A SNP-based linkage map of Phaseolus vulgaris constructed via the genotyping-by-sequencing approach.

Crop models need to be calibrated for each different genotype, thereby yielding a set of genotype-specific parameters (GSPs). This signifies the fact that these GSPs contain genetic information. Our goal is to extract this genetic information via QTL analysis of a RIL population, and turn the GSPs into mathematical functions of the genotype. This conversion is expected to facilitate genotype-based prediction of the phenotype. To fulfill our objective, we have constructed a robust SNP-based linkage map in common bean based on a [Mesoamerican x Andean] RIL population comprised of 188 individuals using the genotyping-by-sequencing (GBS) technique, but without a reference genome sequence. The map is comprised of 11 linkage groups, 1118 GBS-based SNP markers, 200 RFLP (BNG) markers and 12 Glycine max-intron based SNP markers. The map covers 1228 cM (Kosambi function; LOD 8). Filtering out co-segregating markers yielded a total of 699 unique co-dominant marker loci with an average marker interval of 1.7 cM. Seven QTLs controlling time from emergence to first anthesis have already been identified utilizing this map.