Characterization of genetic heterogeneity within accessions in the USDA soybean germplasm collection

Abstract

Soybean breeding relies on the use of wild (Glycine soja Sieb. and Zucc.) and domesticated [Glycine max (L.) Merr.] germplasm for trait improvement. Soybeans are selfpollinating and accessions can be maintained as pure lines, however within-accession genetic variation has been observed in previous studies of some landraces and elite cultivars. The objective of this study was to characterize within-line variation in the accessions housed in the USDA Soybean Germplasm Collection. This collection includes over 20,000 accessions, each previously genotyped using the SoySNP50K Chip. Each SoySNP50K genotype was developed by pooling approximately three individuals per accession. Therefore, clusters of SNPs called as heterozygous within an accession can be inferred to represent putative regions of heterogeneity between the three individuals sampled. In this study, we found high-probability intervals of heterogeneity in 4% of the collection, representing 870 accessions. Heterogeneous loci were found on every chromosome and, collectively, covered 98.4% of the soybean genome and 99% of the gene models. Sanger sequencing confirmed regions of genomic heterogeneity among a subset of ten accessions. This dataset provides useful information and considerations for users of crop germplasm seed banks. Furthermore, the heterogeneous accessions and/or loci represent a unique genetic resource that is immediately available for forward and reverse genetics studies.

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

“…Looking beyond Wm82, approximately 4% of the USDA soybean germplasm collection exhibits inherent within-accession heterogeneity (Mihelich et al, 2020). Notably, the 4% estimate is based on a comparison of ∼3 individual plants per accession.…”

“…Subsequent bulk harvesting in the later stages of the breeding process allowed the heterozygous loci to segregate and differentially fix these loci among different sub-lineages within the bulked population. This type of intracultivar heterogeneity is common in soybean breeding, as cultivars are essentially maintained as collection of near-isogenic sub-lines (Mihelich et al, 2020). In Wm82, (Haun et al, 2011) provided a thorough characterization of intracultivar heterogeneity at a molecular level.…”

Validation of Novel spot blotch disease resistance alleles identified in unexplored wheat (Triticum aestivum L.) germplasm lines through KASP markers

“…The theoretical heterozygosity does reduce to < 1% in inbred lines, while observed heterozygosity in landraces, varieties or other inbred lines in wheat has been reported to be up to 20% in various studies [54,77]. Further, in various plant species residual heterozygosity have been found to be associated with higher gene densities and recombination rates underlining the complex genetic architecture [78,79].…”

Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing

“…Also, the most genetically redundant samples were relative to the whole set of samples assayed, and there is no solid threshold to group samples with and without genetic redundancy. Moreover, we did not examine within-accession variation, as such variation was expected to be low [ 42 ] for soybean with an outcrossing rate of 1–2% [ 43 , 44 ]. In spite of this, we cannot rule out the effects, if any, of the within-accession variation on the estimation of pairwise dissimilarity and duplication identification.…”