Genome-wide Association Study,Copy Number Variations And Selection Signatures Detect For Sheep With Different Types Of Tails

Chinese indigenous sheep can be classified into three types based on tail morphology,fat-tailed,fat-rumped,and thin-tailed sheep.The tails of fat-tailed and fat-rump-tailed sheep are the result of breeding by humans and natural selection from wild thin-tail sheep.Climate,human needs and the way of selection are play an important role during the process of domestication and selection.At the same time,the tail of sheep are significant economic traits in sheep,has been attracting the attention of scholars breeding.In the past,the fat of sheep tail had an important role for itself and humanbeings,but at present,with the change of consumption concept and the improvement of pastoral feed conditions,the role of the fat of sheep tail is not important and bring economic pressure to the production.Thus,analyzing genomic variations by SNP Beadchip data of sheep with different type of tails,searching the differences of the genetic basis of them.In this study,the Illumina Ovine SNP600 Beadchip data of 120 sheep with different type of tail were used for Genome-wide association analysis,Copy number variation and selection of signature detection,and enrichment of candidate genes function.1 Genome-wide association studies for tail type traits of three breeds sheep40 large tail han sheep,40 Altay sheep and 40 Tibetan sheep were obtained respectively from sheep farms located in liaocheng,shan dong province,Altal,xinjiang and tuanzhu,gan su province.Genotyping was conducted through Illumina OvineSNP600 BeadChip.After quality control,119 sheep and 538762 SNPs left.Generalized mixed linear model(GLM)method,Tassel software was used to carry out the GWAS on tail shape of large-tailed Han sheep(LH),Altay sheep(ALT),and Tibetan sheep(Tib).The results indicatied that a total 31 genome-wide significant SNPs associated with type of tail traits were detected,all of which distributed on chrl?2?7?10?13?15 and 19 respectively.For significant SNPS loci,determine its physical location,and screening of candidate genes within section.By combining information of previously reported and annotated biological functional genes,we identified SPAG17,Tbx15,VRTN,NPC2,BMP2 and PDGFD as the most promising candidate genes for type of tail traits.2 Genome-wide Detection of Copy Number Variations(CNVs)in sheepPennCNV was employed to detect genome-wide CNVs among sheep with three different types of tails.In large-tailed Han sheep(LH),Altay sheep(ALT),and Tibetan sheep(Tib),a total of 371,301,and 66 CNV regions(CNVRs)with lengths of 71.3 5 Mb,51.65 Mb,and 10.56 Mb were detected,respectively.490 CNV Regions(CNVRs)were acquired by aggregating overlapping CNVs,including 90 gain,390 loss and 7 both(gain and loss within the same region)events.According to the location of these CNVRs,we drew a map of genomic CNVRs in 26 pairs of autosomal chromosomes of sheep.Ten CNVRs were randomly chosen for confirmation,of which 8 were successfully validated.A great difference was found in the CNVR numbers among the three breeds,CNVRs were much more in LH and ALT than Tib.Series of CNVRs function analysis were carried out,some of the candidate genes in CNVRs were predicted for fat metabolism,and associated with climate-driven adaptive evolution.3 Genome-wide Detection of Selection Signatures in sheepFST and XPEHH methods were employed to detect selection signature between breed pair,FST method found that the selection signature between fat-tailed-thin tail pairs and fat-rumped-thin tail pairs more than fat-tailed-fat-rumped pairs,67 significant SNPs and 44 selection regions were found only between big tail and thin tail.Tatal length is 10.10Mb;average length is 0.233Mb.According the analysis of gene annotation and enrichment,some genes related with fat were found,such as JAZF1,GEM,PRNP,BMP2,PPP1CC,PDGFD,MC4R,GPR124 and ADRB3.XPEHH analysis showed that 231 and 179 SNP loci were positively selected in the large-tail sheep and the Altay sheep.The region close to(<50kb)each significant SNP was set a selected area.In light of the analysis of gene annotation and enrichment,some genes in those regions were found related with fat,such as CPT1A,CA4,CLPS,BMP2,KLF3,RETN,WNT,INSR,IRS1,CPT1A,SLC27A2,SLC27A4,PRKAG1,JAZF1,MC4R,BMP8B,CPT2,FABP3,SLC27A4,KLF11,PRKAG2,BMPR1B,SLC27A5,FOXP1,FGFR1.The Two methods have overlapping selection regions.Through gene annotation and enrichment analysis,it is found that JAZF1,BMP2 and MC4R genes are associated with adipogenesis in these overlapping regions.