Construction and comparison of three reference-quality genome assemblies for soybean
Abstract
Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. Themore »
- Authors:
-
[1];
[11];
more »
- Univ. of Missouri, Columbia, MO (United States); Lincoln Univ., Jefferson City, MO (United States)
- US Dept. of Agriculture (USDA)., Ames, IA (United States)
- The Univ. of Western Australia, Crawley, WA (Australia)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Iowa State Univ., Ames, IA (United States)
- HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
- Chinese Univ. of Hong Kong (China)
- Bionano Genomics, San Diego, CA (United States)
- NRGene Ltd., Ness Ziona (Israel)
- Univ. of Missouri, Columbia, MO (United States)
- International Crops Research Inst. for the Semi‐Arid Tropics (ICRISAT), Patancheru (India)
- School of Biological Sciences The University of Western Australia Crawley 6009 WA Australia
- US Dept. of Agriculture (USDA)., Beltsville, MD (United States)
- Univ. of Minnesota, St. Paul, MN (United States)
- Univ. of Georgia, Athens, GA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); USDA
- OSTI Identifier:
- 1619141
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The Plant Journal
- Additional Journal Information:
- Journal Volume: 100; Journal Issue: 5; Journal ID: ISSN 0960-7412
- Publisher:
- Society for Experimental Biology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; glycine max; glycine soja; soybean; genome assembly; domestication; comparative genomics
Citation Formats
Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y. ‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, and Nguyen, Henry T. Construction and comparison of three reference-quality genome assemblies for soybean. United States: N. p., 2019.
Web. doi:10.1111/tpj.14500.
Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y. ‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, & Nguyen, Henry T. Construction and comparison of three reference-quality genome assemblies for soybean. United States. https://doi.org/10.1111/tpj.14500
Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y. ‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, and Nguyen, Henry T. Wed .
"Construction and comparison of three reference-quality genome assemblies for soybean". United States. https://doi.org/10.1111/tpj.14500. https://www.osti.gov/servlets/purl/1619141.
@article{osti_1619141,
title = {Construction and comparison of three reference-quality genome assemblies for soybean},
author = {Valliyodan, Babu and Cannon, Steven B. and Bayer, Philipp E. and Shu, Shengqiang and Brown, Anne V. and Ren, Longhui and Jenkins, Jerry and Chung, Claire Y. ‐L. and Chan, Ting‐Fung and Daum, Christopher G. and Plott, Christopher and Hastie, Alex and Baruch, Kobi and Barry, Kerrie W. and Huang, Wei and Patil, Gunvant and Varshney, Rajeev K. and Hu, Haifei and Batley, Jacqueline and Yuan, Yuxuan and Song, Qijian and Stupar, Robert M. and Goodstein, David M. and Stacey, Gary and Lam, Hon‐Ming and Jackson, Scott A. and Schmutz, Jeremy and Grimwood, Jane and Edwards, David and Nguyen, Henry T.},
abstractNote = {Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.},
doi = {10.1111/tpj.14500},
journal = {The Plant Journal},
number = 5,
volume = 100,
place = {United States},
year = {2019},
month = {8}
}
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