Genome Wide Genetic Variation Mining And Selection Signal Analysis Of Minxian Black Fur Sheep

Minxian black fur sheep is a kind of Tibetan black fur sheep,which is famous for producing black fur.The quality and population of Minxian black fur sheep continue to decline due to the decline of fur market demand,the deterioration of production area environment and the backward feeding and management methods.Using modern biological technology to evaluate the genetic variation information of livestock and poultry not only promotes the research of genetic diversity of livestock and poultry,but also has important significance for the sustainable development of animal husbandry.Hence,Illumina novaseq 6000 sequencing platform was used to mine the genomic variation information of Minxian black fur sheep,including the detection and annotation of SNPs（Single nucleus polymers）,In Dels（Insertion and Deletion）and CNVs（Copy number variations）,and combined with the published whole genome resequencing data of Tan sheep for selection clearance analysis and candidate region gene function enrichment analysis.In addition,the SNPs information of the sample was filtered with high reliability and the mutation sites of relevant genes were selected for verification.The main results are as follows:1.In this study,498.40 Gb of clean data were obtained from Minxian black fur sheep and 496.98 Gb of clean data were obtained from Tan sheep.The average depth of individual sequencing was 27×,the alignment rate with the reference genome（Qar v.1.0）was 99.17%,and the genome coverage was 96.88%.There are 10.63 Mb SNPs and 1837202 In Dels in Minxian black fur sheep.There are 10.77 Mb SNPs and1851338 In Dels in Tan sheep.After annotation,most SNPs and In Dels were located in the intergenic region.11638 CNVRs were obtained from Minxian black fur sheep.The total fragment size of CNVRs was 42.98 Mb,accounting for about 1.64%of the sheep genome sequence.12725 CNVRs were obtained from Tan sheep.The total fragment size of CNVRs was 57.97 Mb,accounting for about 2.21%of the sheep genome sequence.2.Based on the SNP information of Minxian black fur sheep,fixed selection index(F_ST)and nucleotide polymorphism（π）were used for selective clearance analysis.After merging the candidate areas filtered by the two parameters,select the top 5%window(F_ST>0.268,θπ>1.905)as the selection region,277 selection regions and 630 candidate genes were finally obtained.After KEGG functional enrichment analysis of the candidate genes,it was found that they were mainly enriched in important biological processes such as hair growth,immune response,bone growth and seasonal reproduction of sheep.3.The highly reliable mutation sites were obtained by filtering the SNP mutation information.The site mutation information of keratin 25（KRT25）,melanocortin 1receptor（MC1R）and oculocutaneous albinism type II gene（OCA2）were studied.It was found that KRT25 gene had a missense mutation of c.1091A>T:p.Q364L in exon 6,and MC1R had two missense mutations in exon 1,which were c.218T>A:p.M73K and c.361G>A:p.D121N,respectively.There was a missense mutation c.77C>T:p.T26M in exon 2 in OCA2 gene.In conclusion,after high-depth sequencing analysis of the genome of Minxian black fur sheep,this study annotated 630 candidate genes that regulate the important physiological and biochemical reactions and metabolic processes of Minxian black fur sheep.The present research provided basic data for the future research on the Germplasm Characteristics of Minxian black fur sheep and the screening of specific markers,and have great significance to the protection of germplasm resources of local sheep breeds and the sustainable development of animal husbandry.