Genetic diversity of local chicken breeds（groups） in Guizhou based on SNP chip

【Objective】This study aimed to analyze the genetic diversity of Guizhou local chicken breeds（groups） and determine the genetic relationship among breeds, so as to provide reference for the protection and innovative utilization of Guizhou local chicken breeds resources. 【Method】A total of 66 blood samples were collected from four Guizhou local chicken breeds（groups） Xianglushan chicken（SL）, Yaoshan chicken（YS）, Qiandongnan Xiaoxiang chicken（XX） and Weining chicken（WN）. SNP loci detection for the four Guizhou local chicken breeds（groups） was conducted based on Jingxin No.1 chicken 55 K SNP chip. The genetic diversity, population structure and genetic relationship of the four Guizhou local chicken breeds（groups） were analyzed using Plink v1.90, VCFtools v0.1.17 and Admixture v1.3, respectively. 【Result】The effective population content（Ne） among the four Guizhou local chicken breeds（groups） ranged from 3.1 to 3.2, and the expected heterozygosity（He） was all lower than the observed heterozygosity（Ho）. The polymorphism information content（PIC） rankings were as follows: Weining chicken（0.8583）＞Yaoshan chicken（0.8350）＞Qiandongnan Xiaoxiang chicken（0.8123）＞Lushan chicken（0.8001）, all above 0.50, indicating that the four Guizhou local chicken breeds（groups） were highly polymorphic and rich in genetic diversity. The phylogenetic tree based on the identity by state（IBS） genetic distance matrix showed that Xianglushan chicken had the longest branch and Weining chicken had the shortest branch. The results of principal component analysis（PCA） showed that the boundaries between the four Guizhou local chicken breeds（groups） were clear, and there was no mutual penetration between the breeds（groups）. In the Admixture progenitor analysis, the optimal group clustering occurred when the number of ancestor clusters（K）=2, indicating that Xianglushan chicken, Yaoshan chicken, Qiandongnan chicken and Weining chicken had two common ancestors. The population differentiation coefficient（F_st） among the four Guizhou local chicken breeds（groups） was close to 0.05, indicating that there was no obvious differentiation among the groups. The results of G matrix kinship analysis of four Guizhou local chicken breeds（groups） were consistent with the results of IBS genetic distance analysis. The interindividual kinship and genetic distance between Xianglushan chicken individuals were the closest, whereas those between Weining chicken individual were the farthest. 【Conclusion】The four Guizhou local chicken breeds（groups） exhibit rich genetic diversity with clear boundaries between breeds（groups）, and there is no mutual penetration phenomenon.However, there is risk of inbreeding among some breeds（groups） in the kinship. Therefore, it is neccesary to improve breeding methods of Xianglushan chickens and Qiandongnan Xiaoxiang chickens in the future breeding work, appropriately increase the number of groups and the male-to-female ratio to avoid inbreeding decline.