基于全基因组信息鉴定中国荷斯坦牛产奶性状基因及功能注释

Identification and Annotation of Genes Affecting Milk Production Traits in Chinese Holstein Based on GWAS

前期研究基于中国荷斯坦牛女儿设计资源群体,采用Illumina公司Bovine50K微珠芯片对产奶性状进行了全基因组关联分析(GWAS),利用传递不平衡(L1-TDT)和回归分析(MMRA)2种统计分析方法共同检测到35个显著SNPs位点。本研究旨在基于该GWAS结果进一步对产奶性状基因进行鉴定及功能注释。基于牛基因组序列草图(Btau4.2),采用生物信息学和比较基因组学方法进行显著SNPs位置候选基因筛查和功能预测。分析发现,12个SNPs位点位于基因内部,23个位于基因侧翼,最终鉴定到28个位置候选基因,并确定了其物理位置、基因类型及潜在功能。基因功能可归纳为6种类型:调节机体营养成分代谢和平衡、细胞骨架或基质成分、调节细胞增殖和周期及凋亡、参与细胞信号转导和盐离子通道构成、具有激酶活性、参与mRNA转录调控或翻译调控。该研究为进一步鉴定中国荷斯坦牛产奶性状主效基因及功能验证打下了基础。

The previous genome-wide association studies （GWAS） with Illumina Bovine50K chip have identified 35 significant SNPs associated with one or multiple milk production traits in a Chi- nese Holstein population from Beijing region with daughter design. The purpose of this study was to determine potential genes affecting milk yield and milk composition and function annotation based on such GWAS results. Through bioinformatics and comparative genomics analysis, poten- tial genes screening and function prediction were performed. Twelve of 35 significant SNPs were located within genes and 23 were in the flanking region based on Btau 4.2 database. As a result, total 28 genes corresponding to the aforementioned 35 SNPs were determined. The functions of such genes were classified into 6 categories, including regulating body metabolism and nutrient balance, cytoskeleton or extracellular matrix, regulation of proliferation, cell cycle and apopto- sis, cell signal transduction and saltion channel composition, kinase activity, mRNA transcription and translation regulation, transportation or transduction, transcription and translation regula-tion of fat granule protein. The findings could be useful for further investigations on gene identi- fication and function validation for milk production traits in dairy cattle.