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

Alleles Centromere / genetics Disease Resistance / genetics Fabaceae / genetics Genetic Variation Genetics, Population Genome, Plant Genotype Haplotypes Hardness Multigene Family Phylogeny Polymorphism, Single Nucleotide Quantitative Trait Loci Repetitive Sequences, Nucleic Acid Seed Bank / classification Sequence Inversion Telomere / genetics

Glycine max Glycine soja comparative genomics domestication genome assembly soybean

Journal

The Plant journal : for cell and molecular biology

ISSN: 1365-313X

Titre abrégé: Plant J

Pays: England

ID NLM: 9207397

Informations de publication

Date de publication:
12 2019

Historique:

received: 27 12 2018

revised: 10 07 2019

accepted: 17 07 2019

pubmed: 23 8 2019

medline: 31 7 2020

entrez: 22 8 2019

Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1111/tpj.14500 PMID: 31433882

pubmed: 31433882

doi: 10.1111/tpj.14500

doi:

Banques de données

GENBANK

['GCA_002905335']

Types de publication

Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

Pagination

1066-1082

Informations de copyright

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