A high density soybean genetic map by SLAF sequence. Glycine max

A genetic map provides an important foundation for quantitative trait loci (QTL) fine mapping. However, the utility of genetic linkage maps rests on the types and numbers of polymorphic markers used. Next generation sequencing technology makes it possible to obtain thousands of SNPs throughout the genome that are potential markers for high-density genetic maps. Consequently, several cheap methods for SNP discovery and high throughput genotyping have been developed, such as RADseq (restriction site-associated sequencing), double digest RADseq, and two-enzyme genotyping-by-sequencing (GBS). Recently, Sun et al. developed specific length amplified fragment (SLAF) sequencing (SLAF-seq) as a high-resolution strategy for large-scale de novo SNP discovery and genotyping. This approach has been successfully used to create a genetic map for common carp (Cyprinus carpio L.); it was the highest-density genetic map yet for any organism without a reference genome sequence. In this study, we used SLAF-seq to generate genotype data and subsequently constructed a high-density genetic map of soybean.