Genetic characterization of Taiwan commercial native chickens ascertained by microsatellite markers

Taiwan commercial native chickens have played a vital role in the domestic market due to Taiwanese traditional cooking style and culture. This study investigated the genetic characterization and population structure of 10 Taiwan commercial native chicken populations, together with two exotic breeds and one population of red jungle fowl, using 22 microsatellites. The results showed that Taiwan commercial native chickens generally harbored high genetic diversity but lower than that of red jungle fowl population in terms of number of alleles and gene diversity. The neighbor-joining tree revealed a poor resolution with only two branches showing bootstrap values above 70%. Based on Bayesian clustering approach, thirteen populations were inferred into eight distinct clusters namely Game bird, B strain, L2 strain, White Broiler and White Leghorn with an average proportion of membership higher than 0.90 and the values higher than 0.85 for red jungle fowl, Hakka chicken and Hakka strain while four remaining breeds were closely related together. The population structure showed Taiwan commercial natives chickens are more admixed, in contrast to occidental highly productive breeds. The high genetic variation within breed as shown in the results of the analysis of molecular variance, facilitated by gene exchanges, did not allow discriminating in an efficient way. This suggests that the genetic pool of Taiwan commercial native chickens is well distributed among breeds and therefore there is a good potential for adaptation to new environmental conditions or markets. Some populations, namely L2 strain and B strain showed very high inbreeding coefficient and thus could be considered at risks. Therefore, management needs to be taken into account for the populations, to prevent inbreeding depression and maintain genetic diversity.