplasm into their programs.
Verma, Sujeet; Bassil, NV; Weg, Eric Van De; Harrison, RJ; Monfort, Amparo; Hidalgo, JM; Amaya, Iraida; Denoyes, Beatrice; Mahoney, L; Davis, Tom M
Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa Journal Article
In: Acta Hortic, vol. 1156, pp. 75-82, 2017, ISBN: 9462611521.
@article{802,
title = {Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa},
author = { Sujeet Verma and NV Bassil and Eric Van De Weg and RJ Harrison and Amparo Monfort and JM Hidalgo and Iraida Amaya and Beatrice Denoyes and L Mahoney and Tom M Davis},
url = {https://doi.org/10.17660/ActaHortic.2017.1156.10},
isbn = {9462611521},
year = {2017},
date = {2017-01-01},
journal = {Acta Hortic},
volume = {1156},
pages = {75-82},
abstract = {The Axiom® IStraw90 SNP (single nucleotide polymorphism) array was developed to enable high-throughput genotyping in allo-octoploid cultivated strawberry (Fragaria ×ananassa). However, high cost ($ 80-105 sample-1) limits throughput for certain applications. On average the IStraw90 has yielded 50 to 60% usable data points, defined as PHR (Poly High Resolution) and NMH (No Minor Homozygote) marker classes. Thus, an array is needed with a higher percentage of usable data points at a lower cost. We initiated an effort to identify IStraw90 SNP markers that were genetically mapped in one or more strawberry populations from research programs around the world. Seven programs participated in this endeavor. A total of 41,183 SNP probes were submitted to Affymetrix for quality check, 38,506 of which were accommodated on the Axiom® IStraw35 384HT design. In order to assess the performance of the Axiom® IStraw35 384HT array, 384 DNA samples from the University of Florida strawberry breeding program were assayed at a cost of $ 50 per sample, all inclusive. The performance of the array met expectations. More than 87% of markers belonged to the PHR and NMH categories. This array is expected to provide high-quality genome scanning at a more affordable price for strawberry researchers worldwide.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Axiom® IStraw90 SNP (single nucleotide polymorphism) array was developed to enable high-throughput genotyping in allo-octoploid cultivated strawberry (Fragaria ×ananassa). However, high cost ($ 80-105 sample-1) limits throughput for certain applications. On average the IStraw90 has yielded 50 to 60% usable data points, defined as PHR (Poly High Resolution) and NMH (No Minor Homozygote) marker classes. Thus, an array is needed with a higher percentage of usable data points at a lower cost. We initiated an effort to identify IStraw90 SNP markers that were genetically mapped in one or more strawberry populations from research programs around the world. Seven programs participated in this endeavor. A total of 41,183 SNP probes were submitted to Affymetrix for quality check, 38,506 of which were accommodated on the Axiom® IStraw35 384HT design. In order to assess the performance of the Axiom® IStraw35 384HT array, 384 DNA samples from the University of Florida strawberry breeding program were assayed at a cost of $ 50 per sample, all inclusive. The performance of the array met expectations. More than 87% of markers belonged to the PHR and NMH categories. This array is expected to provide high-quality genome scanning at a more affordable price for strawberry researchers worldwide.
2016
Mahoney, Lise L.; Sargent, Daniel J.; Abebe-Akele, F.; Wood, Dave J.; Ward, Judson A.; Bassil, Nahla V.; Hancock, James F.; Folta, Kevin M.; Davis, Thomas M.
In: The Plant Genome, vol. 9, no. 2, 2016, (doi: 10.3835/plantgenome2015.08.0071).
@article{472,
title = {A High-Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae, Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing},
author = { Lise L. Mahoney and Daniel J. Sargent and F. Abebe-Akele and Dave J. Wood and Judson A. Ward and Nahla V. Bassil and James F. Hancock and Kevin M. Folta and Thomas M. Davis},
url = {https://dl.sciencesocieties.org/publications/tpg/articles/9/2/plantgenome2015.08.0071},
year = {2016},
date = {2016-03-01},
journal = {The Plant Genome},
volume = {9},
number = {2},
abstract = {Fragaria iinumae Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for F. iinumae. The F. iinumae linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter "Array"), and genotyping by sequencing (GBS). The F2 generation mapping population was derived by selfing F. iinumae hybrid F1D, the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the Fragaria vesca ssp. vesca L. ’Hawaii 4’ pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between F. iinumae and F. vesca, and/or to F. vesca genomic assembly errors. The Fii map provides a basis for anchoring a F. iinumae genome assembly as a prerequisite for constructing a second diploid reference genome for Fragaria.},
note = {doi: 10.3835/plantgenome2015.08.0071},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fragaria iinumae Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for F. iinumae. The F. iinumae linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter "Array"), and genotyping by sequencing (GBS). The F2 generation mapping population was derived by selfing F. iinumae hybrid F1D, the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the Fragaria vesca ssp. vesca L. ’Hawaii 4’ pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between F. iinumae and F. vesca, and/or to F. vesca genomic assembly errors. The Fii map provides a basis for anchoring a F. iinumae genome assembly as a prerequisite for constructing a second diploid reference genome for Fragaria.
Liu, Bo; Poulsen, Elizabeth G.; Davis, Thomas M.
Insight into octoploid strawberry (Fragaria) subgenome composition revealed by GISH analysis of pentaploid hybrids Journal Article
In: Genome, vol. 59, no. 2, pp. 79-86, 2016, (https://doi.org/10.1139/gen-2015-0116).
@article{473,
title = {Insight into octoploid strawberry (Fragaria) subgenome composition revealed by GISH analysis of pentaploid hybrids},
author = { Bo Liu and Elizabeth G. Poulsen and Thomas M. Davis},
url = {http://www.nrcresearchpress.com/doi/full/10.1139/gen-2015-0116$#$.WMbNFDvytEY},
year = {2016},
date = {2016-02-01},
journal = {Genome},
volume = {59},
number = {2},
pages = {79-86},
abstract = {As the product of interspecific hybridization between its two ancestral octoploid (2n = 8x = 56) species (Fragaria chiloensis and F. virginiana), the cultivated strawberry (F. ×ananassa) is among the most genomically complex of crop plants, harboring subgenomic components derived from as many as four different diploid ancestors. To physically visualize the octoploids’ subgenome composition(s), we launched molecular cytogenetic studies using genomic in situ hybridization (GISH), comparative GISH (cGISH), and rDNA-FISH techniques. First, GISH resolution in Fragaria was tested by using diploid and triploid hybrids with predetermined genome compositions. Then, observation of an octoploid genome was implemented by hybridizing chromosomes of pentaploid (2n = 5x = 35) hybrids from F. vesca × F. virginiana with genomic DNA probes derived from diploids (2n = 2x = 14) F. vesca and F. iinumae, which have been proposed by phylogenetic studies to be closely related to the octoploids yet highly divergent from each other. GISH and cGISH results indicated that octoploid-derived gametes (n = 4x = 28) carried seven chromosomes with hybridization affinities to F. vesca, while the remaining 21 chromosomes displayed varying affinities to F. iinumae, indicating differing degrees of subgenomic contribution to the octoploids by these two putatively ancestral diploids. Combined rDNA-FISH revealed severe 25S rDNA loss in both the F. vesca- and F. iinumae-like chromosome groups, while only the prior group retained its 5S loci.},
note = {https://doi.org/10.1139/gen-2015-0116},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
As the product of interspecific hybridization between its two ancestral octoploid (2n = 8x = 56) species (Fragaria chiloensis and F. virginiana), the cultivated strawberry (F. ×ananassa) is among the most genomically complex of crop plants, harboring subgenomic components derived from as many as four different diploid ancestors. To physically visualize the octoploids’ subgenome composition(s), we launched molecular cytogenetic studies using genomic in situ hybridization (GISH), comparative GISH (cGISH), and rDNA-FISH techniques. First, GISH resolution in Fragaria was tested by using diploid and triploid hybrids with predetermined genome compositions. Then, observation of an octoploid genome was implemented by hybridizing chromosomes of pentaploid (2n = 5x = 35) hybrids from F. vesca × F. virginiana with genomic DNA probes derived from diploids (2n = 2x = 14) F. vesca and F. iinumae, which have been proposed by phylogenetic studies to be closely related to the octoploids yet highly divergent from each other. GISH and cGISH results indicated that octoploid-derived gametes (n = 4x = 28) carried seven chromosomes with hybridization affinities to F. vesca, while the remaining 21 chromosomes displayed varying affinities to F. iinumae, indicating differing degrees of subgenomic contribution to the octoploids by these two putatively ancestral diploids. Combined rDNA-FISH revealed severe 25S rDNA loss in both the F. vesca- and F. iinumae-like chromosome groups, while only the prior group retained its 5S loci.
Letscher, R. T.; Primeau, F.; Moore, J. K.
Nutrient budgets in the subtropical ocean gyres dominated by lateral transport Journal Article
In: Nature Geoscience, vol. 9, pp. 815-819, 2016.
@article{2516,
title = {Nutrient budgets in the subtropical ocean gyres dominated by lateral transport},
author = {R. T. Letscher and F. Primeau and J. K. Moore},
url = {https://www.nature.com/articles/ngeo2812},
year = {2016},
date = {2016-01-01},
journal = {Nature Geoscience},
volume = {9},
pages = {815-819},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Romera-Castillo, C.; Letscher, R. T.; Hansell, D. A.
New nutrients exert fundamental control on DOC accumulation in the surface Atlantic Ocean Journal Article
In: Proceedings of the National Academy of Sciences, USA, vol. 113, no. 38, pp. 10497-10502, 2016.
