Genetic diversity and population structure in the reciprocal cross between a broiler line and indigenous chickens

This study was performed to evaluate the population structure by genome-wide analysis using the Illumina 60K chicken Beadchip. One F2 population derived from the reciprocal cross between Arian fast-growing chickens and Urmia slow-growing indigenous fowls and consisting of 312 F2 birds was investigated. Quality control procedures, population clustering using the multidimensional scaling (MDS) method and allele frequency assessment in half-sib groups were applied. Then the population structure was considered, as provided by the outputs of MDS, Heatmap and neighbor-joining tree, which were consistent with structure analyses by clustering the birds into eight sub-populations of K1 to K8. The average expected heterozygosity in all half-sib families was K1 = 0.4677, K2 = 0.4635, K3 = 0.4949, K4 = 0.5235, K5 = 0.4613, K6 = 0.4273, K7 = 0.4618, and K8 = 0.4459, respectively. The heterozygosity values were found to be higher than 42% for all the eight clusters in this study, indicating a relatively high genetic variability within the groups. The fixation index (F-st) among F2 chicken clusters ranged from 0.01 to 0.29. One possible explanation for the high estimated F-st (>0.1) can be a signal of selection in the present population. Our findings can be applied in future GWASs, conservation plans and genetic improvement programs of chickens.