基于全基因组重测序筛选湖羊四乳头性状相关基因的初步研究

发布时间：2018-03-22 18:15

本文选题：基因组　切入点：重测序　出处：《西北农林科技大学》2017年硕士论文　论文类型：学位论文

【摘要】：部分绵羊具有四个或更多的乳头,但有关这一性状的遗传机理研究报道较少。为了探究其遗传差异,本研究对四乳头湖羊基因组进行了重测序分析,筛选出与该性状相关的候选基因。1、采集四乳头湖羊(试验组)和两乳头湖羊(对照组)血液样本,提取血样DNA进行全基因组重测序,测序结果与绵羊参考基因组(Ovis aries Oar_3.1)比对,结果表明:(1)使用GATK算法比对测序结果,查找湖羊基因组的突变位点。其中在基因编码区中,试验组中共有42001个SNP/InDel位点,对照组共有50010个SNP/InDel位点。(2)对SNP/InDel位点进行维恩分析,得到试验组湖羊特有的SNP/InDel位点39个,提示这些突变位点可能是四乳头性状的潜在关联位点。(3)对试验组特有的39个SNP/InDel位点进行注释,共计注释到21个基因。并对这21个基因进行GO富集分析和KEGG通路分析,涉及物质代谢、免疫应答、细胞生长、机体发育和信号通路等功能。2、对湖羊基因组重测序得到试验组中的33个SNP位点进行了验证,利用Sanger测序法和SNaPshot技术对变异位点进行SNP分型,结果表明:(1)与参考基因组对比,33个变异位点中,有18个位点碱基没有发生改变,15个位点发生了碱基变化。其中ZEB1基因中sheep13-32879407位点和DEPDC7基因中sheep15-61871375位点试验组相比于对照组存在较高的突变率。sheep13-32879407GC位点在四乳头样本中的突变率为91%,在对照组中的突变率为30%;sheep15-61871375GC位点在四乳头样本中的突变率为72%,在对照组中的突变率为29%。(2)对ZEB1基因的sheep13-32879407GC位点与湖羊四乳头发育等级进行关联分析。在总样本中,基因型CC和GC分别比基因型GG个体拥有更高的四乳头等级(P0.01)。在试验组中,基因型CC和GC分别比基因型GG个体拥有更高的四乳头等级(P0.05)。说明这两个基因型的个体四乳头发育更好。对DEPDC7基因的sheep15-61871375AC位点与湖羊四乳头等级进行关联分析。在总样本中,基因型CC和AC分别比基因型GG个体拥有更高的四乳头等级(P0.01),说明这两个基因型个体的四乳头发育更好。综上所述,ZEB1和DEPDC7基因可作为四乳头性状的候选基因。
[Abstract]:Some sheep have four or more nipples, but there are few studies on the genetic mechanism of this trait. The candidate gene. 1. Blood samples were collected from four-tipped Hu sheep (test group) and two nipple lake sheep (control group). The whole genome was sequenced by DNA. The results were compared with that of sheep reference genome Ovis aries Oar3.1). The results showed that GATK algorithm was used to compare the results of sequencing and to find mutation sites in Hu sheep genome. In the gene coding region, there were 4 200 SNP/InDel loci in the experimental group and 50010 SNP/InDel loci in the control group. 39 SNP/InDel loci specific to Hu sheep were obtained in the experiment group, indicating that these mutation sites may be the potential association sites for tetra nipple traits.) the 39 SNP/InDel loci of the test group were annotated. A total of 21 genes were annotated. The 21 genes were analyzed by go enrichment analysis and KEGG pathway analysis, involving substance metabolism, immune response and cell growth. In this study, 33 SNP loci in the experimental group were confirmed by re-sequencing of the Hu sheep genome. Sanger sequencing and SNaPshot techniques were used to type the mutation loci. The results showed that: 1) compared with the reference genome, 33 mutation loci, The mutation rate of sheep13-32879407 locus in ZEB1 gene and sheep15-61871375 locus in DEPDC7 gene was higher than that in control group. The mutation rate was 91. The mutation rate in the control group was 30 sheep15-61871375GC in the four nipple samples, and the mutation rate in the control group was 29.2. The relationship between the sheep13-32879407GC locus of the ZEB1 gene and the development grade of the fourth nipple of Hu sheep was analyzed. Genotype CC and GC had higher levels of four nipples (P0.01) than genotype GG. In the trial group, the four nipple levels of CC and GC were higher than those of genotype GG. The genotype CC and GC had higher four nipple grade (P0.05) than those of genotype GG, which indicated that the four nipples of the two genotypes had better development. The sheep15-61871375AC loci of the DEPDC7 gene were correlated with the four nipple grades of Hu sheep. The genotype CC and AC had higher four nipple grade (P0.01) than those of genotype GG, which indicated that the four nipples of the two genotypes had better development. In conclusion, ZEB1 and DEPDC7 genes could be used as candidate genes for the tetra nipple traits.
【学位授予单位】：西北农林科技大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S826

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