本文選題：家畜 + 選擇信號�。� 參考：《中國農(nóng)業(yè)大學(xué)》2016年博士論文

【摘要】：選擇信號(selection signature)是選擇作用遺留在基因組上的印跡。在家畜基因組上進行選擇信號檢測有助于揭示選擇作用的潛在遺傳機制,以及造成家畜表型差異的遺傳基礎(chǔ)。本研究針對牛和豬這兩種家畜進行了選擇信號的研究。中國荷斯坦牛和西門塔爾牛的全基因組選擇信號檢測。基于牛的Illumina 770K芯片數(shù)據(jù),采用三種互補的方法進行選擇信號檢測,即LRH (long-range haplotype),XP-EHH (cross-population extended haplotype homozygosity)和FST統(tǒng)計量。研究成功構(gòu)建了中國荷斯坦和西門塔爾群體的選擇信號圖譜。對受選擇區(qū)域進行基因注釋發(fā)現(xiàn)了一系列具有重要生物學(xué)意義的候選基因,比如GHR, MC1R和LEP。這些基因主要與產(chǎn)奶性狀、生長性狀、繁殖性狀和免疫反應(yīng)相關(guān)。此外,研究還發(fā)現(xiàn)在基因組的外顯子上富集有低FST值且低等位基因頻率的遺傳突變,表明外顯子區(qū)域受到強烈的凈化選擇作用。歐洲豬與中國豬之間的群體分化與混合。利用1,157頭家豬和野豬的Illumina 60K芯片數(shù)據(jù),本研究應(yīng)用了主成分分析(principal component analysis, PCA), ADMIXTURE分析,TreeMix分析和f統(tǒng)計量。試驗結(jié)果證實了中國地方豬種被引入到歐洲豬種。而且,不同歐洲豬種含有不同含量的中國豬種遺傳成分。研究結(jié)果還表明,被引入到歐洲的中國豬主要是來自中國南方的地方豬種,與巴馬香豬和東山豬有相近的遺傳關(guān)系。但是,在歐洲豬種中也同樣可以檢測到來自中國東部豬種的遺傳成分。丹麥杜洛克豬中檢測適應(yīng)性基因滲入。研究分析了來自丹麥杜洛克豬、巴馬香豬、梅山豬和歐洲野豬的全基因組測序數(shù)據(jù)。以巴馬香豬、梅山豬和歐洲野豬作為供體群體,并利用ChromoPainter軟件推斷杜洛克豬基因組上每一個等位基因的起源,即祖先群體。在杜洛克豬基因組上,如果一個區(qū)域含有大量來自中國豬種的祖先成分,則以此作為選擇信號,將該區(qū)域作為適應(yīng)性基因滲入的候選區(qū)域。研究結(jié)果表明,在杜洛克豬基因組上普遍存在對來自中國豬種的單倍型的選擇。功能分析表明這些來自中國豬種的單倍型對杜洛克豬的性能起到了改良作用,比如生長性狀,繁殖性狀和外貌特征。綜上,本研究得出了以下結(jié)論：第一,在家畜基因組上進行選擇信號檢測發(fā)現(xiàn)了許多具有重要生物功能的候選基因。第二,用于檢測選擇掃蕩的常用方法通�？梢杂行У貦z測家畜基因組上的選擇信號。但是,家畜基因組本身的特殊性也會影響這些方法的效力,比如家畜基因組上強烈的連鎖不平衡,凈化選擇和基因滲入等。第三,選擇信號的強度依賴于受選擇性狀的類型。通常,外貌特征和生產(chǎn)性狀更容易表現(xiàn)出強烈的選擇信號。
[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.
【學(xué)位授予單位】：中國農(nóng)業(yè)大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：S828;S823

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