Genome-wide Association Study For Wool Production Traits In Chinese Merino Sheep (Xinjiang Type )

Wool yield and quality traits determine the value of fine wool,and affecting to efficiency of wool industry.Discovery and identification of genes or markers affecting wool yield and quality traits of fine sheep were the important direction and task of sheep genetic breeding.In this study,we performed a GWA study mainly based on fiber diameter,staple length,stretched length,rate of stretched length and greasy fleece weight of Chinese Merino sheep(Xinjiang type).The present study is to perform Linkage Disequilibrium(LD)and Genome-Wide Association Studies(GWAS)to detect candidate genes and markers associated with wool production traits for molecular breeding of fine wool sheep.1.Chinese Merino(Xinjiang type)is well-known fine wool sheep breed.However,the extent of LD across the genome remains unexplored.In this study,we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino(Xinjiang type)sheep by Illumina Ovine SNP50 BeadChip.The marker-QC(quality control)process included three steps:(i)control of the call rate(? 0.95);(ii)minor allele frequency(MAF)(? 0.05);(iii)correspondence with the Hardy-Weinberg equilibrium(HWE)(P-value > 0.00001).These parameters were calculated using Plink v1.07.After quality control,we identified 46,062 SNPs in Chinese Merino(Xinjiang type)sheep distributed over 26 autosomal chromosomes.A moderate level of LD(r2? 0.25)across the whole genome was observed at short distances of 0 – 10 KB.we found 280 genes in linkage disequilibriumregion,of which 47 genes were involved in biological processes related to wool traits,also explain chinese merino in the advantage of wool traits.Further,the ancestral effective population size(Ne)was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations,which is consistent with the history of Chinese Merino sheep breeding,initiated in the 1970 s.We also noted that even when the effective population size was estimated across different single chromosomes,Ne only ranged from 140.36 to 183.33 at 5 generations in the past,exhibiting a rapid decrease compared with that at 10 generations in the past.These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity.Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.2.Using Illumina OvineSNP50 BeadChip,First,we performed SNPs genotyping and Phenotypic measurement of Chinese Merino sheep(Xinjiang type)and Germany merino sheep phenotyped for fiber diameter(728),staple length(364),stretched length(364),rate of stretched length(364),greasy fleece weight(364).Next,The quality of wool traits were normal distribution test,in test: stretched length and greasy fleece weight with normal distribution,fiber diameter,staple length,rate of stretched length does not the normal distribution,unnormal distribution of the phenotype was analyzed by BoxCox,which is in accordance with the normal distribution.Again,And the group was the principal component analysis(PCA),found that the stratification in the choice of the resource population,so in the construction of MLM and GLM model,Q-Q plot analysis,In the MLM,observation value and expected value of the basis line were same,that population structure does not exist after correction of population stratification,also shows that the population stratification does not bring influence to the analysis of false positive.After,the construction of the relationship matrix of two groups as a covariate in the mixed linear model,to reduce the false positives caused by genetic relationship.and then,The association analysis revealed 35 significant SNPs.We found 41 gene,and MLH1,CDH3,STXBP6,UBASH3 A,et al,which are skin and/or hair follicle development genes,may be candidate genes of wool quality traits in Merino sheep.The results will contribute to identify candidate genes for wool production traits,and facilitate the potential utilization of genes involved wool traits in merino sheep in future Finally,in two populations,Stretched length of AA genetype were significant differences BB and AB.Stretched length of BB genetype were no significant differences AB.In two populations,BB genetype genotypic frequency is higher,AA genetype genotypic frequency is lower.Also proved German Merino sheep and Chinese Merino sheep(Xinjiang type)were same genetic background,the further explains genome-wide association analysis in the two merino sheep for wool quality mark is correct.Conclusion:This study Using Illumina OvineSNP50 BeadChip,Motivated by mining major candidate genes across ovine genome,the present study is to perform LDand GWAS to detect genes associated with wool production traits.The platform of two breeds merino genome association analysis was constructed.By gene chip technology and high-throughput genotyping technology,we reveals China Merino(Xinjiang type)SNPs distribution,and candidate genes associated with hair quality traits.