Development of a High Density SNP-Based Linkage Map of Phaseolus vulgaris using the Genotyping-by-Sequencing Approach

Crop models comprise complex interrelated mathematical functions which require calibration for each different genotype. Such calibration yields a set of genotype-specific parameters, and underscores the fact that these parameters contain genetic information. Our goal is to extract this genetic information via QTL analysis, and turn the model parameters into mathematical functions of the genotype, thereby facilitating genotype-based prediction of the phenotype. Incorporation of genetic information into crop model requires identification of gene(s)/QTLs controlling different stages of growth and development of the crop. With this objective in mind, we have constructed a robust high-density SNP-based linkage map in common bean based on an [Andean x Mesoamerican] RIL population comprised of 174 individuals. This map was constructed using the genotyping-by-sequencing (GBS) technique, but without a reference genome sequence. Seventy percent of the 3000 SNPs detected between the parents were excluded because they were found in duplicated/repetitive sequences, or were missing in 10% of the RILs. Added to the 851 GBS-based SNP markers were 115 BNG (RFLP) markers and 11 intron based SNP markers. The map contains 977 markers distributed among 11 linkage groups, and covers 720 cM (Kosambi function; LOD 8). Filtering out co-segregating markers yielded a total of 516 unique marker loci with an average marker interval of 1.39 cM. The high density of this linkage map will provide vital resolution required for identifying QTLs for development of a Gene-based Crop Model.