Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

Allopolyploidy is a common feature in many angiosperm genera. The perennial wild relatives of soybean in the genus Glycine include at least nine recently formed (within the last million years) allopolyploid taxa. This study examined three allopolyploid and four diploid progenitor taxa using genome-wide single nucleotide polymorphisms (SNPs) and network analysis. Genotyping by sequencing (GBS) was used to generate SNPs and results were compared with previous analyses from transcriptome data. Three lanes of Illumina sequencing produced genotypes for 70 accessions and an alignment of 22 806 SNPs across eight taxa with no missing data. The alignment combined with network analysis confirmed results from previous studies. In addition, the extended sampling made possible by GBS identified accessions that have either been misclassified or samples that came from mixed seed stocks. The most intriguing results are the discovery of previously unrecognized substructure within diploid taxa, and the likelihood that allopolyploids were derived from particular subgroups. Separation of allopolyploid SNPs into SNPs derived from homoeologous progenitor species indicate that allopolyploids no longer share genotypes with their diploid progenitors but have evolved separately long enough for signals from direct progenitor genotypes to be obscured.