Molecular genetic identification of Wuzhishan Ant Chicken which is a newly discovered resource in Hainan

Beginning in 2021, when China conducts the third national livestock and poultry genetic resources census, Wuzhishan ant chicken was first discovered in Wuzhishan City, Hainan Province, and there is no relevant research report. In order to clarify that Wuzhishan ant chicken may be a new livestock genetic resource in China, this study used the second-generation whole genome resequencing technology to analyze the genetic resources of four indigenous chickens in Hainan Island (Wuzhishan ant chicken, Wenchang chicken, Danzhou chicken and Bawangling chicken) and the Longshengfeng chicken which is partly similar in appearance to Wuzhishan ant chicken were studied nationwide, and their molecular markers were screened. A total of 21,586,378 SNP sites and 4,253,341 InDel sites were screened out. The results of genome diversity index analysis showed that Wuzhishan ant chicken MAF (0.1382), PIC (0.1615), Ho (0.1657) and He (0.1957) were the highest among the five test groups. The LD of Wuzhishan ant chicken is less than 0.1, and the decay rate is the fastest. The Fst values of all groups are between 0.05-0.15, showing a moderate degree of genetic differentiation. In the principal component analysis and phylogenetic tree, Wuzhishan ant chicken formed a branch compared with other groups. The above results showed that Wuzhishan ant chicken had obvious differences in population differentiation, genetic distance and population structure compared with the other four groups, and had higher genetic diversity, which may be a new genetic resource of livestock and poultry at the molecular level. This study laid the foundation for the excavation and identification of livestock genetic resources in China.