Genetic Structure And Genomic Selection Signature Analysis Of Populations At Domestic And International Sheep

Sheep were one of the earliest domesticated animals.The domestic sheep have changed greatly in physiological,behavioral and morphological phenotypes compared with their wild ancestors during the long selection process.There are many breeds and abundant genetic resources of sheep in China,which are valuable materials for studying the genetic mechanism of sheep domestication.In the present study,we performed whole genome resequencing of 4 Chinese native breeds（10 individuals per breed）and 6 cultivated breeds（10 individuals per breed）,and combined with the publicly available genomic data of Asiatic mouflon,African indigenous breeds,Chinese indigenous breeds and cultivated breeds.In total,the genomic data were collected including 17 Asiatic mouflon and 308 domestic sheep from around the world,these data were used for population genetic structure and genomic selection footprints analysis to identify genomic regions and key genes that were selected for sheep during domestication and improvement.The main results are as follows:（1）According to the sequencing and integration of genomic data from the public database,a total of 7.25 Tb genome data was obtained,the average depth of sequencing was 11.18×,the average mapping rate was 97.11%,and the average coverage was 96.23%.After GATK detection,a total of 11013087 high-quality SNPs were obtained for subsequent analysis.（2）The results of population genetic structure analysis showed that 17 Asiatic mouflon wild sheep and 308 domestic sheep were clearly divergence,but there was significant gene flow.The 325 individuals involved in this study were divided into four groups,namely,Asiatic mouflon,African indigenous breeds,Chinese indigenous breeds and cultivated breeds.Among them,Chinese indigenous breeds are divided into three branches:Mongolian sheep,Tibetan sheep and Kazak sheep,which are consistent with their geographical distribution and morphological characteristics.（3）We integrated 308 domestic sheep genome data as a set of data,compared with wild sheep genome data,and the fixation index(F_ST)statistical methods was used to scan the autosomal and X chromosome,a total of 89 selective regions were identified,and harbored 453 genes,these genes mainly related to visual,auditory and neural development.The selection signal analysis between 30 domestic sheep breeds and wild sheep showed that all 30 breeds were selected in the region of 54.3-54.525Mb and 50.325-50.55 Mb on chromosome 1 and 13.The genes related to vision,such as PANK2 and RNF24 genes,and the genes related to immunity,such as IFI44 and IFI44L.These results indicated that the genes related to sensory ability and immunity were strongly selected during early domestication.（4）By comparing the genomic selection signals of wild sheep,native sheep breeds and cultivated breeds,a domestication and improvement process of wild sheep,native breeds and cultivated breeds was established.Wild sheep compared with native breeds,the selected genes were mainly related to vision and fat deposition,native breeds compared with cultivated breeds,the selected genes were mainly related to growth and development（FGF9 and CDH1 genes）and coat color（MITF and KIT genes）.The results showed that the selection of agronomic traits such as growth and coat color was more important in the breeding process than in the domestication process.（5）The three genes with the highest selection value were screened out by selection signature analysis of fat tail type and thin tail type sheep populations and combined with GWAS results.The expression of PDGFD and BMP2 genes in the ultralarge tail fat tissue was significantly higher than that in the ultrasmall tail fat tissue by q PCR.Subsequently,BMP2 gene g.48979196 C>G was genotyping using KASPar technology,the result showed polymorphism in Hu sheep population,which was extremely significantly correlated with the weight of tail fat weight and the relative weight of tail fat in Hu sheep.