Construction and comparison of three reference-quality genome assemblies for soybean

Babu Valliyodan, Steven B Cannon, Philipp E Bayer, Shengqiang Shu, Anne V Brown, Longhui Ren, Jerry Jenkins, Claire Yik-Lok Chung, Ting-Fung Chan, Christopher G Daum, Christopher Plott, Alex Hastie, Kobi Baruch, Kerrie W Barry, Wei Huang, Gunvant Patil, Rajeev K Varshney, Haifei Hu, Jacqueline Batley, Yuxuan Yuan & 10 others Qijian Song, Robert M Stupar, David M Goodstein, Gary Stacey, Hon-Ming Lam, Scott A Jackson, Jeremy Schmutz, Jane Grimwood, David Edwards, Henry T Nguyen

Research output: Contribution to journalArticle

Abstract

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, the closest wild relative of G. max. The G. max assemblies are for widely used U.S. 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 SNPs/kb between Wm82 and Lee, and 4.7 SNPs/kb between these lines and G. soja. SNP distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgressions and haplotype structure. Comparisons against the U.S. germplasm collection shows 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 ~40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and ~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 soybean's domestication and improvement, serving as a basis for future research and crop improvement efforts for this important crop species. This article is protected by copyright. All rights reserved.

Original languageEnglish
Number of pages39
JournalThe Plant Journal
DOIs
Publication statusE-pub ahead of print - 21 Aug 2019

Fingerprint

Glycine soja
genome assembly
Soybeans
Genome
soybeans
Glycine max
domestication
Single Nucleotide Polymorphism
chromosomes
loci
wild relatives
germplasm conservation
crops
introgression
haplotypes
ancestry
genes
nucleotides
alleles
Glycine

Cite this

Valliyodan, Babu ; Cannon, Steven B ; Bayer, Philipp E ; Shu, Shengqiang ; Brown, Anne V ; Ren, Longhui ; Jenkins, Jerry ; Chung, Claire Yik-Lok ; 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. In: The Plant Journal. 2019.
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abstract = "We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, the closest wild relative of G. max. The G. max assemblies are for widely used U.S. 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 SNPs/kb between Wm82 and Lee, and 4.7 SNPs/kb between these lines and G. soja. SNP distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgressions and haplotype structure. Comparisons against the U.S. germplasm collection shows 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 ~40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and ~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 soybean's domestication and improvement, serving as a basis for future research and crop improvement efforts for this important crop species. This article is protected by copyright. All rights reserved.",
author = "Babu Valliyodan and Cannon, {Steven B} and Bayer, {Philipp E} and Shengqiang Shu and Brown, {Anne V} and Longhui Ren and Jerry Jenkins and Chung, {Claire Yik-Lok} and Ting-Fung Chan and Daum, {Christopher G} and Christopher Plott and Alex Hastie and Kobi Baruch and Barry, {Kerrie W} and Wei Huang and Gunvant Patil and Varshney, {Rajeev K} and Haifei Hu and Jacqueline Batley and Yuxuan Yuan and Qijian Song and Stupar, {Robert M} and Goodstein, {David M} and Gary Stacey and Hon-Ming Lam and Jackson, {Scott A} and Jeremy Schmutz and Jane Grimwood and David Edwards and Nguyen, {Henry T}",
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Valliyodan, B, Cannon, SB, Bayer, PE, Shu, S, Brown, AV, Ren, L, Jenkins, J, Chung, CY-L, Chan, T-F, Daum, CG, Plott, C, Hastie, A, Baruch, K, Barry, KW, Huang, W, Patil, G, Varshney, RK, Hu, H, Batley, J, Yuan, Y, Song, Q, Stupar, RM, Goodstein, DM, Stacey, G, Lam, H-M, Jackson, SA, Schmutz, J, Grimwood, J, Edwards, D & Nguyen, HT 2019, 'Construction and comparison of three reference-quality genome assemblies for soybean' The Plant Journal. https://doi.org/10.1111/tpj.14500

Construction and comparison of three reference-quality genome assemblies for soybean. / Valliyodan, Babu; Cannon, Steven B; Bayer, Philipp E; Shu, Shengqiang; Brown, Anne V; Ren, Longhui; Jenkins, Jerry; Chung, Claire Yik-Lok; 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.

In: The Plant Journal, 21.08.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Construction and comparison of three reference-quality genome assemblies for soybean

AU - Valliyodan, Babu

AU - Cannon, Steven B

AU - Bayer, Philipp E

AU - Shu, Shengqiang

AU - Brown, Anne V

AU - Ren, Longhui

AU - Jenkins, Jerry

AU - Chung, Claire Yik-Lok

AU - Chan, Ting-Fung

AU - Daum, Christopher G

AU - Plott, Christopher

AU - Hastie, Alex

AU - Baruch, Kobi

AU - Barry, Kerrie W

AU - Huang, Wei

AU - Patil, Gunvant

AU - Varshney, Rajeev K

AU - Hu, Haifei

AU - Batley, Jacqueline

AU - Yuan, Yuxuan

AU - Song, Qijian

AU - Stupar, Robert M

AU - Goodstein, David M

AU - Stacey, Gary

AU - Lam, Hon-Ming

AU - Jackson, Scott A

AU - Schmutz, Jeremy

AU - Grimwood, Jane

AU - Edwards, David

AU - Nguyen, Henry T

PY - 2019/8/21

Y1 - 2019/8/21

N2 - We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, the closest wild relative of G. max. The G. max assemblies are for widely used U.S. 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 SNPs/kb between Wm82 and Lee, and 4.7 SNPs/kb between these lines and G. soja. SNP distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgressions and haplotype structure. Comparisons against the U.S. germplasm collection shows 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 ~40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and ~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 soybean's domestication and improvement, serving as a basis for future research and crop improvement efforts for this important crop species. This article is protected by copyright. All rights reserved.

AB - We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, the closest wild relative of G. max. The G. max assemblies are for widely used U.S. 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 SNPs/kb between Wm82 and Lee, and 4.7 SNPs/kb between these lines and G. soja. SNP distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgressions and haplotype structure. Comparisons against the U.S. germplasm collection shows 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 ~40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and ~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 soybean's domestication and improvement, serving as a basis for future research and crop improvement efforts for this important crop species. This article is protected by copyright. All rights reserved.

U2 - 10.1111/tpj.14500

DO - 10.1111/tpj.14500

M3 - Article

JO - The Plant Journal

JF - The Plant Journal

SN - 0960-7412

ER -