@article{2515,
title = {New nutrients exert fundamental control on DOC accumulation in the surface Atlantic Ocean},
author = {C. Romera-Castillo and R. T. Letscher and D. A. Hansell},
url = {http://www.pnas.org/content/113/38/10497.short},
year = {2016},
date = {2016-01-01},
journal = {Proceedings of the National Academy of Sciences, USA},
volume = {113},
number = {38},
pages = {10497-10502},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sargent, DJ; Yang, Y; Šurbanovski, N; Bianco, L; Buti, M; Velasco, R; Giongo, L; Davis, TM
In: Plant Science, vol. 242, no. 4, pp. 140-150, 2016, ISBN: 0168-9452, (https://doi.org/10.1016/j.plantsci.2015.07.004).
@article{488,
title = {HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria ×ananassa)},
author = { DJ Sargent and Y Yang and N {Š}urbanovski and L Bianco and M Buti and R Velasco and L Giongo and TM Davis},
url = {http://www.sciencedirect.com/science/article/pii/S0168945215300108?via%3Dihub},
isbn = {0168-9452},
year = {2016},
date = {2016-01-01},
journal = {Plant Science},
volume = {242},
number = {4},
pages = {140-150},
publisher = {Elsevier},
abstract = {The cultivated strawberry, Fragaria × ananassa possesses a genetically complex allo-octoploid genome. Advances in genomics research in Fragaria, including the release of a genome sequence for F. vesca, have permitted the development of a high throughput whole genome genotyping array for strawberry, which promises to facilitate genetics and genomics research. In this investigation, we used the Axiom® IStraw90® array for linkage map development, and produced a linkage map containing 8,407 SNP markers spanning 1,820 cM. Whilst the linkage map provides good coverage of the genome of both parental genotypes, the map of ‘Monterey’ contained significantly fewer mapped markers than did that of ‘Darselect’. The array contains a novel marker class known as haploSNPs, which exploit homoeologous sequence variants as probe destabilization sites to effectively reduce marker ploidy. We examined these sites as potential indicators of subgenomic identities by using comparisons to allele states in two ancestral diploids. On this basis, haploSNP loci could be inferred to be derived from F. vesca, F. iinumae, or from an unknown source. When the identity classifications of haploSNPs were considered in conjunction with their respective linkage map positions, it was possible to define two discrete subgenomes, while the remaining homoeologues of each chromosome could not be partitioned into two discrete subgenomic groupings. These findings suggested a novel hypothesis regarding octoploid strawberry subgenome structure and evolutionary origins},
note = {https://doi.org/10.1016/j.plantsci.2015.07.004},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The cultivated strawberry, Fragaria × ananassa possesses a genetically complex allo-octoploid genome. Advances in genomics research in Fragaria, including the release of a genome sequence for F. vesca, have permitted the development of a high throughput whole genome genotyping array for strawberry, which promises to facilitate genetics and genomics research. In this investigation, we used the Axiom® IStraw90® array for linkage map development, and produced a linkage map containing 8,407 SNP markers spanning 1,820 cM. Whilst the linkage map provides good coverage of the genome of both parental genotypes, the map of ‘Monterey’ contained significantly fewer mapped markers than did that of ‘Darselect’. The array contains a novel marker class known as haploSNPs, which exploit homoeologous sequence variants as probe destabilization sites to effectively reduce marker ploidy. We examined these sites as potential indicators of subgenomic identities by using comparisons to allele states in two ancestral diploids. On this basis, haploSNP loci could be inferred to be derived from F. vesca, F. iinumae, or from an unknown source. When the identity classifications of haploSNPs were considered in conjunction with their respective linkage map positions, it was possible to define two discrete subgenomes, while the remaining homoeologues of each chromosome could not be partitioned into two discrete subgenomic groupings. These findings suggested a novel hypothesis regarding octoploid strawberry subgenome structure and evolutionary origins
2015
Bassil, Nahla V; and, Thomas M Davis
Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa Journal Article
In: BMC Genomics, vol. 16, no. 155, 2015, (doi: 10.1186/s12864-015-1310-1).
@article{474,
title = {Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa},
author = { Nahla V Bassil and Thomas M Davis and et al.},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1310-1},
year = {2015},
date = {2015-03-01},
journal = {BMC Genomics},
volume = {16},
number = {155},
abstract = {Background
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.
Results
About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.
Conclusions
The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.},
note = {doi: 10.1186/s12864-015-1310-1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.
Results
About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.
Conclusions
The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.
Results
About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.
Conclusions
The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
Letscher, R. T.; Knapp, A. N.; James, A.; Carlson, C. A.; Santoro, A. E.; Hansell, D. A.
Microbial community composition and nitrogen availability influence DOC remineralization in the South Pacific Gyre Journal Article
In: Marine Chemistry, vol. 177, pp. 325-334, 2015.
@article{2514,
title = {Microbial community composition and nitrogen availability influence DOC remineralization in the South Pacific Gyre},
author = {R. T. Letscher and A. N. Knapp and A. James and C. A. Carlson and A. E. Santoro and D. A. Hansell},
url = {http://www.sciencedirect.com/science/article/pii/S0304420315300104},
year = {2015},
date = {2015-01-01},
journal = {Marine Chemistry},
volume = {177},
pages = {325-334},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Letscher, R. T.; Moore, J. K.
In: Global Biogeochemical Cycles, vol. 29, pp. 325-340, 2015.
@article{2513,
title = {Preferential remineralization of dissolved organic phosphorus and non-Redfield DOM dynamics in the global ocean: Impacts on marine productivity, nitrogen fixation, and carbon export},
author = {R. T. Letscher and J. K. Moore},
url = {http://onlinelibrary.wiley.com/doi/10.1002/2014GB004904/full},
year = {2015},
date = {2015-01-01},
journal = {Global Biogeochemical Cycles},
volume = {29},
pages = {325-340},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Letscher, R. T.; Moore, J. K.; Teng, Y. C.; Primeau, F.
Variable C:N:P stoichiometry of marine dissolved organic matter cycling in the Community Earth System Model Journal Article
In: Biogeosciences, vol. 12, pp. 209-221, 2015.
@article{2512,
title = {Variable C:N:P stoichiometry of marine dissolved organic matter cycling in the Community Earth System Model},
author = {R. T. Letscher and J. K. Moore and Y. C. Teng and F. Primeau},
url = {https://www.biogeosciences.net/12/209/2015/bg-12-209-2015.html},
year = {2015},
date = {2015-01-01},
journal = {Biogeosciences},
volume = {12},
pages = {209-221},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ogunro, O. O.; Burrows, S. M.; Elliott, S.; Frossard, A. A.; Hoffman, F.; Letscher, R. T.; Moore, J. K.; Russell, L. M.; Wang, S.; Wingenter, O. W.
Global distribution and surface activity of macromolecules in offline simulations of marine organic chemistry Journal Article
In: Biogeochemistry, vol. 168, pp. 1-32, 2015.
@article{2511,
title = {Global distribution and surface activity of macromolecules in offline simulations of marine organic chemistry},
author = {O. O. Ogunro and S. M. Burrows and S. Elliott and A. A. Frossard and F. Hoffman and R. T. Letscher and J. K. Moore and L. M. Russell and S. Wang and O. W. Wingenter},
url = {https://link.springer.com/article/10.1007/s10533-015-0136-x},
year = {2015},
date = {2015-01-01},
journal = {Biogeochemistry},
volume = {168},
pages = {1-32},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vining, KJ; Davis, TM; Jamieson, AR; Mahoney, LL
Germplasm resources for verticillium wilt resistance breeding and genetics in strawberry (Fragaria) Journal Article
In: Journal of Berry Research, vol. 5, no. 4, pp. 183-195,, 2015, (DOI: 10.3233/JBR-150096).
@article{1429,
title = {Germplasm resources for verticillium wilt resistance breeding and genetics in strawberry (Fragaria)},
author = { KJ Vining and TM Davis and AR Jamieson and LL Mahoney},
url = {http://content.iospress.com/articles/journal-of-berry-research/jbr096},
year = {2015},
date = {2015-01-01},
journal = {Journal of Berry Research},
volume = {5},
number = {4},
pages = {183-195,},
abstract = {BACKGROUND: The fungal disease verticillium wilt has been recognized as an obstacle to strawberry production since its initial description in 1931. The full potential of genetic resistance as a solution to this problem has yet to be determined or realized.
OBJECTIVE: Our investigations are concerned with defining new sources of resistance to verticillium wilt disease in cultivated and wild strawberry germplasm, and with advancing genetic studies on the basis of resistance/susceptibility.
METHODS: We screened 23 diploid, 1 decaploid, and 26 octoploid Fragaria (strawberry) germplasm accessions and cultigens for response to root-dip inoculation with Verticillium dahliae. isolate V1. Pedigree relationships of 10 studied cultigens were examined. Crosses were performed between resistant and susceptible accessions. RESULTS: Variability in inoculation response existed within and between species at diploid and octoploid levels. Very or moderately resistant accessions were found within each of three diploid and three octoploid species. Moderately or very susceptible accessions were documented within F. vesca and each octoploid species. Segregation for resistance/susceptibility was evident in progeny populations. CONCLUSIONS: The verticillium wilt resistance ratings reported here and discussed in relation to prior studies adds to the body of publically available knowledge about sources of wilt resistance and susceptibility in Fragaria germplasm},
note = {DOI: 10.3233/JBR-150096},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: The fungal disease verticillium wilt has been recognized as an obstacle to strawberry production since its initial description in 1931. The full potential of genetic resistance as a solution to this problem has yet to be determined or realized.
