摘要
耳型是山羊的一个品种标准性状,但有关山羊耳型变异的遗传机制尚不清楚。利用来自西藏自治区仲巴县的正常耳和小耳藏山羊群体及前期测定的5个山羊群体的基因组序列,采用比较基因组学鉴定影响山羊耳朵大小的遗传位点。100 kb窗口大小和25 kb步长滑动窗口的全基因组FST以及HP比值的结果显示,2号染色体56.475~56.575 Mb基因组区域在两种耳型藏山羊之间分化程度最高(FST=0.36)。在该窗口内,30个SNPs位点的等位基因频率差异较大(△AF>0.5),特别是其中1个SNP位点(chr2:56559507,C>T)的△AF高达0.87。在7号染色体45.05~59.76 Mb区域内,受选择基因数量多达52个。对离异值窗口包含的372个基因进行富集分析,SPINK5、TCOF1、PPARD等基因显著富集在10个与哺乳动物耳朵发育相关的表型条目中;特别是SPINK5基因上游5kb处2个SNPs(c.-4283A>G、c.-4295G>A)的等位基因频率差异高达0.9和0.83。主成分分析结果表明,仲巴地区藏山羊的遗传组成与低海拔地方山羊品种更接近;而措勤地区藏山羊的遗传组成与其他山羊品种区别较大。初步鉴定到与藏山羊耳型变异相关的基因组区域,为深入研究山羊耳朵发育的分子机制提供依据;并揭示出不同地区藏山羊群体遗传组成存在较大差异。
Ear size is one of the breed standard traits in goats,but the genetic mechanisms of the phenotypic variations of ear types in goats remains elusive.In this study,we applied comparative genomic analysis to investigate the genetic loci which affected the ear size in the Tibetan goats with normaland small ears sampled from Zhongba county,as well as genome sequence data from five other goat breeds.The genome-wide FST values and HP ratios in sliding 100 kb windows with a step size of 25 kb showed that the genomic region from 56.475 to 56.575 Mb on chromosome 2 was most differentiated(FST=0.36)between the Tibetan goats with normal ears and small ears.In this window,the allele frequency differences of 30 SNPs were large(△AF>0.5),and the△AF of one SNP(chr2:56559507,C>T)was obviously high as 0.87.The number of selected genes was as many as 52 in the region spanning 45.05-59.76 Mb on chromosome 7.Based on the enrichment analysis for the total 372 genes overlapped with the outlier windows,many genes,including SPINK5,TCOF1 and PPARD,were significantly enriched in 10 MGI-MP terms that were involved in mammalian ear development.In addition,the allele frequency differences of the two SNPs(c.-4283 A>G,c.-4295 G>A)in the region surrounding SPINK5 was 0.9 and 0.83,respectively.The principal component analysis showed that the genetic composition of the Tibetan goats from Zhongba county was close to that of low-land goat breeds,whereas the genetic composition of the Tibetan goats from Coqen county was different from other goat breeds.In this study,the genetic loci contributing to the phenotypic variation of the ear size in goats were identified,which provided a reference for the investigation of molecular mechanism underlying the ear development in goats.Furthermore,we revealed that the genetic compositions of Tibetan goats from different areas in the Qinghai-Tibetan plateau were largely different.
作者
钟杰
李利
宋天增
张红平
郭家中
ZHONG Jie;LI Li;SONG Tianzeng;ZHANG Hongping;GUO Jiazhong(College of Animal Science and Technology,Sichuan Agricultural University,Chengdu 611130,China;Institute of Animal Science,Tibet Academy of Agricultural and Animal Husbandry Science,Lhasa 850009,China)
出处
《西北农业学报》
CAS
CSCD
北大核心
2019年第11期1742-1749,共8页
Acta Agriculturae Boreali-occidentalis Sinica
基金
国家重点研发计划专项(2018YFD0502002)
国家自然科学基金(31860623).
