基于高密度SNP芯片的香猪产仔数性状基因筛选和鉴定

发布时间：2018-06-03 12:11

本文选题：香猪 + SNP　；参考：《贵州大学》2016年博士论文

【摘要】：猪是一种重要的经济动物,不但能为人类提供充足的动物蛋白,还能作为优良的人类疾病研究模型。繁殖性状是猪最为重要的经济性状之一,其中产仔数是衡量母猪繁殖能力高低的关键性状。产仔数性状不仅影响母猪的繁殖力,而且直接影响养猪业的经济效益,因此对产仔数性状的研究成为当前研究的重点和热点。产仔数性状是数量性状,由主效基因和多个微效基因所共同调控。随着国内外研究人员的努力,目前已成功定位了雌激素受体和促卵泡激素β亚基两个与猪繁殖性状相关的主效基因,此外,部分微效基因如骨桥蛋白,催乳素受体基因等也陆续被发现,但是还有大量的微效基因有待发现。香猪是黔东南月亮山区农民最主要的经济来源之一,其产仔数较低,平均只有6.7头,但是变异范围较大,产仔数从3~21头都有,但是目前对于香猪的产仔数变异机理还不清楚。随着人类基因组计划和人类单倍型计划的完成,高密度的芯片越来越多地应用到畜牧业当中。因此本文采用Illumina Porcine SNP60K芯片,首次对贵州本地特色的香猪群体进行产仔数性状的全基因组关联分析和拷贝数变异研究,挖掘影响香猪产仔数性状的重要候选基因以及相关的功能位点,掌握其产仔数变异的遗传机理,在SNP水平和CNV水平为下一步的遗传改良提供科学依据取得的主要研究结果包括:1、香猪产仔数性状全基因组关联分析本研究以98从江香猪为研究材料,通过Illumina Porcine SNP60K芯片对61565个SNP位点进行基因分型,采用混合线性模型对香猪产仔数性状进行全基因组关联研究,筛选与目标性状显著关联的SNP位点,进一步寻找与香猪繁殖相关的候选基因。分型后的原始数据经过严格的质控之后,采用Plink软件进行基于无关个体的全基因组关联分析。分析结果经Bonferroni校正之后,筛选到与香猪产仔数性状显著关联的SNP位点25个,(P1.77E-06),潜在关联SNP位点7个(1.77E-06P3.55E-05)。通过AS-PCR验证,所有位点均与芯片分型结果一致。对显著SNP位点上下游100 kb的基因进行检索,共检索到基因70个,其中13个包含关联SNP位点,这些基因富集在16个显著的GO条目中,影响病毒应答、嗅觉受体、防御反应、细胞外基质、干扰素受体结合、细胞因子结合等生物学过程。筛选得到ZEB1、PDIA4、MARCKS、HDAC2、CDC42、FSH-β、PRSS21等基因与动物的繁殖有关,可能是香猪产仔数性状的潜在候选基因。2、香猪全基因组拷贝数变异检测本研究基于Illumina Porcine SNP60K芯片数据,采用PennCNV软件从全基因组水平扫描香猪的CNVs,寻找不同产仔性能香猪之间的拷贝数变异作为分子标记,进一步从全基因水平挖掘候选基因的拷贝数变异对表型性状的影响。通过一系列严格的质控之后,共得到包含172个CNVRs的香猪全基因组拷贝数变异草图,总长达到80.41Mb,大小约占猪基因组的2.98%。172个CNVRs中增加型97个;缺失型65个;缺失和增加共存型10个。有97个CNVRs与之前报道的完全或部分重叠,剩下的75个有可能是新发现的拷贝数变异区间。群体分析发现82个CNVRs是高产香猪特有的,而低产特有的只有13个。对CNVRs涉及的基因进行功能注释,发现ADAMTS-1、AR、KIT、MED 12、PN-1和SOD1与繁殖有关且只在高产群体中存在拷贝数变异。此外,克隆了拷贝数变异候选基因ADAMTS-1,包含8个内含子和9个外显子区域。该基因第七外显子5996位存在多态性,在香猪中以BB基因型为主,而西方猪种中以AA或AB型为主。高产和低产两个香猪群体中的ADAMTS-1基因的拷贝数都是复制型为主,但存在拷贝数的差异,高产香猪群体中的拷贝数增加较多,多为三个或三个以上拷贝,而低产群体中多为双拷贝,高产和低产群体中缺失型的个体分别有3头和16头。结果表明低产群体中的拷贝数低于高产群体。本文通过以上研究发现了与香猪产仔数性状显著关联的SNP位点和候选基因,为后续候选基因的功能验证,分子育种,揭示香猪繁殖力调控机理奠定基础。首次绘制得到香猪全基因组拷贝数变异草图,为进一步研究香猪表型差异与拷贝数变异之间的关系提供理论依据。而ADAMTS-1基因的拷贝数变异以及第七外显子5996位的多态性可能是影响香猪繁殖力的重要因素之一。
[Abstract]:Pig is an important economic animal, which not only provides sufficient animal protein for human beings, but also can be used as a good model of human disease research. Reproductive traits are one of the most important economic traits of pigs. The number of litter is the key trait to measure the breeding ability of sows. The study of the number of litter size has become the focus and hot spot in the present study. The number of litter size traits is a quantitative trait, which is regulated by the main gene and the multiple micro effect genes. With the efforts of researchers at home and abroad, two of the estrogen receptor and the follicle stimulating hormone beta subunit have been successfully located. In addition, some micro effective genes, such as osteopontin and prolactin receptor genes, have been discovered in succession, but there are still a large number of micro effective genes to be found. The fragrant pig is one of the most important economic sources of farmers in the Qiandongnan moon mountain area, with a lower litter size and an average of only 6.7, but the range of variation is larger. The number of litter is from 3~21, but the variation mechanism of the litter size is unclear. With the completion of the human genome project and the human haplotype program, the high density chip is more and more applied to the animal husbandry. Therefore, this paper uses the Illumina Porcine SNP60K core for the first time to the local characteristics of the Guizhou pig population. Complete genome association analysis and copy number variation study of litter size traits, excavating important candidate genes and related functional sites affecting litter size traits of fragrant pigs, mastering the genetic mechanism of litter size variation, and providing scientific basis for the next step of genetic improvement at SNP level and CNV level: 1, The whole genome association analysis of the litter size traits of Xiang pig 98 from Jiangxiang pig as the research material, 61565 SNP loci were genotyping by Illumina