OBJECTIVE: Our investigations are concerned with defining new sources of resistance to verticillium wilt disease in cultivated and wild strawberry germplasm, and with advancing genetic studies on the basis of resistance/susceptibility.
METHODS: We screened 23 diploid, 1 decaploid, and 26 octoploid Fragaria (strawberry) germplasm accessions and cultigens for response to root-dip inoculation with Verticillium dahliae. isolate V1. Pedigree relationships of 10 studied cultigens were examined. Crosses were performed between resistant and susceptible accessions. RESULTS: Variability in inoculation response existed within and between species at diploid and octoploid levels. Very or moderately resistant accessions were found within each of three diploid and three octoploid species. Moderately or very susceptible accessions were documented within F. vesca and each octoploid species. Segregation for resistance/susceptibility was evident in progeny populations. CONCLUSIONS: The verticillium wilt resistance ratings reported here and discussed in relation to prior studies adds to the body of publically available knowledge about sources of wilt resistance and susceptibility in Fragaria germplasm
OBJECTIVE: Our investigations are concerned with defining new sources of resistance to verticillium wilt disease in cultivated and wild strawberry germplasm, and with advancing genetic studies on the basis of resistance/susceptibility.
METHODS: We screened 23 diploid, 1 decaploid, and 26 octoploid Fragaria (strawberry) germplasm accessions and cultigens for response to root-dip inoculation with Verticillium dahliae. isolate V1. Pedigree relationships of 10 studied cultigens were examined. Crosses were performed between resistant and susceptible accessions. RESULTS: Variability in inoculation response existed within and between species at diploid and octoploid levels. Very or moderately resistant accessions were found within each of three diploid and three octoploid species. Moderately or very susceptible accessions were documented within F. vesca and each octoploid species. Segregation for resistance/susceptibility was evident in progeny populations. CONCLUSIONS: The verticillium wilt resistance ratings reported here and discussed in relation to prior studies adds to the body of publically available knowledge about sources of wilt resistance and susceptibility in Fragaria germplasm
2014
Mathey, MEGAN M; Mookerjee, Sonali; Mahoney, Lise L.; Finn, Chad E; Serce,; Davis, Thomas M.; Stewart, Philip J; Whitaker, Vance M; Jamieson, AR; Bassil, Nahla V.; Amaya, Iraida; Denoyes-Rothan, Beatrice; Hummer, Kim E; Sargent, Daniel J.; Weg, Eric Van De; Iezzoni, Amy F
Using general and specific combining ability to further advance strawberry (Fragaria sp.) breeding Journal Article
In: Acta Hort, vol. 1049, pp. 193-200, 2014.
@article{10949,
title = {Using general and specific combining ability to further advance strawberry (Fragaria sp.) breeding},
author = { MEGAN M Mathey and Sonali Mookerjee and Lise L. Mahoney and Chad E Finn and Serce and Thomas M. Davis and Philip J Stewart and Vance M Whitaker and AR Jamieson and Nahla V. Bassil and Iraida Amaya and Beatrice Denoyes-Rothan and Kim E Hummer and Daniel J. Sargent and Eric Van De Weg and Amy F Iezzoni},
year = {2014},
date = {2014-01-01},
journal = {Acta Hort},
volume = {1049},
pages = {193-200},
abstract = {Strawberry is one of the five fruit crops included in the USDA-funded multiinstitutional and trans-disciplinary project, "RosBREED: Enabling Marker- Assisted Breeding in Rosaceae". A Crop Reference Set (CRS) was developed of 900 genotypes and seedlings from 40 crosses representing the breadth of relevant diversity and encompassing founders used in breeding the domesticated strawberry. Individual native species and cultivar genotypes were included along with 10 progeny from 36 of the crosses of genotypes representing eastern and western North American and European short day and remontant cultivars. This CRS has been phenotyped in five U.S. states. Over 14 fruit quality traits have been studied, as well as remontancy, truss size, peduncle length, crop estimate, plant architecture, and disease resistance. The phenotyping conducted in the first growing season showed considerable variability amongst the genotypes and the locations for all of the characteristics. General and specific combining ability variance components were determined from the populations in order to provide breeders with guidance on the most effective breeding strategies for incorporating the superior traits from this germplasm into their programs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Strawberry is one of the five fruit crops included in the USDA-funded multiinstitutional and trans-disciplinary project, "RosBREED: Enabling Marker- Assisted Breeding in Rosaceae". A Crop Reference Set (CRS) was developed of 900 genotypes and seedlings from 40 crosses representing the breadth of relevant diversity and encompassing founders used in breeding the domesticated strawberry. Individual native species and cultivar genotypes were included along with 10 progeny from 36 of the crosses of genotypes representing eastern and western North American and European short day and remontant cultivars. This CRS has been phenotyped in five U.S. states. Over 14 fruit quality traits have been studied, as well as remontancy, truss size, peduncle length, crop estimate, plant architecture, and disease resistance. The phenotyping conducted in the first growing season showed considerable variability amongst the genotypes and the locations for all of the characteristics. General and specific combining ability variance components were determined from the populations in order to provide breeders with guidance on the most effective breeding strategies for incorporating the superior traits from this germplasm into their programs.
Zhang, Qian; Folta, Kevin M; Davis, Thomas M
In: BMC Plant Biol, vol. 14, pp. 23, 2014, ISSN: 1471-2229, (DOI: https://doi.org/10.1186/1471-2229-14-23).
@article{476,
title = {Somatic embryogenesis, tetraploidy, and variant leaf morphology in transgenic diploid strawberry (Fragaria vesca subspecies vesca &$#$39;Hawaii 4&$#$39;).},
author = { Qian Zhang and Kevin M Folta and Thomas M Davis},
url = {https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-14-23},
doi = {10.1186/1471-2229-14-23},
issn = {1471-2229},
year = {2014},
date = {2014-01-01},
journal = {BMC Plant Biol},
volume = {14},
pages = {23},
abstract = {BACKGROUND: The diploid (2n = 2x = 14) strawberry model plant Fragaria vesca ssp. vesca ’Hawaii 4’ was employed for functional analysis of expressed DNA sequences initially identified as being unique to Fragaria and of unknown or poorly understood function. ’Hawaii 4’ is prominent in strawberry research due to its ease of Agrobacterium-mediated transformation and regenerability, and its status as the source of the first complete strawberry genomic sequence. Our studies of a set of transformants have documented intriguing, construct-associated effects on leaf morphology, and provide important and unexpected insights into the performance of the ’Hawaii 4’ transformation and regeneration system.
RESULTS: Following Agrobacterium-mediated transformation of leaf explants with gene constructs carried by Gateway® vectors, plants were regenerated using a modified version of an established ’Hawaii 4’ protocol. Expanding upon the findings of prior studies, we documented that plantlet regeneration was occurring via a somatic embryogenic rather than an organogenic developmental pathway. Among transformants, several variations in leaf morphology were observed. Unexpectedly, a particular leaf variant type, occurring in ~17% of all regenerants independent of construct type, was found to be attributable to tetraploidy. The tetraploidy-associated alteration in leaf morphology could be differentiated from the leaf morphology of diploid regenerants on the basis of a quantitative ratio of leaf dimensions: B/A, where B is the width of the central leaflet and A is the overall width of the trifoliate leaf. Variant effects on leaf morphology of four different transgenic constructs were also documented, and were in all cases distinguishable from the effects of tetraploidy.
CONCLUSIONS: These results define opportunities to optimize the existing ’Hawaii 4’ protocol by focusing on treatments that specifically promote somatic embryogenesis. The reported morphological metric and descriptions will guide future transgenic studies using the ’Hawaii 4’ model system by alerting researchers to the potential occurrence of polyploid regenerants, and to differentiating the effects on leaf morphology due to polyploidy versus transgenic manipulations. Finally, an intriguing spectrum of leaf morphology alterations resulting from manipulation of expressed sequences of uncertain function is documented, providing a foundation for detailed studies of the respective genes and their functional roles.},
note = {DOI: https://doi.org/10.1186/1471-2229-14-23},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: The diploid (2n = 2x = 14) strawberry model plant Fragaria vesca ssp. vesca ’Hawaii 4’ was employed for functional analysis of expressed DNA sequences initially identified as being unique to Fragaria and of unknown or poorly understood function. ’Hawaii 4’ is prominent in strawberry research due to its ease of Agrobacterium-mediated transformation and regenerability, and its status as the source of the first complete strawberry genomic sequence. Our studies of a set of transformants have documented intriguing, construct-associated effects on leaf morphology, and provide important and unexpected insights into the performance of the ’Hawaii 4’ transformation and regeneration system.
RESULTS: Following Agrobacterium-mediated transformation of leaf explants with gene constructs carried by Gateway® vectors, plants were regenerated using a modified version of an established ’Hawaii 4’ protocol. Expanding upon the findings of prior studies, we documented that plantlet regeneration was occurring via a somatic embryogenic rather than an organogenic developmental pathway. Among transformants, several variations in leaf morphology were observed. Unexpectedly, a particular leaf variant type, occurring in ~17% of all regenerants independent of construct type, was found to be attributable to tetraploidy. The tetraploidy-associated alteration in leaf morphology could be differentiated from the leaf morphology of diploid regenerants on the basis of a quantitative ratio of leaf dimensions: B/A, where B is the width of the central leaflet and A is the overall width of the trifoliate leaf. Variant effects on leaf morphology of four different transgenic constructs were also documented, and were in all cases distinguishable from the effects of tetraploidy.
