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

OAR@ICRISAT

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Relation http://oar.icrisat.org/11488/
https://doi.org/10.1111/tpj.14500
doi:10.1111/tpj.14500
 
Title Construction and comparison of three reference‐quality genome assemblies for soybean
 
Creator Valliyodan, B
Cannon, S B
Bayer, P E
Shu, S
Brown, A V
Ren, L
Jenkins, J
Chung, C Y L
Chan, T F
Daum, C G
Plott, C
Hastie, A
Baruch, K
Barry, K W
Huang, W
Patil, G
Varshney, R K
Hu, H
Batley, J
Yuan, Y
Song, Q
Stupar, R M
Goodstein, D M
Stacey, G
Lam, H M
Jackson, S A
Schmutz, J
Grimwood, J
Edwards, D
Nguyen, H T
 
Subject Genetics and Genomics
 
Description 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.
 
Publisher Wiley
 
Date 2019-08
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11488/1/15_Construction%20and%20comparison%20of%20three%20reference-quality%20genome%20assemblies%20for%20soybean.pdf
Valliyodan, B and Cannon, S B and Bayer, P E and Shu, S and Brown, A V and Ren, L and Jenkins, J and Chung, C Y L and Chan, T F and Daum, C G and Plott, C and Hastie, A and Baruch, K and Barry, K W and Huang, W and Patil, G and Varshney, R K and Hu, H and Batley, J and Yuan, Y and Song, Q and Stupar, R M and Goodstein, D M and Stacey, G and Lam, H M and Jackson, S A and Schmutz, J and Grimwood, J and Edwards, D and Nguyen, H T (2019) Construction and comparison of three reference‐quality genome assemblies for soybean. The Plant Journal (TSI), 100 (5). pp. 1066-1082. ISSN 0960-7412