牛和猪基因组选择信号研究

发布时间：2018-06-27 18:08

本文选题：家畜 + 选择信号　；参考：《中国农业大学》2016年博士论文

【摘要】：选择信号(selection signature)是选择作用遗留在基因组上的印迹。在家畜基因组上进行选择信号检测有助于揭示选择作用的潜在遗传机制,以及造成家畜表型差异的遗传基础。本研究针对牛和猪这两种家畜进行了选择信号的研究。中国荷斯坦牛和西门塔尔牛的全基因组选择信号检测。基于牛的Illumina 770K芯片数据,采用三种互补的方法进行选择信号检测,即LRH (long-range haplotype),XP-EHH (cross-population extended haplotype homozygosity)和FST统计量。研究成功构建了中国荷斯坦和西门塔尔群体的选择信号图谱。对受选择区域进行基因注释发现了一系列具有重要生物学意义的候选基因,比如GHR, MC1R和LEP。这些基因主要与产奶性状、生长性状、繁殖性状和免疫反应相关。此外,研究还发现在基因组的外显子上富集有低FST值且低等位基因频率的遗传突变,表明外显子区域受到强烈的净化选择作用。欧洲猪与中国猪之间的群体分化与混合。利用1,157头家猪和野猪的Illumina 60K芯片数据,本研究应用了主成分分析(principal component analysis, PCA), ADMIXTURE分析,TreeMix分析和f统计量。试验结果证实了中国地方猪种被引入到欧洲猪种。而且,不同欧洲猪种含有不同含量的中国猪种遗传成分。研究结果还表明,被引入到欧洲的中国猪主要是来自中国南方的地方猪种,与巴马香猪和东山猪有相近的遗传关系。但是,在欧洲猪种中也同样可以检测到来自中国东部猪种的遗传成分。丹麦杜洛克猪中检测适应性基因渗入。研究分析了来自丹麦杜洛克猪、巴马香猪、梅山猪和欧洲野猪的全基因组测序数据。以巴马香猪、梅山猪和欧洲野猪作为供体群体,并利用ChromoPainter软件推断杜洛克猪基因组上每一个等位基因的起源,即祖先群体。在杜洛克猪基因组上,如果一个区域含有大量来自中国猪种的祖先成分,则以此作为选择信号,将该区域作为适应性基因渗入的候选区域。研究结果表明,在杜洛克猪基因组上普遍存在对来自中国猪种的单倍型的选择。功能分析表明这些来自中国猪种的单倍型对杜洛克猪的性能起到了改良作用,比如生长性状,繁殖性状和外貌特征。综上,本研究得出了以下结论：第一,在家畜基因组上进行选择信号检测发现了许多具有重要生物功能的候选基因。第二,用于检测选择扫荡的常用方法通常可以有效地检测家畜基因组上的选择信号。但是,家畜基因组本身的特殊性也会影响这些方法的效力,比如家畜基因组上强烈的连锁不平衡,净化选择和基因渗入等。第三,选择信号的强度依赖于受选择性状的类型。通常,外貌特征和生产性状更容易表现出强烈的选择信号。
[Abstract]:The selection signal (selection signature) is the imprinting left by the selection action on the genome. The detection of selection signal on the animal genome is helpful to reveal the potential genetic mechanism of selection and the genetic basis of the phenotypic difference of livestock. The selection signals of cattle and pigs were studied in this study. Genome-wide selection signal detection of Chinese Holstein and Simmental cattle. Based on the Illumina 770K chip data of cattle, three complementary methods are used to detect the selected signals, namely, LRH (long-range haplotype) XP-EHH (cross-population extended haplotype homozygosity) and FSTstatistics). The selective signal map of Chinese Holstein and Simmental population was successfully constructed. A series of biologically significant candidate genes, such as GHRR, MC1R and LEP, were identified by gene annotation of the selected regions. These genes are mainly related to milk production traits, growth traits, reproductive traits and immune responses. In addition, genetic mutations with low FST value and low isogene frequency were found in the exons of the genome, indicating that the exon region was strongly purified and selected. Population differentiation and mixing between European pigs and Chinese pigs. Using the Illumina 60K chip data of 1157 domestic pigs and wild boars, principal component analysis (principal component analysis,), ADMIXTURE analysis (TreeMix analysis) and f statistics were used in this study. The results confirmed that Chinese local pig breeds were introduced into European pig breeds. Moreover, different European pig breeds contain different genetic components of Chinese pig breeds. The results also showed that the Chinese pigs introduced to Europe were mainly from southern China and had similar genetic relationship with Bama Xiang pig and Dongshan pig. However, genetic components from eastern Chinese pig breeds can also be detected in European pig breeds. Adaptive gene penetration was detected in Duroc pigs. Genomic sequencing data from Duroc, Bama, Meishan and European wild boars were analyzed. Bama Xiang pig, Meishan pig and European wild boar were used as donor population, and the origin of each allele in Duroc pig genome was deduced by using ChromoPainter software. In the Duroc pig genome, if a region contains a large number of ancestral components from Chinese pigs, the region is used as a selection signal, and the region is used as a candidate region for adaptive gene infiltration. The results showed that haplotypes from Chinese pigs were widely selected in the Duroc genome. Functional analysis showed that these haplotypes from Chinese pigs could improve the performance of Duroc pigs such as growth traits reproduction traits and appearance characteristics. In conclusion, the main conclusions are as follows: first, a lot of candidate genes with important biological functions were found by selective signal detection in the animal genome. Second, the common methods used to detect selective sweep are usually effective in detecting the selection signals in livestock genomes. However, the particularity of the animal genome itself will also affect the effectiveness of these methods, such as strong linkage disequilibrium, purification selection and gene infiltration on the livestock genome. Thirdly, the intensity of the selection signal depends on the type of the selected trait. In general, appearance and production traits are more likely to show strong selection signals.
【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S828;S823

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