CONCLUSIONS: These results define opportunities to optimize the existing ’Hawaii 4’ protocol by focusing on treatments that specifically promote somatic embryogenesis. The reported morphological metric and descriptions will guide future transgenic studies using the ’Hawaii 4’ model system by alerting researchers to the potential occurrence of polyploid regenerants, and to differentiating the effects on leaf morphology due to polyploidy versus transgenic manipulations. Finally, an intriguing spectrum of leaf morphology alterations resulting from manipulation of expressed sequences of uncertain function is documented, providing a foundation for detailed studies of the respective genes and their functional roles.
RESULTS: Following Agrobacterium-mediated transformation of leaf explants with gene constructs carried by Gateway® vectors, plants were regenerated using a modified version of an established ’Hawaii 4’ protocol. Expanding upon the findings of prior studies, we documented that plantlet regeneration was occurring via a somatic embryogenic rather than an organogenic developmental pathway. Among transformants, several variations in leaf morphology were observed. Unexpectedly, a particular leaf variant type, occurring in ~17% of all regenerants independent of construct type, was found to be attributable to tetraploidy. The tetraploidy-associated alteration in leaf morphology could be differentiated from the leaf morphology of diploid regenerants on the basis of a quantitative ratio of leaf dimensions: B/A, where B is the width of the central leaflet and A is the overall width of the trifoliate leaf. Variant effects on leaf morphology of four different transgenic constructs were also documented, and were in all cases distinguishable from the effects of tetraploidy.
CONCLUSIONS: These results define opportunities to optimize the existing ’Hawaii 4’ protocol by focusing on treatments that specifically promote somatic embryogenesis. The reported morphological metric and descriptions will guide future transgenic studies using the ’Hawaii 4’ model system by alerting researchers to the potential occurrence of polyploid regenerants, and to differentiating the effects on leaf morphology due to polyploidy versus transgenic manipulations. Finally, an intriguing spectrum of leaf morphology alterations resulting from manipulation of expressed sequences of uncertain function is documented, providing a foundation for detailed studies of the respective genes and their functional roles.
2013
Mathey, M. M.; Mookerjee, S.; Gündüz, K.; Hancock, J. F.; Iezzoni, A. F.; Mahoney, L. L.; Davis, T. M.; Bassil, N. V.; Hummer, K. E.; Stewart, P. J.; Whitaker, V. M.; Sargent, D. J.; Denoyes, B.; Amaya, I.; van de Weg, E.; Finn, C. E.
Large-scale standardized phenotyping of strawberry in RosBREED Journal Article
In: J. Amer. Pom. Soc., vol. 67, no. 4, pp. 205-216, 2013, ( ISSN: 1527-3741).
@article{520,
title = {Large-scale standardized phenotyping of strawberry in RosBREED},
author = { M.M. Mathey and S. Mookerjee and K. Gündüz and J.F. Hancock and A.F. Iezzoni and L.L. Mahoney and T.M. Davis and N.V. Bassil and K.E. Hummer and P.J. Stewart and V.M. Whitaker and D.J. Sargent and B. Denoyes and I. Amaya and E. van de Weg and C.E. Finn},
url = {http://www.pubhort.org/aps/67/v67_n4_a3.htm},
year = {2013},
date = {2013-10-01},
journal = {J. Amer. Pom. Soc.},
volume = {67},
number = {4},
pages = {205-216},
abstract = {In an effort to implement marker-assisted breeding in Rosaceae, many traits need to be characterized in diverse germplasm. The USDA-NIFA Specialty Crop Research Initiative-funded RosBREED project includes breeding programs of four Rosaceae crops (apple, peach, cherry and strawberry). Phenotyping each crop for specific horticultural and commercial traits is an important process needed to translate genomic knowledge through marker-assisted breeding into enhanced breeding efficiency. These data will directly aid in the identification of quantitative trait loci or marker-trait associations that will be used to assist breeding programs in the future. Large-scale, standardized phenotyping protocols have been set up for each crop. The standardized phenotyping protocol for strawberries was agreed upon by the breeding teams in Oregon, Michigan, New Hampshire, California and Florida and includes four trait categories: phenology and other flower-related traits, plant characteristics, fruit characteristics, and fruit chemistry traits. We describe how each of the traits in the categories was evaluated. A summary of mean values for 37 traits of the genotypes planted at the RosBREED locations in 2011 and 2012 is provided. The phenotypic data for widely used founder germplasm that has contributed to current cultivars is available through the “Breeders Toolbox” at the Genome Database for Rosaceae (http://www.rosaceae.org/breeders_toolbox).},
note = {
ISSN: 1527-3741},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In an effort to implement marker-assisted breeding in Rosaceae, many traits need to be characterized in diverse germplasm. The USDA-NIFA Specialty Crop Research Initiative-funded RosBREED project includes breeding programs of four Rosaceae crops (apple, peach, cherry and strawberry). Phenotyping each crop for specific horticultural and commercial traits is an important process needed to translate genomic knowledge through marker-assisted breeding into enhanced breeding efficiency. These data will directly aid in the identification of quantitative trait loci or marker-trait associations that will be used to assist breeding programs in the future. Large-scale, standardized phenotyping protocols have been set up for each crop. The standardized phenotyping protocol for strawberries was agreed upon by the breeding teams in Oregon, Michigan, New Hampshire, California and Florida and includes four trait categories: phenology and other flower-related traits, plant characteristics, fruit characteristics, and fruit chemistry traits. We describe how each of the traits in the categories was evaluated. A summary of mean values for 37 traits of the genotypes planted at the RosBREED locations in 2011 and 2012 is provided. The phenotypic data for widely used founder germplasm that has contributed to current cultivars is available through the “Breeders Toolbox” at the Genome Database for Rosaceae (http://www.rosaceae.org/breeders_toolbox).
Letscher, R. T.; Hansell, D. A.; Carlson, C. A.; Lumpkin, R.; Knapp, A. N.
Dissolved organic nitrogen in the global surface ocean: Distribution and fate Journal Article
In: Global Biogeochemical Cycles, vol. 27, pp. 141-153, 2013.
@article{2510,
title = {Dissolved organic nitrogen in the global surface ocean: Distribution and fate},
author = {R. T. Letscher and D. A. Hansell and C. A. Carlson and R. Lumpkin and A. N. Knapp},
url = {http://onlinelibrary.wiley.com/doi/10.1029/2012GB004449/full},
year = {2013},
date = {2013-01-01},
journal = {Global Biogeochemical Cycles},
volume = {27},
pages = {141-153},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Letscher, R. T.; Hansell, D. A.; Kadko, D.; Bates, N. R.
Dissolved organic nitrogen dynamics in the Arctic Ocean Journal Article
In: Marine Chemistry, vol. 148, pp. 1-9, 2013.
@article{2509,
title = {Dissolved organic nitrogen dynamics in the Arctic Ocean},
author = {R. T. Letscher and D. A. Hansell and D. Kadko and N. R. Bates},
url = {http://www.sciencedirect.com/science/article/pii/S0304420312001168},
year = {2013},
date = {2013-01-01},
journal = {Marine Chemistry},
volume = {148},
pages = {1-9},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hummer, Kim E; Ballington, James R; Finn, Chad E; Davis, Thomas M
Asian germplasm influences on American berry crops Journal Article
In: HortScience, vol. 48, no. 9, pp. 1090-1094, 2013, ISBN: 0018-5345.
@article{487,
title = {Asian germplasm influences on American berry crops},
author = { Kim E Hummer and James R Ballington and Chad E Finn and Thomas M Davis},
url = {http://hortsci.ashspublications.org/content/48/9/1090.full},
isbn = {0018-5345},
year = {2013},
date = {2013-01-01},
journal = {HortScience},
volume = {48},
number = {9},
pages = {1090-1094},
publisher = {American Society for Horticultural Science},
abstract = {Asian germplasm has significantly contributed to berry crops in America in several ways. The American wild octoploid species [Fragaria chiloensis (L.) Mill. and F. virginiana Mill.], and subsequently, the cultivated strawberry (F. ×ananassa Duch. ex Rozier), have benefitted from Asian heritage in the evolutionary time scale. Second, breeders have combined Asian germplasm in crosses for improved fruit cultivars. Third, Asian temperate fruit species have been collected from wild stands in their native ranges, imported, and in some cases improved and are now cultivated in the West or throughout the world. The objectives of this article were to 1) describe evolutionary contributions of Asian species to the American strawberry genome; 2) present examples of breeding Asian species (Rubus L. subgenus Idaeobatus) into cultivated raspberries; and 3) give examples of two Asian fruit species that have been recently introduced and cultivated or that could be developed for cultivation in the United States.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Asian germplasm has significantly contributed to berry crops in America in several ways. The American wild octoploid species [Fragaria chiloensis (L.) Mill. and F. virginiana Mill.], and subsequently, the cultivated strawberry (F. ×ananassa Duch. ex Rozier), have benefitted from Asian heritage in the evolutionary time scale. Second, breeders have combined Asian germplasm in crosses for improved fruit cultivars. Third, Asian temperate fruit species have been collected from wild stands in their native ranges, imported, and in some cases improved and are now cultivated in the West or throughout the world. The objectives of this article were to 1) describe evolutionary contributions of Asian species to the American strawberry genome; 2) present examples of breeding Asian species (Rubus L. subgenus Idaeobatus) into cultivated raspberries; and 3) give examples of two Asian fruit species that have been recently introduced and cultivated or that could be developed for cultivation in the United States.
