The composition and origins of intravarietal genomic heterogeneity in soybean

Authors: HAUN, WILLIAM - University Of Minnesota; Hyten, David; XU, WAYNE - University Of Minnesota; GERHARDT, DANIEL - Roche Nimblegen, Inc; ALBERT, THOMAS - Roche Nimblegen, Inc; RICHMOND, TODD - Roche Nimblegen, Inc; JEDDELOH, JEFFREY - Roche Nimblegen, Inc; SPRINGER, NATHAN - University Of Minnesota; Vance, Carroll; STUPAR, ROBERTM - University Of Minnesota

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/15/2010
Publication Date: 2/1/2011
Citation: Haun, W.J., Hyten, D.L., Xu, W.W., Gerhardt, D.J., Albert, T.J., Richmond, T., Jeddeloh, J.A., Springer, N.M., Vance, C.P., Stupar, R. 2011. The composition and origins of intravarietal genomic heterogeneity in soybean. Plant Physiology. 155:645-655.

Interpretive Summary: Intravarietal genetic heterogeneity refers to the genetic variation present from plant to plant within a named cultivar or variety. Although the phenomenon of intravarietal heterogeneity has long been recognized in crop species it is oftentimes ignored, as most researchers assume that elite cultivars and varieties are composed of relatively homogenous genetic pools. However, a small number of studies have documented that this intravarietal genetic heterogeneity can affect traits observed within soybeans including seed composition, seed weight, maturity, plant height and lodging. Recently the soybean cultivar ‘Williams 82’ was used in the creation of a whole genome reference sequence for soybean and is being used extensively for soybean research. We found that different plants sampled from the soybean variety Williams 82 contained multiple regions of genetic heterogeneity which also had different gene content. Soybean researchers investigating comparative studies of soybean that include Williams 82 as a reference genotype will use this research to help factor in the inherent differences between each Williams 82 individual and the reference genome sequence in their studies.

Technical 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 intravarietal 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 rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’ To explore the genetic basis of intravarietal variation, we investigated the SNP, structural and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variable Kingwa introgression loci and introgression sizes. These regions of genomic heterogeneity have impacted the reference Williams 82 sequence, as these regions consist of a mosaic of Williams and Kingwa assemblies. 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. Furthermore, these data demonstrate 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.