The Whole-genome Genetic Diversity Of Three Cattle Breeds In Guangxi

Guangxi Province is located in the southernmost region of China,with the most humid and prolonged hot summer temperatures.The unique natural conditions and the long-term acclimatization have formed three excellent native cattle breeds(Longlin cattle,Nandan cattle and Weizhou cattle).With the development of next generation sequencing technology,the whole-genome sequencing data of cattle has been accumulated worldwide,and increasingly number of studies have been performed on the genetic diversity of domestic cattle through resequencing.However,there are few studies on the genome-wide genetic diversity of Guangxi native cattle breeds.Here,we investigated the genome-wide genetic diversity of Guangxi native breeds,Longlin(n = 21),Nandan(n = 18),and Weizhou cattle(n = 17)using whole genome re-sequencing,along with some published whole genome sequencing data of Pakistani(n = 18)and Hanwoo cattle(n=15).The main results obtained are as follows:(1)The Guangxi cattle breeds showed plentiful genetic variation.Compared with Hanwoo and Pakistani cattle,the number of Guangxi native cattle breeds is more than 22,212,517 and 11,885,454 in SNP respectively,while 2,413,421 and 1,494,795 in In Del.(2)The three native Guangxi cattle breeds belonged to an independent origin of zebu in southern China.(3)The nucleotide diversity of three cattle breeds of Guangxi was basically consistent.Among the three native Guangxi cattle breeds,Longlin cattle had the lowest LD linkage imbalance,while Weizhou cattle had the highest;ROH analysis showed that Nandan cattle may have inbreeding.(4)The three native Guangxi cattle breeds shared 24,345,302 SNPs and 2,697,399 In Dels.The KEGG functional enrichment analysis of these breeds represented herpes virus resistance genes(TLR2,DDX58,TAP2).Moreover,GO functional enrichment analysis revealed genes related to homophilic cell adhesion via plasma membrane adhesion molecules(NCR3,FAT4)and six genes involved in complement activation.(5)Mitochondrial genome analysis revealed that Bos indicus sub-haplogroup I1 a predominates in the studied cattle breeds of Guangxi,and the proportions in Longlin,Nandan,and Weizhou cattle were 71.43%,66.67%,and 100%,respectively.(6)The male-specific region SNP analysis revealed that the zebu haplotype group Y3 a was dominant in the studied cattle breeds of Guangxi.In summary,this study investigated the genetic diversity and origin of the three cattle breeds of Guangxi.Information generated from this study forms the basis for the protection of the native cattle breeds of Guangxi.