Genome-wide Association Study For Growth And Serum Biochemical Parameters And Construction Of CNV Map In Yak

Meat production is always the key trait in yak breeding.Growth traits and metabolic traits such as serum biochemical parameters are crucial traits affecting yak meat production.Here,we conducted genome-wide association studies(GWAS)to uncover the genetic basis and corresponding candidate genes of growth traits and serum biochemical parameters in 354 yaks using the Illunima Bovine HD Bead Chip.Besides,we also identified the genome-wide copy number variations(CNV)and conducted a GWAS for growth traits using CNV as markers.The results are as follows:1.Three multi-locus GWAS methods were adopted to investigate the genetic mechanisms and potential candidate genes underlying the growth traits such as body weight,withers height,body length,and chest girth at 6th month,12 th month,18 th month,and 30 th month of age in yak.A total of 385 SNPs were found to be significantly associated with at least one traits.Among them,18 SNPs were significantly associated with two different traits,while 3 SNPs were significantly associated with three traits.Besides,116 out of the 385 SNPs were found to be located within or near the previously reported QTLs for growth-related traits.268 protein-coding genes were found to be as the potential candidate genes due to their positions in the genome,and 55 out of them were identified as the key candidate genes for growth traits.2.Three multi-locus GWAS methods were adopted to identify the genetic loci influencing the levels of 11 serum metabolic-related biochemical parameters in yak including serum total protein,albumin,alanine aminotransferase,aspartate aminotransferase,alkaline phosphatase,glutamyl transferase,lactate dehydrogenase,urea,glucose,triglyceride,and total cholesterol.266 SNPs were found to be significantly associated with at least one of the 11 serum metabolic-related biochemical parameters.Among them,16 SNPs were pleiotropic loci associated with two or more traits.These pleiotropic loci might be critical indicators to unravel the underlying molecular mechanisms of serum biochemical parameters in yak.A total of 32 genes were identified as the key candidate genes for these metabolic-related biochemical parameters.3.We identified 1408 CNVRs across the yak genome by using the combination of Penn CNV and CNVRuler software.The total length of the CNVRs was 322.14 Mb,occupying 12.82% of the bovine genome(UMD 3.1).83 out of the 1408 CNVRs were identified as the yak-specific CNVRs.1023 out of the 1408 CNVRs were annotated with 2521 protein coding genes.Functional analysis of the genes harbored in CNVRs showed that the CNVRs may be involved in the adaptation to high altitudes.1246 CNVRs were found to be overlapping with 16354 QTLs involving six trait classes,including reproduction QTLs,production QTLs,meat and carcass QTLs,milk QTLs,exterior QTLs,and health QTLs.4.GWAS for growth traits in yak using CNV as markers identified 1,3,60,3,and 6 significant CNVRs to be associated with body weight at 6th month,body length at 6th month,withers height at 18 th month,body length at 30 th month,and chest girth at 30 th month,respectively.Interestingly,5 CNVRs were found to be significantly associated with at least two of the five traits.The 5 significant CNVRs were CNVR250,CNVR308,CNVR420,CNVR1206 and CNVR1296.The results of the GWAS for growth traits and serum biochemical parameters can provide valuable information to the marker-assisted selection and genomic selection of meat production in yak,and will give novel insights into the mechanisms of the formation of phenotypic variations of the interested complex traits.The genome-wide yak CNV map may not only help to the genetic improvement of economic important traits and investigation of the adaptation to high altitudes,but to a better understand of the genetic variation in yak genome.