Genetic diversity of Hainan cattle population based on whole genome resequencing and screening of candidate genes related to heat adaptation

【Objective】The genetic diversity of Hainan cattle population was analyzed based on whole genome resequencing and candidate genes related to heat adaptation were screened to provide theoretical reference for the protection,development and utilization of local domestic cattle germplasm resources in China.【 Method】FASTP v0.20.0 was used to perform quality control and filtering on the whole genome data of Hainan cattle, Mongolian cattle and Tibetan cattle,BWA was used for sequence alignment, GATK v3.5-0-g36282e4 was used for variation detection, and ANNOVAR Documentation was used to build the database required for annotation. Based on the autosomal SNP loci information, the phylogenetic tree was constructed using the method of MEGA X, and principal component analysis （PCA）, uniform manifold approximation and projection （UMAP） clustering were performed using EIGENSOFT v7.2.1. Structure v2.3.4 was used for population structure analysis and population genetic diversity was studied by calculating nucleotide diversity and linkage disequilibrium decay. The whole genome was scanned using PopGenome, and the nucleotide diversity ratio （θπ） and nucleotide diversity and genetic differentiation coefficient（F_ST） methods were used to screen candidate regions under positive selection in the Hainan cattle genome. The annotated genes were annotated with GO functional annotation and KEGG signal pathway enrichment analysis using DAVID, and genes related to heat adaptation were selected, and the structures and physicochemical properties of their encoded proteins were analyzed. 【Result】A total of 20075403 highquality autosomal SNP loci were detected after quality control. There was no pedigree admixture in the Hainan cattle,Mongolian cattle and Tibetan cattle populations. Compared with Mongolian cattle and Tibetan cattle, Hainan cattle had a faster decay rate of linkage disequilibrium（LD）, higher nucleotide diversity, lower artificial selection intensity and higher population genetic diversity. Using Mongolian cattle and Tibetan cattle as reference populations, a total of 144genes under positive selection were screened in Hainan cattle. A missense mutation of the phosphoinositide 3-kinase regulatory subunit 5 （PIK3R5） gene （AC＿000176.1: 28979868, c.987C＞A, p.331D＞Y） was found in Hainan cattle population, which could cause changes in the secondary structure of PIK3R5 gene mRNA and the secondary structure of PIK3R5 protein.【 Conclusion】The high genetic diversity and low artificial selection intensity of Hainan cattle indicate that they retain rich genetic variation in tropical environment. There are missense mutations in PIK3R5 gene in Hainan cattle,which may affect heat stress response and metabolic regulation through the regulation of PI3K/Akt/mTOR signaling pathway, thereby enhancing their heat adaptation ability.