Analysis of Conservation Priorities and Runs of Homozygosity Patterns for Chinese Indigenous Chicken Breeds

SIMPLE SUMMARY: The abundant animal genetic resources ensure sustainable and successful development of animal husbandry. The lack of appropriate long-term conservation programs, however, leads to the absence of rich genetic diversity in indigenous breeds. We investigated the population structure, genetic distance, contribution priority, and runs of homozygosity (ROH) patterns for eight Chinese indigenous chicken breeds using genomic data. Our analysis showed that Chahua, Xiaoshan, and Wannan three-yellow chickens, should be the top three breeds for conservation priority. Selection signals based on ROH were considered to be associated with meat production traits such as body weight, carcass weight, breast muscle weight, drumstick and thigh percentage. ABSTRACT: To achieve sustainable development of the poultry industry, the effective conservation of genetic resources has become increasingly important. In the present study, we systematically elucidated the population structure, conservation priority, and runs of homozygosity (ROH) patterns of Chinese native chicken breeds. We used a high-density genotyping dataset of 157 native chickens from eight breeds. The population structure showed different degrees of population stratification among the breeds. Chahua chicken was the most differentiated breed from the other breeds (Nei = 0.0813), and the Wannan three-yellow chicken (WanTy) showed the lowest degree of differentiation (Nei = 0.0438). On the basis of contribution priority, Xiaoshan chicken had the highest contribution to the total gene diversity (1.41%) and the maximum gene diversity of the synthetic population (31.1%). WanTy chicken showed the highest contribution to the total allelic diversity (1.31%) and the maximum allelic diversity of the syntenic population (17.0%). A total of 5242 ROH fragments and 5 ROH island regions were detected. The longest ROH fragment was 41.51 Mb. A comparison of the overlapping genomic regions between the ROH islands and QTLs in the quantitative trait loci (QTL) database showed that the annotated candidate genes were involved in crucial economic traits such as immunity, carcass weight, drumstick and leg muscle development, egg quality and egg production, abdominal fat precipitation, body weight, and feed intake. In conclusion, our findings revealed that Chahua, Xiaoshan, and WanTy should be the priority conservation breeds, which will help optimize the conservation and breeding programs for Chinese indigenous chicken breeds.