The aim of the present study was to assess the genetic variation and establish the relationship amongst the six chicken breeds using 9 fluorescently labeled microsatellite markers. The 16 (equal number of sexes) DNA samples from Naked Neck (NN), White Silkies (WS), Commercial Layer (CL) and Broiler (CB), Giriraja (G, a synthetic coloured strain) and Desi (D) populations were genotyped for this study. Seven loci were polymorphic in all of the populations and the number of alleles varying from 3 to 27 per locus and 4.1 to 8.6 per population, respectively, with a total of 134 alleles. The average observed and expected heterozygosity for the populations varied from 0.56 (WS) to 0.76 (CB), and from 0.52 (CL) to 0.74 (D and G) respectively. Some of the populations and loci deviated from Hardy-Weinberg equilibrium. Except NN, all of the other populations were not in gametic disequilibrium for only one pairwise locus combinations. F-statistics indicated that populations are genetically structured (F ST ≈ ө=0.155; R ST =0.240; P<0.001). The F ST and R ST estimates respectively, demonstrated that approximately 85.0 and 66.0 percent of the total genetic variation was because of the genetic differentiation within the populations. Estimates of different genetic distances revealed relatively close genetic similarity between NN and G. In the UPGMA-based phylogenetic tree constructed from different genetic distances, four major clusters obtained: first, NN and G; second, NN, G and CB; third, D and CL and forth, WS in a single cluster. The percentage of occurrences of each group was 100, 100, 66.7 and 55.6, respectively. The estimated time of divergence suggested a separation time of approximately 114 years between NN and G, and a comparatively longer period (477 years) between G and WS. By using different methods, the correct assignment of the individuals to populations was from 60.4 to 89.6%.

Source : IPSACON-2005

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