Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

Babu Valliyodan; Anne V. Brown; Juexin Wang; Gunvant Patil; Yang Liu; Paul I. Otyama; Rex T. Nelson; Tri Vuong; Qijian Song; Theresa A. Musket; Ruth Wagner; Pradeep Marri; Sam Reddy; Allen Sessions; Xiaolei Wu; David Grant; Philipp E. Bayer; Manish Roorkiwal; Rajeev K. Varshney; Xin Liu; David Edwards; Dong Xu; Trupti Joshi; Steven B. Cannon; Henry T. Nguyen

doi:10.1038/s41597-021-00834-w

Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

Babu Valliyodan, Anne V. Brown, Juexin Wang, Gunvant Patil, Yang Liu, Paul I. Otyama, Rex T. Nelson, Tri Vuong, Qijian Song, Theresa A. Musket, Ruth Wagner, Pradeep Marri, Sam Reddy, Allen Sessions, Xiaolei Wu, David Grant, Philipp E. Bayer, Manish Roorkiwal, Rajeev K. Varshney, Xin LiuDavid Edwards, Dong Xu, Trupti Joshi, Steven B. Cannon, Henry T. Nguyen

School of Biological Sciences

Research output: Contribution to journal › Data article › peer-review

39 Citations (Scopus)

Abstract

We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

Original language	English
Article number	50
Journal	Scientific Data
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41597-021-00834-w
Publication status	Published - 2021

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Valliyodan, B., Brown, A. V., Wang, J., Patil, G., Liu, Y., Otyama, P. I., Nelson, R. T., Vuong, T., Song, Q., Musket, T. A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D., Bayer, P. E., Roorkiwal, M., Varshney, R. K., ... Nguyen, H. T. (2021). Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data, 8(1), Article 50. https://doi.org/10.1038/s41597-021-00834-w

@article{b226d0636f1047929d2536e41e5e4ae5,

title = "Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing",

abstract = "We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.",

author = "Babu Valliyodan and Brown, {Anne V.} and Juexin Wang and Gunvant Patil and Yang Liu and Otyama, {Paul I.} and Nelson, {Rex T.} and Tri Vuong and Qijian Song and Musket, {Theresa A.} and Ruth Wagner and Pradeep Marri and Sam Reddy and Allen Sessions and Xiaolei Wu and David Grant and Bayer, {Philipp E.} and Manish Roorkiwal and Varshney, {Rajeev K.} and Xin Liu and David Edwards and Dong Xu and Trupti Joshi and Cannon, {Steven B.} and Nguyen, {Henry T.}",

year = "2021",

doi = "10.1038/s41597-021-00834-w",

language = "English",

volume = "8",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Publishing Group - Macmillan Publishers",

number = "1",

}

Valliyodan, B, Brown, AV, Wang, J, Patil, G, Liu, Y, Otyama, PI, Nelson, RT, Vuong, T, Song, Q, Musket, TA, Wagner, R, Marri, P, Reddy, S, Sessions, A, Wu, X, Grant, D, Bayer, PE, Roorkiwal, M, Varshney, RK, Liu, X, Edwards, D, Xu, D, Joshi, T, Cannon, SB & Nguyen, HT 2021, 'Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing', Scientific Data, vol. 8, no. 1, 50. https://doi.org/10.1038/s41597-021-00834-w

TY - JOUR

T1 - Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

AU - Valliyodan, Babu

AU - Brown, Anne V.

AU - Wang, Juexin

AU - Patil, Gunvant

AU - Liu, Yang

AU - Otyama, Paul I.

AU - Nelson, Rex T.

AU - Vuong, Tri

AU - Song, Qijian

AU - Musket, Theresa A.

AU - Wagner, Ruth

AU - Marri, Pradeep

AU - Reddy, Sam

AU - Sessions, Allen

AU - Wu, Xiaolei

AU - Grant, David

AU - Bayer, Philipp E.

AU - Roorkiwal, Manish

AU - Varshney, Rajeev K.

AU - Liu, Xin

AU - Edwards, David

AU - Xu, Dong

AU - Joshi, Trupti

AU - Cannon, Steven B.

AU - Nguyen, Henry T.

PY - 2021

Y1 - 2021

N2 - We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

AB - We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

UR - http://www.scopus.com/inward/record.url?scp=85100982492&partnerID=8YFLogxK

U2 - 10.1038/s41597-021-00834-w

DO - 10.1038/s41597-021-00834-w

M3 - Data article

C2 - 33558550

AN - SCOPUS:85100982492

SN - 2052-4463

VL - 8

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 50

ER -

Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

Abstract

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