Porcine SNP60K chip. A mixed linear model was used to study the whole genome association of the litter size traits of the fragrant pigs, and to screen the SNP site which was significantly associated with the target characters. After finding the candidate genes related to the reproduction of the pig, the original data after the typing were strictly controlled by the Plink software to analyze the whole genome association based on the unrelated individuals. After the Bonferroni correction, 25 SNP loci, which were significantly associated with the litter size traits of the pigs, were selected, (P1.77E-06), and 7 potential associated SNP loci. (1.77E-06P3.55E-05). Through AS-PCR verification, all loci were consistent with the results of the microchip typing. A total of 70 genes were retrieved for 100 kb in the upper and lower reaches of the significant SNP loci, of which 13 contained associated SNP sites, and these genes were enriched in 16 significant GO entries, affecting the viral response, the olfactory receptor, defense response, and the extracellular matrix. ZEB1, PDIA4, MARCKS, HDAC2, CDC42, FSH- beta, PRSS21 and other genes are related to the reproduction of animals. It may be a potential candidate gene for the litter size of the pig. The whole genome copy number variation detection of Xiang pig is based on Illumina Porcine SNP60K chip data. PennCNV software was used to scan the whole genome level of the CNVs of the fragrant pigs, looking for the copy number variation between the different piglets of different litter size as molecular markers, and further mining the influence of the copy number variation on the candidate genes from the whole gene level to the phenotypic traits. After a series of strict quality control, a total of 172 CNVRs pig whole genes were obtained. The total length of copy number variant sketches reached 80.41Mb, the size of which accounted for 97 of the 2.98%.172 CNVRs in the pig genome, 65 missing, 10 missing and increased coexistence. 97 CNVRs were fully or partially overlapped with previous reports, and the remaining 75 may be the newly discovered copy number variation interval. Group analysis found that 82 CNVRs was high. There are only 13 endemic pigs and only 13 low yield traits. Functional annotation of genes involved in CNVRs found that ADAMTS-1, AR, KIT, MED 12, PN-1 and SOD1 are related to reproduction and have copy number variation only in high yield populations. In addition, the copy number variant candidate gene ADAMTS-1, including 8 introns and 9 exons, has been cloned. Seven exon 5996 was polymorphic, and BB genotypes were dominant in fragrant pigs, while AA or AB type was dominant in Western pigs. The number of copies of ADAMTS-1 genes in two high and low yield pigs were replicative, but there was a difference in copy number. The number of copies in high yield pigs increased more, more than three or more than three copies. There are more than two copies in the low yield population and 3 and 16 in the high and low yield individuals. The results show that the number of copies in the low yield population is lower than that of the high yield population. In this paper, the SNP loci and candidate genes associated with the litter size traits of the pigs were found, and the functional verification of the subsequent candidate genes was found. Seed breeding is the basis for revealing the regulation mechanism of the reproductive power of the pig. The whole genome copy number variant sketch of the Xiang pig is first drawn to provide a theoretical basis for further study of the relationship between the phenotypic and copy number variations of the Xiang pig. The variation of the copy number of the ADAMTS-1 gene and the polymorphism of the seventh exon 5996 may affect the fragrant pigs. One of the important factors of fecundity.
【学位授予单位】：贵州大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S828

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