Genomic Analysis Of Economically Important Production Traits: Coat Color And Fat Tail Traits In Chinese Tan Sheep

The contribution of livestock for food production and economic growth has been quite significant in the globe.Sheep are among the highly contributed livestock species to feed the world population.Initially,sheep were reared mainly for meat production;however,gradually specialized for secondary products such as milk,wool and fur production.Chinese Tan sheep is a unique and typical sheep breed for fur and meat production.The coat colour of the fur and fat content of the meat in its different body part including tail fat are some of the determinant factors for consumers and breeding program of sheep breeds.Therefore,understanding the genetic characteristics of the Tan sheep for its important traits such us coat colour and tail fat is paramount important.Hence this study was designed to perform GWAS to identify genomic region,candidate genes and significant molecular variants associated with coat colour and fat tail phenotypic traits in Chinese Tan sheep.For coat colour phenotype,we used 75 Chinese Tan sheep and ovine 600 K SNP Bead Chip to perform GWAS.We were also performed PCR,q PCR and allele-specific expression analysis using extra Tan sheep samples to validate the GWAS results.Accordingly,we identified two significant SNPs(rs409651063 at 14.232 Mb and rs408511664 at 14.228 Mb)associated with coat colour in the MC1 R gene on chromosome 14 with-log10(P)= 2.47E-14 and 1.00E-13,respectively.The consequence of rs409651063 was a missense variant(g.14231948 G>A)that caused an amino acid change(Asp105Asn),whereas the second SNP(rs408511664)was a synonymous substitution and is an upstream variant(g.14228343G>A).Moreover,the genotype of white sheep was found exclusively homozygous(GG),whereas the genotypes of black-head sheep were mainly heterozygous(GA)in the PCR analysis.In the allele-specific expression analysis of black-head sheep,only the G allele was expressed in the skin covered with white hair,while both the G and A alleles were expressed in the skin covered with black hair.Furthermore,in the q PCR analysis,gene expression(MC1R)was significantly higher in blackhead than white sheep and very significantly higher in heterozygous(GA)sheep than homozygous(GG)individuals.Similarly,for the Fat tail phenotype,we conducted a genome-wide association study to identify candidate genes and genetic variants associated with fat tail in 160 Chinese Tan sheep using the ovine600 K SNP HD Bead Chip.Accordingly,we identified a candidate gene(NISCH)and five SNPs spanning the genomic region 48.344 Mb-48.369 Mb on chromosome 19 which associated with fat tail phenotype.This result was validated using extra Tan sheep samples by PCR and q PCR techniques.Among the genotyped fat tail individuals for SNP chr19?48345414G>A,48% were homozygous(AA),57% individuals were heterozygous(GA)and only 7% individuals revealed homozygous(GG).This finding indicated that the missense mutation that we identified is probably responsible for the large fat tail in Tan sheep.Moreover,we performed q PCR for gene expression analysis using the data collected from Tan sheep embryos found at different developmental stages.From this data,the NISCH expression level was significantly higher in the 60 days developmental stage embryos than the 70 days,and it was very significantly increased from 70 to 90 days developmental stage.As a conclusion,in this study,we identified two significant SNPs and a gene(MC1R)associated with coat colour on chromosome 14,and NISCH gene and molecular variants related to fat tail trait in Tan sheep on chromosome 19 using the ovine 600 K SNP HD Bead Chip.The findings of this study will have significant contributions in elucidating the genetic mechanism underlying the fat tail and coat colour phenotype variation in indigenous Chinese sheep in particular and genetic improvement activities in animal production and reproduction industries in general.