The Whole-genome Genetic Diversity Of Major Cattle Around The Southwest Border Of China

The southwest border of China is bordered by many countries in Southeast Asia,and the complex humanity and geographical environment has created the natural abundant genetic resources here.As the gateway to Southeast Asia,the southwest border area has complex terrain and large span,which led to complex and diverse local breeds.So far,there has been no specialized research on indigenous cattle breeds in the southwest border area of China.Therefore,this study combined with the resequencing data of 93 cattle from 11 breeds in Shigatse,Dehong,Wenshan and Weizhou,Wannan,Burma,India,Pakistan,South Korea and Europe,the whole genome level was analyzed.The autosomal genome,mitochondrial genome and Y chromosome were used for genetic diversity,population genetic structure,paternal and maternal genetic map construction and selection analysis,and the following main research results were obtained:1.The genetic diversity of 11 cultivars was analyzed by nucleotide diversity(π),runs of homozygosity(ROH)and linkage disequilibrium(LD).The results showed that the genetic diversity from high to low was as follows: Chinese Bos indicus > Southwest China hybrid > India-Pakistan Bos indicus > East Asian Bos taurus > European Bos taurus.2.Through the study of the phylogenetic tree of 11 varieties of building component analysis,principal component cluster analysis and ancestors,the results show that the Wenshan cattle and Weizhou cattle around the southwest border are mainly of Chinese Bos indicus ancestry,while Dehong cattle and Burma cattle are of Indian Bos indicus ancestry is predominant.The lineage of Indian Bos indicus is gradually diluted in Burma,Dehong,Wenshan and Weizhou cattle from west to east.3.The patrilineal and maternal genetic maps were constructed on the Y chromosomes of 72 male individuals and the mitochondrial genomes of 81 individuals.According to the results,Wenshan cattle and Weizhou cattle mainly for the Chinese Bos indicus origin,while Dehong cattle and Burma mainly India-Pakistan Bos indicus cattle.Shigatse humped cattle are mainly India-Pakistan Bos indicus origin,mixed with a small amount of African Bos taurus(T1),East Asian Bos taurus(T3)and Western European Bos taurus(Y2a).4.Through selective sweeping analysis of 9 Shigatse humped cattle(at an altitude of4200 meters)and a reference group of 9 Weizhou cattle(at an altitude of 20 meters),the high-altitude Shigatse humped cattle population was identified as being related to melanin deposition,hypoxia adaptation,metabolic pathway,reproducing and radiation resistance and so on related genes and pathways,which are consistent with the breed characteristics of Shigatse humped cattle.This study conducted a systematic assessment of Bos indicus resources around Chinese southwest border from the perspective of the whole genome,and provided a scientific basis for the scientific protection of Bos indicus breed resources and the genetic improvement of local breeds in southwest China,which has important theoretical and practical significance.