2011
Liu, Bo; Davis, Thomas M
Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae). Journal Article
In: BMC Plant Biol, vol. 11, pp. 157, 2011, ISSN: 1471-2229.
@article{477,
title = {Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae).},
author = { Bo Liu and Thomas M Davis},
url = {https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-11-157},
doi = {10.1186/1471-2229-11-157},
issn = {1471-2229},
year = {2011},
date = {2011-11-01},
journal = {BMC Plant Biol},
volume = {11},
pages = {157},
abstract = {BACKGROUND: The genus Fragaria comprises species at ploidy levels ranging from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70). Fluorescence in situ hybridization with 5S and 25S rDNA probes was performed to gather cytogenetic information that illuminates genomic divergence among different taxa at multiple ploidy levels, as well as to explore the evolution of ribosomal RNA genes during polyploidization in Fragaria.
RESULTS: Root tip cells of diploid taxa were typified by two 5S and six 25S rDNA hybridization signals of varying intensities, providing a baseline for comparisons within the genus. In three exceptional diploid genotypes, F. nilgerrensis (CFRA 1358 and CFRA 1825) and F. vesca ’Yellow Wonder’, two 5S but only four 25S rDNA sites were found but with differing site losses. The numbers of 5S and 25S rDNA signals, respectively were three and nine in a triploid F. ×bifera accession, and were four and twelve in three tetraploids, thus occurring in proportional 1.5× and 2× multiples of the typical diploid pattern. In hexaploid F. moschata, a proportional multiple of six 5S rDNA sites was observed, but the number of 25S rDNA sites was one or two less than the proportionate prediction of eighteen. This apparent tendency toward rDNA site loss at higher ploidy was markedly expanded in octoploids, which displayed only two 5S and ten 25S rDNA sites. In the two decaploids examined, the numbers of 5S and 25S rDNA signals, respectively, were four and fifteen in F. virginiana subsp. platypetala, and six and twelve in F. iturupensis.
CONCLUSIONS: Among diploid Fragaria species, a general consistency of rDNA site numbers implies conserved genomic organization, but highly variable 25S signal sizes and intensities and two instances of site loss suggest concurrent high dynamics of rDNA copy numbers among both homologs and non-homologs. General conservation of rDNA site numbers in lower ploidy, but marked site number reductions at higher ploidy levels, suggest complex evolution of rDNA sites during polyploidization and/or independent evolutionary pathways for 6x versus higher ploidy strawberries. Site number comparisons suggest common genomic composition among natural octoploids, and independent origins of the two divergent decaploid accessions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: The genus Fragaria comprises species at ploidy levels ranging from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70). Fluorescence in situ hybridization with 5S and 25S rDNA probes was performed to gather cytogenetic information that illuminates genomic divergence among different taxa at multiple ploidy levels, as well as to explore the evolution of ribosomal RNA genes during polyploidization in Fragaria.
RESULTS: Root tip cells of diploid taxa were typified by two 5S and six 25S rDNA hybridization signals of varying intensities, providing a baseline for comparisons within the genus. In three exceptional diploid genotypes, F. nilgerrensis (CFRA 1358 and CFRA 1825) and F. vesca ’Yellow Wonder’, two 5S but only four 25S rDNA sites were found but with differing site losses. The numbers of 5S and 25S rDNA signals, respectively were three and nine in a triploid F. ×bifera accession, and were four and twelve in three tetraploids, thus occurring in proportional 1.5× and 2× multiples of the typical diploid pattern. In hexaploid F. moschata, a proportional multiple of six 5S rDNA sites was observed, but the number of 25S rDNA sites was one or two less than the proportionate prediction of eighteen. This apparent tendency toward rDNA site loss at higher ploidy was markedly expanded in octoploids, which displayed only two 5S and ten 25S rDNA sites. In the two decaploids examined, the numbers of 5S and 25S rDNA signals, respectively, were four and fifteen in F. virginiana subsp. platypetala, and six and twelve in F. iturupensis.
CONCLUSIONS: Among diploid Fragaria species, a general consistency of rDNA site numbers implies conserved genomic organization, but highly variable 25S signal sizes and intensities and two instances of site loss suggest concurrent high dynamics of rDNA copy numbers among both homologs and non-homologs. General conservation of rDNA site numbers in lower ploidy, but marked site number reductions at higher ploidy levels, suggest complex evolution of rDNA sites during polyploidization and/or independent evolutionary pathways for 6x versus higher ploidy strawberries. Site number comparisons suggest common genomic composition among natural octoploids, and independent origins of the two divergent decaploid accessions.
RESULTS: Root tip cells of diploid taxa were typified by two 5S and six 25S rDNA hybridization signals of varying intensities, providing a baseline for comparisons within the genus. In three exceptional diploid genotypes, F. nilgerrensis (CFRA 1358 and CFRA 1825) and F. vesca ’Yellow Wonder’, two 5S but only four 25S rDNA sites were found but with differing site losses. The numbers of 5S and 25S rDNA signals, respectively were three and nine in a triploid F. ×bifera accession, and were four and twelve in three tetraploids, thus occurring in proportional 1.5× and 2× multiples of the typical diploid pattern. In hexaploid F. moschata, a proportional multiple of six 5S rDNA sites was observed, but the number of 25S rDNA sites was one or two less than the proportionate prediction of eighteen. This apparent tendency toward rDNA site loss at higher ploidy was markedly expanded in octoploids, which displayed only two 5S and ten 25S rDNA sites. In the two decaploids examined, the numbers of 5S and 25S rDNA signals, respectively, were four and fifteen in F. virginiana subsp. platypetala, and six and twelve in F. iturupensis.
CONCLUSIONS: Among diploid Fragaria species, a general consistency of rDNA site numbers implies conserved genomic organization, but highly variable 25S signal sizes and intensities and two instances of site loss suggest concurrent high dynamics of rDNA copy numbers among both homologs and non-homologs. General conservation of rDNA site numbers in lower ploidy, but marked site number reductions at higher ploidy levels, suggest complex evolution of rDNA sites during polyploidization and/or independent evolutionary pathways for 6x versus higher ploidy strawberries. Site number comparisons suggest common genomic composition among natural octoploids, and independent origins of the two divergent decaploid accessions.
Shulaev, Vladimir; Sargent, Daniel J; Crowhurst, Ross N; Mockler, Todd C; Folkerts, Otto; Delcher, Arthur L; Jaiswal, Pankaj; Mockaitis, Keithanne; Liston, A; Mane, Shrinivasrao P; Burns, Paul; Davis, Thomas M; Slovin, Janet P; Bassil, Nahla; Hellens, Roger P; Evans, Clive; Harkins, Tim; Kodira, Chinnappa; Desany, Brian; Crasta, Oswald R; Jensen, Roderick V; Allan, Andrew C; Michael, Todd P; Setubal, Joao Carlos; Celton, Jean-Marc; Rees, D Jasper G; Williams, Kelly P; Holt, Sarah H; Rojas, Juan Jairo Ruiz; Chatterjee, Mithu; Liu, Bo; Silva, Herman; Meisel, Lee; Adato, Avital; Filichkin, Sergei A; Troggio, Michela; Viola, Roberto; Ashman, Tia-Lynn; Wang, Hao; Dharmawardhana, Palitha; Elser, Justin; Raja, Rajani; Priest, Henry D; Bryant, Douglas W; Fox, Samuel E; Givan, Scott A; Wilhelm, Larry J; Naithani, Sushma; Christoffels, Alan; Salama, David Y; Carter, Jade; Girona, Elena Lopez; Zdepski, Anna; Wang, Wenqin; Kerstetter, Randall A; Schwab, Wilfried; Korban, Schuyler S; Davik, Jahn; Monfort, Amparo; Denoyes-Rothan, Beatrice; Arus, Pere; Mittler, Ron; Flinn, Barry; Aharoni, Asaph; Bennetzen, Jeffrey L; Salzberg, Steven L; Dickerman, Allan W; Velasco, Riccardo; Borodovsky, Mark; Veilleux, Richard E; Folta, Kevin M
The genome of woodland strawberry (Fragaria vesca) Journal Article
In: Nat Genet, vol. 43, no. 2, pp. 109-16, 2011, ISSN: 1546-1718.
@article{484,
title = {The genome of woodland strawberry (Fragaria vesca)},
author = { Vladimir Shulaev and Daniel J Sargent and Ross N Crowhurst and Todd C Mockler and Otto Folkerts and Arthur L Delcher and Pankaj Jaiswal and Keithanne Mockaitis and A Liston and Shrinivasrao P Mane and Paul Burns and Thomas M Davis and Janet P Slovin and Nahla Bassil and Roger P Hellens and Clive Evans and Tim Harkins and Chinnappa Kodira and Brian Desany and Oswald R Crasta and Roderick V Jensen and Andrew C Allan and Todd P Michael and Joao Carlos Setubal and Jean-Marc Celton and D Jasper G Rees and Kelly P Williams and Sarah H Holt and Juan Jairo Ruiz Rojas and Mithu Chatterjee and Bo Liu and Herman Silva and Lee Meisel and Avital Adato and Sergei A Filichkin and Michela Troggio and Roberto Viola and Tia-Lynn Ashman and Hao Wang and Palitha Dharmawardhana and Justin Elser and Rajani Raja and Henry D Priest and Douglas W Bryant and Samuel E Fox and Scott A Givan and Larry J Wilhelm and Sushma Naithani and Alan Christoffels and David Y Salama and Jade Carter and Elena Lopez Girona and Anna Zdepski and Wenqin Wang and Randall A Kerstetter and Wilfried Schwab and Schuyler S Korban and Jahn Davik and Amparo Monfort and Beatrice Denoyes-Rothan and Pere Arus and Ron Mittler and Barry Flinn and Asaph Aharoni and Jeffrey L Bennetzen and Steven L Salzberg and Allan W Dickerman and Riccardo Velasco and Mark Borodovsky and Richard E Veilleux and Kevin M Folta},
url = {http://www.nature.com/ng/journal/v43/n2/full/ng.740.html},
doi = {10.1038/ng.740},
issn = {1546-1718},
year = {2011},
date = {2011-02-01},
journal = {Nat Genet},
volume = {43},
number = {2},
pages = {109-16},
abstract = {The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
Letscher, R. T.; Hansell, D. A.; Kadko, D.
