Genotyping by sequencing GBS of 2139 F2 hybrid accessions derived from crossing cultivated ICCV96029 by wild accessions of both Cicer reticulatum and Cicer echinospermum. Cicer

NAM populations utilize the framework of common reference design to produce synthetic mapping populations that take advantage of both historic and recent recombination events such that marker density requirement is kept low while having higher allelic richness and statistical power. Pursuant of this aim, and keeping in mind that our goal is to introgress favourable alleles from wild populations into cultivated varieties, crosses of two wild chickpea species, C. echinospermum and C. reticulatum, called wild founders, were made with three different elite cultivars. In the present analysis, we examine hybrid crosses of wild founders with the elite cultivar, ICCV96029. Limiting ourselves to species divergent markers, we conduct an association study with six continuous phenotypes including important traits like yield and shattering index. This reveals important features of the genomic architecture underlying these traits. Additionally, by breaking down the association analysis by population, we locate markers that may be active in a population specific manner. Finally, by conducting a PCA-based selection scan, we identify distortion regions that may indicate potential incompatibility loci.