Whole-genome Genetic Diversity And Selective Signals In Hunan And Hubei Indigenous Cattle

Hunan and Hubei provinces are geographically in the hinterland of southern China which is a mixed area of Chinese indicine and East Asian taurine cattle.Hunan and Hubei indigenous cattle belong to southern cattle group,but their origins are complex,and the identification and distinction of breeds in Chinese cattle breeds and indigenous breeds is rather vague.The origin,evolution,taxonomy,and genetic diversity of the indigenous cattle in Hunan and Hubei mainly remain in the description of body shape and appearance.In order to accurately identify and evaluate the local cattle resources in Hunan and Hubei,it is necessary to conduct in-depth analysis from the whole genome level.Therefore,this study collected two Hunan indigenous cattle breeds（17 Xiangnan cattle,24 Xiangxi cattle）and three Hubei indigenous cattle breeds（10 Yiling cattle,7 Zaobei cattle,9 Huangpi cattle）,and downloaded whole-genome resequencing data of Chinese indicine（5 Wannan cattle,4Guangfeng cattle,5 Wenshan cattle）,Indian indicine（10 cattle）,East Asian taurine cattle（10Hanwoo cattle）,European taurine cattle（9 Angus cattle,8 Simmental cattle）,and representative breed of 12 Qinchuan cattle in China.To construct a genetic map of indigenous cattle breeds in Hunan and Hubei,and to study their genetic diversity,population genetic structure and genomic selection regions The following main research results were obtained:（1）The Xiangnan cattle only has Chinese indicine cattle ancestry,the other four breeds have principally Chinese indicine cattle ancestry and also contain taurine cattle ancestry,and the indicine cattle ancestry components decrease sequentially from low latitude to high latitude.（2）The genetic diversity of mtDNA and Y chromosome of indigenous cattle in Hunan and Hubei was high.Both the paternal and maternal origins have indicine and taurine cattle ancestry,and the indicine ancestry was the main line.Specifically,the Xiangnan cattle belong to the pure Chinese indicine lineage.The Xiangxi Cattle,Yiling Cattle and Zaobei Cattle are mainly of Chinese indicine pedigree,which may have been mixed with taurine cattle ancestry during the domestication process.Huangpi cattle are also mainly of Chinese indicine ancestry,which may have been mixed with the ancestry of Eurasian taurine cattle under the introduction and hybridization of modern times.（3）Hunan and Hubei indigenous cattle breeds have fewer ROH fragments than taurine cattle breeds,among which the cattle breeds in Hubei are slightly lower than those of Chinese indicine and Indian indicine,while those in Hunan cattle were slightly higher than those of Chinese indicine and Indian indicine.The inbreeding coefficient of indigenous cattle breeds in Hunan and Hubei is only higher than that of Chinese indicine,and the nucleotide diversity is second only to that of Chinese indicine.The above results show that the indigenous cattle in Hunan and Hubei have rich genetic diversity,but the degree of selection was not very high.（4）Theθπand CLR methods were used to find candidate regions for positive selection within the breeds of Hunan and Hubei indigenous cattle,and 210（Xiangnan cattle）,108（Yiling cattle）,80（Zaobei cattle）and 49（Huangpi cattle）were identified,respectively.Candidate genes were analyzed for enrichment.Candidate genes and related pathways related to reproduction and immune response were identified in Xiangnan cattle;candidate genes and related pathways related to muscle meat quality were identified in Yiling cattle;Candidate genes and related pathways related to growth and development were identified in Zaobei cattle,which were consistent with the germplasm characteristics of each breed.By comparing the differences in candidate genes,the differences in the direction of selection among different breeds were shown.（5）Through single-group detection（CLR andθπ）methods and F_STand XPEHH analysis methods on 24 Xiangxi cattle and 12 Qinchuan cattle in the reference group,2225（θπ）,182（CLR）,1264(F_ST)and 553（XPEHH）candidate genes were detected respectively.And found positive selection regions of genes related to heat tolerance（DNAJC8）and performance（VGLL2,WASF2,SLC9A1）,meat quality（EYA3,MYH10,GPR3,etc.）,skin barrier（SFN,PALLD,KDF1,FA2H）and candidate genes and related pathways related to immunity（PTAFR,JAK2,etc.）.The excellent adaptability of Xiangxi cattle was demonstrated from different aspects.In this study,the germplasm characteristics and excellent characteristics of indigenous cattle in Hunan and Hubei were mined from the whole-genome level,and provided theoretical basis for the targeted and efficient breeding of indigenous cattle in Hunan and Hubei.