| As a typical hybrid cattle breed,the complex lineage composition of Yunling cattle makes it have the excellent variety characteristics from different ancestral groups,but there are relatively few studies on the potential genetic mechanism of these excellent variety characteristics.According to the variety advantages of Yunling cattle,such as fast growth speed,strong immune disease resistance and strong adaptability,this study conducted genome-wide association（GWAS）analysis on the body appearance and blood physiological and biochemical traits（15 body traits,ear size,brindle coat color and red topline,navel length and blood physiological and biochemical traits）of Yunling cattle,and obtained the following innovative results:1.Based on the whole genome sequence data of Yunling cattle and Brahman cattle,the genome-wide association analysis was conducted on 15 body traits of those cattle.The results showed that 9 body traits had significant signal loci(P<5×10-8),involving 18candidate genes.For ischium width,the most significant SNP(P=6.60×10-9)was assigned to LCORL,a famous gene controlling body size.For chest width,the most significant SNP P=9.77×10-9)was located upstream of BMP5.For chest circumference,frontal width,body oblique length,tube circumference,chest depth and rump length,the most significant loci were located in NAV3,LSAMP,STXBP3,TUSC1,IZUMO3,DOK5,SLX4IP,CAMK1D,CDYL2,DYNLRB2 and ACACA genes,respectively.In addition,the gene CNTNAP5 significantly associated with cross height(P=4.33×10-8)showed extreme IHS and CLR values.The LIMCH1 gene significantly correlated with frontal width(P=3.49×10-8)showed extreme IHS values and decreased nucleotide diversity.2.Genome wide association analysis of 158 cattle ear size traits showed a region on chromosome 6 between 36.79 and 38.80 Mb included 4 significant SNPs that were significantly associated with ear size.The most significant locus(P=1.30×10-8)was a missense mutation（NC＿037333.1:g.36880294 A>G）on the seventh exon of IBSP.At the same time,the statistical analysis of the IBSP missense genotype among different cattle breeds showed that the GG genotype is presented in Bos indicus with large ear size and that the AA genotype is presented in Bos taurus,which has small ear size.Three genotypes are presented in hybrid cattle,which lives in the south of China and has complex ear size.Furthermore,this missense mutation could alter the 3D structure of its protein,which may change the function of the protein.The expression levels of IBSP in ear tissues of large-and small-ear cattle were significantly different.In nearly 70 vertebrate species except Bos taurus,mouse deer and white lipped deer,this mutation is conserved.3.GWAS analysis of brindle coat color and topline phenotype of Yunling cattle showed that the formation of brindle coat color and topline phenotype was not affected by the population structure and lineage composition of the variety.The GWAS result of brindle coat color traits showed that the significant signal region contained SEXT and BMP7 genes,The GWAS results of topline phenotype trait showed that the significant signal on chromosome 18 was a missense mutation site of MC1R gene.The missense mutation of MC1R gene may be one of the important factors leading to the less enrichment of melanin in the back hair of Yunling and Dabieshan cattle and the formation of yellow and white striped topline.4.The navel length of Yunling cattle and Brahman cattle was significant difference,and the navel length of Yunling cattle was less than that of Brahman cattle.GWAS results showed that ABLIM3,PPARA,HMGA2,FAM184B and SLCA24A5 were candidate genes for the navel length trait,and the navel length trait was controlled by multiple genes.The intron mutation site of ABLIM3 gene was an important molecular marker of cattle navel length trait.5.Based on the blood physiological and biochemical indexes of Yunling cattle,GWAS analysis found that seven index traits had significant correlation loci.For lipid traits,the results showed that the most significant signals were located on PRL22L1 and SLC7A14genes on chromosome 1,while the genes involved in the other significant loci were XPOT,SLC16A7,SCAI,SYT14 and ATP2B2.For GWAS on metabolic and protein related parameters,the resulrs showed that the significant locus related to bilirubin was located on NHSL1,which showed an antagonistic relationship with biological hypertension.For GWAS analysis on erythrocyte related parameters,we found that the genes significantly related to erythrocyte distribution width traits were NAV3,LSAMP,STXBP3,TUSC1,IZUMO3,DOK5,SLX4IP,CAMK1D,CDYL2,DYNLRB2 and ACACA.GWAS analysis of leukocyte related parameters showed that the genes significantly related to leukocyte count traits were BOLA,BOLA-DQB and BOLA-DQA5.These three genes were famous bovine leukocyte antigen genes and play an important role in many immune diseases of cattle.GWAS analysis of traits related to trace element parameters found that the gene significantly related to cysteine traits was CIITA,which played an important role in the immune regulation of organisms and played a certain role in the defense mechanism against tick invasion.In this study,GWAS analysis was carried out on the body appearance and blood physiological and biochemical traits of Yunling cattle at the whole genome level,and a large number of candidate genes and molecular markers significantly related to the variety advantages of Yunling cattle,such as tall body,fast growth speed and strong immune and disease resistance,which laid a foundation for the genomic selection breeding of Yunling cattle and other yellow cattle breeds and provided a scientific basis for the molecular breeding of Yunling cattle. |
PDF Full Text Request