Rapid removal of terrigenous dissolved organic carbon over the Eurasian shelves of the Arctic Ocean Journal Article
In: Marine Chemistry, vol. 123, pp. 78-87, 2011.
@article{2508,
title = {Rapid removal of terrigenous dissolved organic carbon over the Eurasian shelves of the Arctic Ocean},
author = {R. T. Letscher and D. A. Hansell and D. Kadko},
url = {http://www.sciencedirect.com/science/article/pii/S0304420310001052},
year = {2011},
date = {2011-01-01},
journal = {Marine Chemistry},
volume = {123},
pages = {78-87},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Millero, F. J.; Huang, F.; Woosley, R. J.; Letscher, R. T.; Hansell, D. A.
Effect of dissolved organic carbon and alkalinity on the density of Arctic Ocean waters Journal Article
In: Aquatic Geochemistry, vol. 17, no. 4-5, pp. 311-326, 2011.
@article{2507,
title = {Effect of dissolved organic carbon and alkalinity on the density of Arctic Ocean waters},
author = {F. J. Millero and F. Huang and R. J. Woosley and R. T. Letscher and D. A. Hansell},
url = {https://link.springer.com/article/10.1007/s10498-010-9111-2},
year = {2011},
date = {2011-01-01},
journal = {Aquatic Geochemistry},
volume = {17},
number = {4-5},
pages = {311-326},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sargent, Daniel J; Kuchta, Paulina; Girona, Elena Lopez; Zhang, Hailong; Davis, Thomas M; Celton, Jean-Marc; Marchese, Annalisa; Korbin, Malgorzata; Folta, Kevin M; Shulaev, Vladimir
Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence Journal Article
In: The Plant Genome, vol. 4, no. 3, pp. 165-177, 2011, ISBN: 1940-3372, (Supplemental files: http://www.crops.org/publications/tpg).
@article{1428,
title = {Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence},
author = { Daniel J Sargent and Paulina Kuchta and Elena Lopez Girona and Hailong Zhang and Thomas M Davis and Jean-Marc Celton and Annalisa Marchese and Malgorzata Korbin and Kevin M Folta and Vladimir Shulaev},
url = {https://dl.sciencesocieties.org/publications/tpg/articles/4/3/165},
isbn = {1940-3372},
year = {2011},
date = {2011-01-01},
journal = {The Plant Genome},
volume = {4},
number = {3},
pages = {165-177},
publisher = {Crop Science Society of America},
abstract = {The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria ×ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physical map, using predominantly SSR markers to order scaffolds via anchoring to a comprehensive linkage map. This report complements and expands resolution of the Fragaria spp. reference map and refines the scaffold ordering of the F. vesca genome sequence using newly devised tools. The results of this study provide two significant resources: (i) the concurrent validation of a substantial set of SSRs associated with these previously unmapped regions of the Fragaria spp. genome and (ii) the precise placement of previously orphaned genomic sequence. Together, these resources improve the resolution and completeness of the strawberry genome sequence, making it a better resource for downstream studies in Fragaria spp. and the family Rosaceae.},
note = {Supplemental files: http://www.crops.org/publications/tpg},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria ×ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physical map, using predominantly SSR markers to order scaffolds via anchoring to a comprehensive linkage map. This report complements and expands resolution of the Fragaria spp. reference map and refines the scaffold ordering of the F. vesca genome sequence using newly devised tools. The results of this study provide two significant resources: (i) the concurrent validation of a substantial set of SSRs associated with these previously unmapped regions of the Fragaria spp. genome and (ii) the precise placement of previously orphaned genomic sequence. Together, these resources improve the resolution and completeness of the strawberry genome sequence, making it a better resource for downstream studies in Fragaria spp. and the family Rosaceae.
2010
Davis, Thomas M; Shields, Melanie E; Zhang, Qian; Tombolato-Terzić, Denise; Bennetzen, Jeffrey L; Pontaroli, Ana C; Wang, Hao; Yao, Qin; SanMiguel, Phillip; Folta, Kevin M
An examination of targeted gene neighborhoods in strawberry Journal Article
In: BMC Plant Biol, vol. 10, pp. 81, 2010, ISSN: 1471-2229.
@article{479,
title = {An examination of targeted gene neighborhoods in strawberry},
author = { Thomas M Davis and Melanie E Shields and Qian Zhang and Denise Tombolato-Terzi{ć} and Jeffrey L Bennetzen and Ana C Pontaroli and Hao Wang and Qin Yao and Phillip SanMiguel and Kevin M Folta},
url = {https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-10-81},
doi = {10.1186/1471-2229-10-81},
issn = {1471-2229},
year = {2010},
date = {2010-05-01},
journal = {BMC Plant Biol},
volume = {10},
pages = {81},
abstract = {BACKGROUND: Strawberry (Fragaria ssp.) is the familiar name of a group of economically important crop plants and wild relatives that also represent an emerging system for the study of gene and genome evolution. Its small stature, rapid seed-to-seed cycle, transformability and miniscule basic genome make strawberry an attractive system to study processes related to plant physiology, development and crop production; yet it lacks substantial genomics-level resources. This report addresses this deficiency by characterizing 0.71 Mbp of gene space from a diploid species (F. vesca). The twenty large genomic tracks (30-52 kb) captured as fosmid inserts comprise gene regions with roles in flowering, disease resistance, and metabolism.
RESULTS: A detailed description of the studied regions reveals 131 Blastx-supported gene sites and eight additional EST-supported gene sites. Only 15 genes have complete EST coverage, enabling gene modelling, while 76 lack EST support. Instances of microcolinearity with Arabidopsis thaliana were identified in twelve inserts. A relatively high portion (25%) of targeted genes were found in unanticipated tandem duplications. The effectiveness of six FGENESH training models was assessed via comparisons among ab initio predictions and homology-based gene and start/stop codon identifications. Fourteen transposable-element-related sequences and 158 simple sequence repeat loci were delineated.
CONCLUSIONS: This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Strawberry (Fragaria ssp.) is the familiar name of a group of economically important crop plants and wild relatives that also represent an emerging system for the study of gene and genome evolution. Its small stature, rapid seed-to-seed cycle, transformability and miniscule basic genome make strawberry an attractive system to study processes related to plant physiology, development and crop production; yet it lacks substantial genomics-level resources. This report addresses this deficiency by characterizing 0.71 Mbp of gene space from a diploid species (F. vesca). The twenty large genomic tracks (30-52 kb) captured as fosmid inserts comprise gene regions with roles in flowering, disease resistance, and metabolism.
RESULTS: A detailed description of the studied regions reveals 131 Blastx-supported gene sites and eight additional EST-supported gene sites. Only 15 genes have complete EST coverage, enabling gene modelling, while 76 lack EST support. Instances of microcolinearity with Arabidopsis thaliana were identified in twelve inserts. A relatively high portion (25%) of targeted genes were found in unanticipated tandem duplications. The effectiveness of six FGENESH training models was assessed via comparisons among ab initio predictions and homology-based gene and start/stop codon identifications. Fourteen transposable-element-related sequences and 158 simple sequence repeat loci were delineated.
CONCLUSIONS: This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.
RESULTS: A detailed description of the studied regions reveals 131 Blastx-supported gene sites and eight additional EST-supported gene sites. Only 15 genes have complete EST coverage, enabling gene modelling, while 76 lack EST support. Instances of microcolinearity with Arabidopsis thaliana were identified in twelve inserts. A relatively high portion (25%) of targeted genes were found in unanticipated tandem duplications. The effectiveness of six FGENESH training models was assessed via comparisons among ab initio predictions and homology-based gene and start/stop codon identifications. Fourteen transposable-element-related sequences and 158 simple sequence repeat loci were delineated.
CONCLUSIONS: This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.
Orcheski, Benjamin B; Davis, Thomas M
An enhanced method for sequence walking and paralog mining: TOPO(R) Vector-Ligation PCR. Journal Article
In: BMC Res Notes, vol. 3, pp. 61, 2010, ISSN: 1756-0500.
@article{480,
title = {An enhanced method for sequence walking and paralog mining: TOPO(R) Vector-Ligation PCR.},
author = { Benjamin B Orcheski and Thomas M Davis},
url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-3-61},
doi = {10.1186/1756-0500-3-61},
issn = {1756-0500},
year = {2010},
date = {2010-03-01},
journal = {BMC Res Notes},
volume = {3},
pages = {61},
abstract = {BACKGROUND: Although technological advances allow for the economical acquisition of whole genome sequences, many organisms’ genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO(R) Vector-Ligation PCR (or TVL-PCR) that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining.
FINDINGS: TVL-PCR exploits the ligation efficiency of the pCR(R)4-TOPO(R) (Invitrogen, Carlsbad, California) vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3’ adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes.
