Analysis Genetic Diversity Of 12 Features Chicken Breeds From Southwest China By Microsatellite Markers

Genetic diversity within and among 12 chicken breeds in southwest China were assessed using 20 microsatellite DNA loci. Allele frequency, number of observed alleles (Na), number of effective alleles (Ne), expected heterozygosity(He), observed heterozygosity (Ho), and polymorphic information content (PIC) , number of private alleles(NPA) were calculated among other genetic diversity parameters. NJ and UPGMA phylogenetic trees were reconstructed using Nei's DA and DS genetic distances. The genetic differentiation of these populations was estimated using principal component analysis and FSTAT software. Some results and conclusions are made as follows:A total of 226 alleles were detected in 368 samples of the 12 populations, of which locus of LEI0234 had the highest Na of 24, while locus of MCW0037 had least Na of 6. The estimates of average Na, Ne , PIC and He per locus among the 12 populations were 7.879, 40.21,0.501 - 0.82 and 0.563-0.849respectively. The PIC values all of 20 loci were larger than 0.5. 20 loci deviated significantly from the Hardy-Weinberg equilibrium in 12 populations (P<0.05),locus of MCW0014 was deviated significantly from the Hardy-Weinberg equilibrium in all 12 populations (P<0.05), loci of MCW0111 and MCW0067 were deviated significantly from the Hardy-Weinberg equilibrium in 11 populations (P<0.05), locus of LEI0166 was just deviated significantly from the Hardy-Weinberg equilibrium in 3 populations (P<0.05).Genetic diversity was high in all 12 populations with estimates of average polymorphic information content (PIC) per population of 0.668. The highest PIC was 0.75 in the Chayu Tibetan population while the lowest PIC was 0.582 in the Daninghe population;while estimates of average expected heterozygosity (He) per population of 0.701. The highest He was 0.759 in the Pingbian Silkies population and the lowest He was 0.612 in the Tibetan chicken population. The genetic differentiation in the 12 population showed that only 11.7% of the total genetic variance existed among population. Dendrogram analysis showed that the genetic distances and genetic relationships between the 12 populations were consistent with their geographic distribution. The Chayu Tibetan chicken and Daninghe chicken had the most distant genetic distances with the highest DA and Ds estimate of 0.4624 and 0.9813. While Gongshan chicken and Wuding chicken had the closest genetic distance with the lowest DA and Ds estimate of 0.1358 and 0.1126. Clustering analyses revealed six populations from Yunnan province were clustered as two group, one branch was located in southern Yunnan, including Pingbian Silkies, Menghai Bantam and Mengla chahua; the other was located in north Yunnan of the, including Gongshan chicken and Wuding chicken, populations from Tibet were between the two branch.