Genomics

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The composition and origins of intravarietal genomic heterogeneity in soybean


ABSTRACT: Soybean is a self-pollinating crop species that has relatively low nucleotide polymorphism rates compared to other crop plant species. Despite the appearance of a low intervarietal nucleotide polymorphism rate, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some varieties. ‘Williams 82,’ the soybean variety used to produce the reference genome sequence, was derived from backcrossing a phytophthora root rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’ To explore the genetic basis of intravarietal variation, we investigated the nucleotide, structural and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. Collectively, these findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intravarietal genetic heterogeneity may be much greater than previously assumed. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are utilizing or working towards developing a reference genome sequence.

ORGANISM(S): Glycine max

PROVIDER: GSE25294 | GEO | 2010/12/14

SECONDARY ACCESSION(S): PRJNA134895

REPOSITORIES: GEO

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