Abstract
Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the low rate of nucleotide polymorphisms, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some cultivars. Williams 82, the soybean cultivar 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 intracultivar 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. 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 intracultivar genetic heterogeneity may be significant. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are developing or utilizing a reference genome sequence.
Highlights
Intra-cultivar genetic heterogeneity refers to the genetic variation present from plant to plant within a named cultivar or variety
The phenomenon of intra-cultivar heterogeneity has long been recognized in crop species (Byth and Weber, 1968) it is oftentimes ignored, as most researchers assume that elite cultivars are composed of relatively homogenous genetic pools (Fasoula and Boerma, 2007)
Variation based on differential segregation should be identifiable in the parental lines, while variation generated de novo would be expected to be unique to the cultivar and not preferentially shared with either parent. To test these hypotheses and dissect the origin of the Williams 82 genomic heterogeneity, Williams 82 individuals and parental lines were genotyped using the Illumina Infinium iSelect SoySNP50 chip consisting of 44,299 informative single nucleotide polymorphism (SNP) designed for soybean (Figure 1)
Summary
Intra-cultivar genetic heterogeneity refers to the genetic variation present from plant to plant within a named cultivar or variety. The phenomenon of intra-cultivar heterogeneity has long been recognized in crop species (Byth and Weber, 1968) it is oftentimes ignored, as most researchers assume that elite cultivars are composed of relatively homogenous genetic pools (Fasoula and Boerma, 2007). A small number of studies have documented the phenotypic consequences of intra-cultivar genetic heterogeneity in inbred crop accessions, including studies in tobacco (Gordon and Byth, 1972), maize (Higgs and Russell, 1968; Tokatlidis, 2000), wheat (Tokatlidis et al, 2004) and cotton (Tokatlidis et al, 2008). Assuming that the population remains intact, each plant lineage will eventually fix almost all of the segregating loci in the homozygous state of either parent. The population will maintain some degree of plant to plant variation due to the heterogeneity at these loci
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