Study Of Genetic Diversity Of 11 Chicken Populations From China And Abroad By 20 Microsatellite Loci

Genetic diversity within and differentiation among 11 chicken breeds (three indigenous chicken populations from Papua New Guinea, five indigenous chicken populations from China and three commercial breeds also sampled in China) and one red junglefowl population (Hainan, China) were assessed using 20 autosome microsatellite DNA loci. Allele frequency, number of observed alleles (Na), number of effective alleles (Ne), heterozygosity (H), and polymorphic information content (PIC) were calculated. NJ and UPGMA phylogenetic trees were reconstructed using Nei's DS and DA genetic distances. The genetic structure of these populations was further estimated using principal component analysis and STRUCTURE program. Some results and conclusions were obtained as follows:A total of 213 alleles were detected in 588 samples within the 12 populations, of which locus LEI0234 had the highest Na of 27 and MCW0222 had 5 alleles. The estimates of average Na, Ne and PIC per locus among the 12 populations were 10.65±5.30, 2.954±0.089 and 0.526 - 0.680, respectively. Except for the loci of LEI0166, MCW0216, MCW0248, MCW0222, MCW0014, MCW0067 and MCW0081 with PIC values ranging from 0.4 to 0.5, the PIC values of the other loci were larger than 0.5. Apart from locus of MCW0216, the rest of the 19 loci deviated significantly from the Hardy-Weinberg equilibrium in one to six populations (P < 0.05). Among the populations, there were 1 to 12 loci deviated significantly from the Hardy-Weinberg equilibrium in 1 to 12 populations (P < 0.05).Genetic diversity was high in all 12 populations with estimation of average expected heterozygosity (He) was 0.615. The highest He was 0.680 in the PMA population witch from Papua New Guinea while the lowest He was 0.526 in the Lohmann Brown. AMOVA analysis showed that the genetic variations between the red junglefowl and all domestic chicken populations, and between the commercial breeds and indigenous chicken populations were existed, while mostly of them was existed between individuals.The patterns of Nei's DS and DA genetic distances between the populations were similar. The highest DA was 0.460 between the red junglefowl and the Lohmann Brown while Hy-line Brown and Lohmann Brown had the lowest DA of 0.064. Clustering and principal component analyses and population genetic structure estimation revealed seven groups among the 12 populations: Hy-line Brown and Lohmann Brown; Arbor Acres broiler; Huining and Minqin populations in Gansu, China; Dehua Black in Fujiang, China; Beijing Fatty and Silkie in Fujian, China; PMA, PAL and PPO chickens in Papua New Guina; red junglefowls.