| Sheep,one of the earliest domesticated animals,play vital roles in economic animals for providing meat,dairy and wool products.The demand for mutton is increasing because of its characteristics with high protein,low cholesterol and low fat.However,the annual mutton production in China exceeds supply which makes it impossible to quickly supply the market.Screening genetic markers related with sheep meat performance for genetic improvement of breeds is an important technique to improve sheep meat performance.In this study,two sheep breeds with different meat production performance(local breed,Small-Tail Han Sheep and cultivated breed,Suffolk)were selected to analyze the selective signature based on the whole genome resequencing data,combined with the reported Quantitative Trait Locus(QTL)and Genome-Wide Association Study(GWAS)information to screen the variant sites related with meat production performance,The high-throughput KASP genotyping method for the selected variation sites was established.The results are as follows:(1)A total of 30,370,984 single nucleotide polymorphisms(SNPs)were obtained based on 9 Small-Tail Han Sheep and 9 Suffolk sheep with the genome-wide data of 324.265 Gb compared with the sheep reference genome(Texel,OAR-V3.1).The obtained SNPs were analyzed by population genetic analysis.The differences between the small-tailed Han sheep and Suffolk were found by principal component analysis(PCA).Linkage disequilibrium(LD)analysis revealed that the LD decay distance of the Suffolk population is larger than that of Small-Tail Han Sheep.(2)Based on the variant information between the small-tailed Han sheep and the Suffolk genome,the population F-statistics(Fst)was calculated for selective signature analysis.A total of 51 regions containing 89 candidate genes with higher signal strength and ZFst value greater than 5 were selected.These candidate genes which are related to growth and development,disease and disease resistance,adaptability,milk quality,reproduction,wool,horns and coat color traits etc.In addition,Using top5%corresponding ZFst value as critical value,the gene ontology enrichment(GO)analysis of the genes in the selected region larger than this value was carried out.the results of gene ontology(GO)enrichment analysis showed that the selected genes in the selected region were mainly related to the activity of G protein conjugated nucleotide receptor and G protein conjugated nucleotide receptor(P<0.01).The KEGG pathway analysis indicated that the selected genes in the selected regions were associated with olfactory conduction,arachidonic acid metabolism and systemic lupus pathways(P<0.01).The genes related to meat production traits screened by selection signal analysis overlapped with the genes in meat production trait QTLs were confirmed as candidate genes and KAT2B and SGPP2 genes were identified.Three different SNP sites were screened in KAT2B and SGPP2 genes,and they are rs161725730 A>G missense variant site of KAT2B gene on chromosome 1,intron variant site of 75278 G>C and 79756 G>C of SGPP2 gene on chromosome 2,named K1,S1 and S2 respectively.(3)A DNA pool respectively containing five small-tailed Han sheep DNA samples and five Suffolk DNA samples was sequenced by direct sequencing respectively.The sequencing results identified three SNP sites named K1,S1 and S2.KASP genotyping was used for the DNA samples of sheep on K1,S1 and S2 site,and a high-throughput KASP genotyping method was established for K1,S1 and S2 site.The results of detection showed that the main genotypes at K1,S1,and S2 were AA,GG,and GG,in small-tailed Han sheep respectively,corresponding genotype frequencies were 0.63,0.8 and 0.8,while were GG,CC,and CC in Suffolk and Dorset,respectively.The corresponding genotype frequencies in Suffolk were 0.5,0.53 and 0.53.The corresponding genotype frequencies in Dorset were 0.5,0.7 and 0.7.These results indicated that K1,S1 and S2 sites were likely to be important variant site to affect sheep meat traits.In summary,this study used the whole genome data of small-tailed Han sheep and Suffolk for selection signal analysis and screened three variant sites that affected sheep meat traits,providing theoretical basis and technical support for molecular marker breeding of sheep breeds. |