CONCLUSIONS: TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Although technological advances allow for the economical acquisition of whole genome sequences, many organisms’ genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO(R) Vector-Ligation PCR (or TVL-PCR) that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining.
FINDINGS: TVL-PCR exploits the ligation efficiency of the pCR(R)4-TOPO(R) (Invitrogen, Carlsbad, California) vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3’ adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes.
CONCLUSIONS: TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.
FINDINGS: TVL-PCR exploits the ligation efficiency of the pCR(R)4-TOPO(R) (Invitrogen, Carlsbad, California) vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3’ adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes.
CONCLUSIONS: TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.
Davis, TM; Shields, ME; Reinhard, AE; Reavey, PA; Lin, J; Zhang, H; Mahoney, LL
Chloroplast DNA inheritance, ancestry, and sequencing in Fragaria Journal Article
In: Acta Hortic, vol. 859, pp. 221-228, 2010, ISBN: 9066052287.
@article{490,
title = {Chloroplast DNA inheritance, ancestry, and sequencing in Fragaria},
author = { TM Davis and ME Shields and AE Reinhard and PA Reavey and J Lin and H Zhang and LL Mahoney},
url = {http://www.actahort.org/books/859/859_25.htm},
isbn = {9066052287},
year = {2010},
date = {2010-01-01},
journal = {Acta Hortic},
volume = {859},
pages = {221-228},
abstract = {In the emerging era of Next Generation (NextGen) technologies, molecular markers will continue to play important roles in research requiring targeted genotyping rather than global sequencing. Using chloroplast DNA (cpDNA) markers, we generated the first evidence confirming that cpDNA is maternally inherited in Fragaria, and defined likely diploid sources of the chloroplast genomes harbored by the Fragaria hexaploid, octoploid, and decaploid allopolyploid species. As a resource for future research on Fragaria cpDNA, we used a NextGen sequencing approach to assemble a draft sequence of the Fragaria vesca subsp. americana ‘Pawtuckaway’ chloroplast genome.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In the emerging era of Next Generation (NextGen) technologies, molecular markers will continue to play important roles in research requiring targeted genotyping rather than global sequencing. Using chloroplast DNA (cpDNA) markers, we generated the first evidence confirming that cpDNA is maternally inherited in Fragaria, and defined likely diploid sources of the chloroplast genomes harbored by the Fragaria hexaploid, octoploid, and decaploid allopolyploid species. As a resource for future research on Fragaria cpDNA, we used a NextGen sequencing approach to assemble a draft sequence of the Fragaria vesca subsp. americana ‘Pawtuckaway’ chloroplast genome.
Mahoney, LL; Quimby, ML; Shields, ME; Davis, TM
Mitochondrial DNA transmission, ancestry, and sequences in Fragaria Proceedings
vol. 859, 2010, ISBN: 9066052287.
@proceedings{491,
title = {Mitochondrial DNA transmission, ancestry, and sequences in Fragaria},
author = { LL Mahoney and ML Quimby and ME Shields and TM Davis},
url = {http://www.actahort.org/books/859/859_35.htm},
isbn = {9066052287},
year = {2010},
date = {2010-01-01},
journal = {Acta Hortic},
volume = {859},
pages = {301-308},
abstract = {Of the three plant genomic components (nuclear, plastid, and mitochondrial) the mitochondrial DNA (mtDNA) has received the least research attention. We describe a phylogenetically informative sequence in the matR gene region of the Fragaria (strawberry) mtDNA, and the first mtDNA marker developed for this economically important genus. The sequence was obtained from a fosmid genomic library clone of F. vesca subsp. americana ‘Pawtuckaway’. New mtDNA PCR primer sets work on members of the Rosaceae family, and have potential for broad applicability in the angiosperms. An informative mtDNA CAPS (cleaved amplified polymorphic site) marker provided evidence that mtDNA was transmitted maternally in two interspecific crosses, and that diploid F. iinumae is the likely mtDNA donor to the octoploid species F. chiloensis and F. virginiana, but not to decaploid F. iturupensis. We expanded the database of Fragaria mtDNA sequence by assembling a 67 kb mtDNA contig from Illumina 36 bp paired-end reads from ‘Pawtuckaway’, providing a basis to develop additional mtDNA markers.},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
Of the three plant genomic components (nuclear, plastid, and mitochondrial) the mitochondrial DNA (mtDNA) has received the least research attention. We describe a phylogenetically informative sequence in the matR gene region of the Fragaria (strawberry) mtDNA, and the first mtDNA marker developed for this economically important genus. The sequence was obtained from a fosmid genomic library clone of F. vesca subsp. americana ‘Pawtuckaway’. New mtDNA PCR primer sets work on members of the Rosaceae family, and have potential for broad applicability in the angiosperms. An informative mtDNA CAPS (cleaved amplified polymorphic site) marker provided evidence that mtDNA was transmitted maternally in two interspecific crosses, and that diploid F. iinumae is the likely mtDNA donor to the octoploid species F. chiloensis and F. virginiana, but not to decaploid F. iturupensis. We expanded the database of Fragaria mtDNA sequence by assembling a 67 kb mtDNA contig from Illumina 36 bp paired-end reads from ‘Pawtuckaway’, providing a basis to develop additional mtDNA markers.
Folta, Kevin M; Clancy, Maureen A; Chamala, Srikar; Brunings, Asha M; Dhingra, Amit; Gomide, Leandro; Kulathinal, Rob J; Peres, Natalia; Davis, Thomas M; Barbazuk, W Brad
A transcript accounting from diverse tissues of a cultivated strawberry Journal Article
In: The Plant Genome, vol. 3, no. 2, pp. 90-105, 2010, ISBN: 1940-3372.
@article{489,
title = {A transcript accounting from diverse tissues of a cultivated strawberry},
author = { Kevin M Folta and Maureen A Clancy and Srikar Chamala and Asha M Brunings and Amit Dhingra and Leandro Gomide and Rob J Kulathinal and Natalia Peres and Thomas M Davis and W Brad Barbazuk},
url = {https://dl.sciencesocieties.org/publications/tpg/articles/3/2/90},
isbn = {1940-3372},
year = {2010},
date = {2010-01-01},
journal = {The Plant Genome},
volume = {3},
number = {2},
pages = {90-105},
publisher = {Crop Science Society of America},
abstract = {Strawberry (Fragaria spp.) is a valuable fruit crop as well as an outstanding system for studying functional genomics in plants. The goal of this study was to substantially increase and analyze the available expressed sequence information in the genus by examining the transcriptome of the cultivated strawberry (Fragaria × ananassa Duchesne). To maximize transcript diversity and discovery, plants representing an octoploid strawberry cultivar were subjected to a broad range of treatments. Plant materials were pooled by tissue type. cDNA pools were sequenced by the Roche-454 GS-FLX system and assembled into over 32,000 contigs. Predictions of cellular localization and function were made by associating assembled contigs to annotated homologs, and the tissue pool tags provided a means to assess the overall expression pattern for any given transcript. Contigs comprised of reads originating from only one organ type and those present equally in all plant organs were both identified. Bacterial and fungal sequences found in the strawberry samples provide a metagenomic survey of the microbial community of a greenhouse strawberry plant. This study utilized an innovative assembly strategy on pooled tissues, thus providing a foundation for developing tissue-specific tools, an opportunity to identify alleles for marker-assisted selection, a reference of strawberry gene annotations, and a basis for comparative transcriptomics between cultivated strawberry, its diploid ancestors, and the wider Rosaceae family.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Strawberry (Fragaria spp.) is a valuable fruit crop as well as an outstanding system for studying functional genomics in plants. The goal of this study was to substantially increase and analyze the available expressed sequence information in the genus by examining the transcriptome of the cultivated strawberry (Fragaria × ananassa Duchesne). To maximize transcript diversity and discovery, plants representing an octoploid strawberry cultivar were subjected to a broad range of treatments. Plant materials were pooled by tissue type. cDNA pools were sequenced by the Roche-454 GS-FLX system and assembled into over 32,000 contigs. Predictions of cellular localization and function were made by associating assembled contigs to annotated homologs, and the tissue pool tags provided a means to assess the overall expression pattern for any given transcript. Contigs comprised of reads originating from only one organ type and those present equally in all plant organs were both identified. Bacterial and fungal sequences found in the strawberry samples provide a metagenomic survey of the microbial community of a greenhouse strawberry plant. This study utilized an innovative assembly strategy on pooled tissues, thus providing a foundation for developing tissue-specific tools, an opportunity to identify alleles for marker-assisted selection, a reference of strawberry gene annotations, and a basis for comparative transcriptomics between cultivated strawberry, its diploid ancestors, and the wider Rosaceae family.
2009
Vining, Kelly; Davis, Thomas
Isolation of a Ve homolog, mVe1, and its relationship to Verticillium wilt resistance in Mentha longifolia (L.) Huds. Journal Article
In: Mol Genet Genomics, vol. 282, no. 2, pp. 173-84, 2009, ISSN: 1617-4623.
