Construction of Genetic Maps for Glycine latifolia by High-Throughput Sequencing

Like many widely cultivated crops, soybean (Glycine max) has a relatively narrow genetic base.  In contrast, soybean’s 26 distant perennial relatives in the subgenus Glycine are more genetically diverse and display desirable traits not present in cultivated soybean. For example, high levels of resistance to Sclerotinia sclerotiorum, the cause of Sclerotinia stem rot, have been identified in G. latifolia and other perennial wild Glycine species, whereas only low levels of resistance have been identified in G. max. To generate molecular resources for gene mapping and identification in a perennial Glycine species, Illumina sequence data from G. latifolia accessions resistant or susceptible to S. sclerotiorum were compared.  These sequences generated a large number of single nucleotide polymorphism (SNP) markers in a very cost effective manner. Utilizing the G. max genome sequence as a reference, nine TaqMan and 384 GoldenGate G. latifolia SNP assays were selected and analyzed in an F₂ population of 92 individuals. All TaqMan markers, and 85% of the polymorphic GoldenGate markers were linked to markers in the linkage groups predicted from the G. max genome sequence. These results showed that high-density SNP markers can be identified and validated in perennial species of Glycine and used to compare the genome organizations of two species within the genus. To extend these studies, Illumina genotyping-by-sequencing libraries were created from an additional 94 G. latifolia F₂ individuals for a total of 186 F₂ individuals.