@article{482,
title = {Isolation of a Ve homolog, mVe1, and its relationship to Verticillium wilt resistance in Mentha longifolia (L.) Huds.},
author = { Kelly Vining and Thomas Davis},
url = {https://link.springer.com/article/10.1007/s00438-009-0454-6},
doi = {10.1007/s00438-009-0454-6},
issn = {1617-4623},
year = {2009},
date = {2009-08-01},
journal = {Mol Genet Genomics},
volume = {282},
number = {2},
pages = {173-84},
abstract = {As a step toward greater understanding of the genetics of verticillium wilt resistance in plants, we report the sequencing of a candidate wilt resistance gene, mVe1, from the mint diploid model species, Mentha longifolia (Lamiaceae). mVe1 is a putative homolog of tomato (Solanum lycopersicum L.) verticillium wilt (Ve) resistance genes. The mVe1 gene has a coding region of 3,051 bp. The predicted mVe1 protein contains a leucine-rich repeat domain, a common feature of plant disease resistance proteins. We compared 13 mVe1 alleles from three mint species. These alleles shared 96.2-99.6% nucleotide identity. We analyzed four M. longifolia populations segregating with respect to mVe1 alleles and wilt resistance versus susceptibility and found one association between mVe1 genotype and wilt phenotype. We conclude that mVe1 may play a role in mint verticillium wilt resistance, but variation for resistance in our segregating progenies is likely polygenic. Therefore, further investigations of mVe1 and identification of additional candidate genes are both warranted.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
As a step toward greater understanding of the genetics of verticillium wilt resistance in plants, we report the sequencing of a candidate wilt resistance gene, mVe1, from the mint diploid model species, Mentha longifolia (Lamiaceae). mVe1 is a putative homolog of tomato (Solanum lycopersicum L.) verticillium wilt (Ve) resistance genes. The mVe1 gene has a coding region of 3,051 bp. The predicted mVe1 protein contains a leucine-rich repeat domain, a common feature of plant disease resistance proteins. We compared 13 mVe1 alleles from three mint species. These alleles shared 96.2-99.6% nucleotide identity. We analyzed four M. longifolia populations segregating with respect to mVe1 alleles and wilt resistance versus susceptibility and found one association between mVe1 genotype and wilt phenotype. We conclude that mVe1 may play a role in mint verticillium wilt resistance, but variation for resistance in our segregating progenies is likely polygenic. Therefore, further investigations of mVe1 and identification of additional candidate genes are both warranted.
Hummer, KE; Richards, C; Davis, TM; Njuguna, W; Bassil, NV
Genetic diversity of Japanese strawberry species based on microsatellite markers Journal Article
In: Acta Hortic, vol. 842, pp. 581-584, 2009, ISBN: 9066056428.
@article{494,
title = {Genetic diversity of Japanese strawberry species based on microsatellite markers},
author = { KE Hummer and C Richards and TM Davis and W Njuguna and NV Bassil},
url = {https://www.researchgate.net/profile/Nahla_Bassil/publication/225690470_Genetic_diversity_of_diploid_Japanese_strawberry_species_based_on_microsatellite_markers/links/00b4952ebf41423187000000.pdf},
isbn = {9066056428},
year = {2009},
date = {2009-01-01},
journal = {Acta Hortic},
volume = {842},
pages = {581-584},
abstract = {The United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, is a genebank that preserves strawberry genetic resources. The Fragaria L. collection consists of more than 1700 accessions of 17 species from 37 countries. In 2004, Asian diploid species, F. iinumae Makino and F. nipponica Makino, were collected during an expedition to Hokkaido, Japan. An ancestor of F. iinumae may be a progenitor of the “B” genome for octoploid strawberry species. The objective of this study was to evaluate the diversity of these two species using microsatellite markers. We report preliminary results obtained from SSR analysis of 139 accessions based on 20 SSRs. A higher genetic diversity was observed in F. nipponica, which tends to be cross pollinated, than in F. iinumae, which tends to be self-pollinated. This study identified putative hybrids between F. iinumae and F. nipponica as well as an unexpected octoploid accession from Hokkaido, Japan. The hybrid nature of these accessions and the possible source of this octoploid accession will be further evaluated using chloroplast and nuclear markers as well as morphological traits.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, is a genebank that preserves strawberry genetic resources. The Fragaria L. collection consists of more than 1700 accessions of 17 species from 37 countries. In 2004, Asian diploid species, F. iinumae Makino and F. nipponica Makino, were collected during an expedition to Hokkaido, Japan. An ancestor of F. iinumae may be a progenitor of the “B” genome for octoploid strawberry species. The objective of this study was to evaluate the diversity of these two species using microsatellite markers. We report preliminary results obtained from SSR analysis of 139 accessions based on 20 SSRs. A higher genetic diversity was observed in F. nipponica, which tends to be cross pollinated, than in F. iinumae, which tends to be self-pollinated. This study identified putative hybrids between F. iinumae and F. nipponica as well as an unexpected octoploid accession from Hokkaido, Japan. The hybrid nature of these accessions and the possible source of this octoploid accession will be further evaluated using chloroplast and nuclear markers as well as morphological traits.
Sargent, Daniel J; Davis, Thomas M; Simpson, David W
Strawberry (Fragaria spp.) structural genomics Book Chapter
In: Genetics and genomics of Rosaceae, pp. 437-456, Springer, 2009.
@inbook{495,
title = {Strawberry (Fragaria spp.) structural genomics},
author = { Daniel J Sargent and Thomas M Davis and David W Simpson},
url = {https://link.springer.com/chapter/10.1007/978-0-387-77491-6_21},
year = {2009},
date = {2009-01-01},
booktitle = {Genetics and genomics of Rosaceae},
pages = {437-456},
publisher = {Springer},
organization = {Springer},
abstract = {The genus Fragaria has a basic chromosome number of seven (x=7) (Ichijima, 1926), and four main fertility groups are recognized: the diploids (2n=2x=14) which include the model species for the genus, F. vesca, (Oosumi et al., 2006) amongst the 14 described species; the tetraploids (2n=4x=28) including F. orientalis; the single hexaploid species F. moschata (2n=6x=42); and four octoploid species (2n=8x=56): F. chiloensis, F. iturupensis, F. virginiana and the hybrid cultivated strawberry, F. ×ananassa.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
The genus Fragaria has a basic chromosome number of seven (x=7) (Ichijima, 1926), and four main fertility groups are recognized: the diploids (2n=2x=14) which include the model species for the genus, F. vesca, (Oosumi et al., 2006) amongst the 14 described species; the tetraploids (2n=4x=28) including F. orientalis; the single hexaploid species F. moschata (2n=6x=42); and four octoploid species (2n=8x=56): F. chiloensis, F. iturupensis, F. virginiana and the hybrid cultivated strawberry, F. ×ananassa.
Pontaroli, Ana Clara; Rogers, Rebekah L.; Zhang, Qian; Shields, Melanie E.; Davis, Thomas M.; Folta, Kevin M.; SanMiguel, Phillip; Bennetzen, Jeffrey L.
Gene Content and Distribution in the Nuclear Genome of Fragaria vesca Journal Article
In: The Plant Genome, vol. 2, no. 1, pp. 93-101, 2009.
@article{483,
title = {Gene Content and Distribution in the Nuclear Genome of Fragaria vesca},
author = { Ana Clara Pontaroli and Rebekah L. Rogers and Qian Zhang and Melanie E. Shields and Thomas M. Davis and Kevin M. Folta and Phillip SanMiguel and Jeffrey L. Bennetzen},
url = {http://dx.doi.org/10.3835/plantgenome2008.09.0007},
doi = {10.3835/plantgenome2008.09.0007},
year = {2009},
date = {2009-01-01},
journal = {The Plant Genome},
volume = {2},
number = {1},
pages = {93-101},
publisher = {Crop Science Society of America},
address = {Madison, WI},
abstract = {Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ~4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ~1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ~200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ~4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ~1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ~200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.
Mahoney, L; Davis, TM; Curran-Celentano, J
Investigation of Cyanidin and Pelargonidin Contents in the Genus Fragaria L. Journal Article
In: Acta Hortic, vol. 842, pp. 915-918, 2009, ISBN: 9066056428.
@article{492,
title = {Investigation of Cyanidin and Pelargonidin Contents in the Genus Fragaria L.},
author = { L Mahoney and TM Davis and J Curran-Celentano},
url = {http://www.actahort.org/books/842/842_202.htm},
isbn = {9066056428},
year = {2009},
date = {2009-01-01},
journal = {Acta Hortic},
volume = {842},
pages = {915-918},
abstract = {The fruit cyanidin (Cyn) and pelargonidin (Plr) contents in 73 Fragaria accessions were assayed using a modified HPLC method, and % Cyn (Cyn as % of Cyn-plus-Plr) values were calculated. Plr content increased during fruit ripening, while Cyn content held steady. Consistent with previous studies, % Cyn was comparatively low (5-20%) among twelve F. ×ananassa cultivars, but was >40% in diploid F. vesca. Importantly, three F. chiloensis accessions had greater than 50% Cyn, and ssp. lucida CFRA1691 had the overall highest Cyn content: 707 μg/g FDW. An F1 population of ‘Bountiful’ × ‘Pink Panda’ segregated for both Cyn and Plr contents. Our investigation identifies useful germplasm, offering promise for increasing Cyn content and antioxidant potential through introgressive breeding.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The fruit cyanidin (Cyn) and pelargonidin (Plr) contents in 73 Fragaria accessions were assayed using a modified HPLC method, and % Cyn (Cyn as % of Cyn-plus-Plr) values were calculated. Plr content increased during fruit ripening, while Cyn content held steady. Consistent with previous studies, % Cyn was comparatively low (5-20%) among twelve F. ×ananassa cultivars, but was >40% in diploid F. vesca. Importantly, three F. chiloensis accessions had greater than 50% Cyn, and ssp. lucida CFRA1691 had the overall highest Cyn content: 707 μg/g FDW. An F1 population of ‘Bountiful’ × ‘Pink Panda’ segregated for both Cyn and Plr contents. Our investigation identifies useful germplasm, offering promise for increasing Cyn content and antioxidant potential through introgressive breeding.
