本文選題：豬　切入點(diǎn)：飼料利用效率　出處：《中國(guó)農(nóng)業(yè)科學(xué)院》2016年博士論文

【摘要】：飼料成本占養(yǎng)豬成本的60%以上,尤其在集約化大群飼養(yǎng)的情況下,效率利用效率是飼養(yǎng)成本高低的決定性因素之一。所以通過遺傳學(xué)手段,獲得重要的候選基因,對(duì)飼料利用效率指標(biāo)進(jìn)行遺傳改良,是我們尚待解決的重要問題。由于飼料利用效率的主效基因及調(diào)控機(jī)制研究還尚不清楚,本研究對(duì)已報(bào)道的候選基因進(jìn)行分析,確定主要的候選基因及因果突變位點(diǎn);再利用全基因組關(guān)聯(lián)分析的方法篩選杜洛克群體飼料利用效率相關(guān)性狀的候選基因;并通過RNA-seq手段對(duì)RFI高低組的垂體組織進(jìn)行轉(zhuǎn)錄本表達(dá)量分析,獲得重要的調(diào)控通路及網(wǎng)絡(luò)。主要的研究如下:1.對(duì)已報(bào)道的RFI性狀候選基因MAP3K5和GPX2進(jìn)行深入研究。由于MAP3K5基因還沒有全長(zhǎng),所以我們首先擴(kuò)增獲得了MAP3K5基因的mRNA 5451bp全長(zhǎng),分析了基因結(jié)構(gòu)及組織表達(dá)情況。并發(fā)現(xiàn)RFI高低組中,MAP3K5基因的拷貝數(shù)也存在顯著的差異。MAP3K5基因的2個(gè)SNP位點(diǎn)與RFI性狀顯著相關(guān),1個(gè)SNP位點(diǎn)與FCR性狀顯著相關(guān),1個(gè)SNP位點(diǎn)與ADG性狀顯著相關(guān)。擴(kuò)增發(fā)現(xiàn)了GPX2基因外顯子及5’flank區(qū)的7個(gè)SNP位點(diǎn),這些位點(diǎn)在本杜洛克群體中與RFI性狀并無(wú)顯著的關(guān)聯(lián),但與豬100kgBF等生長(zhǎng)性狀顯著相關(guān),且分型個(gè)體的背部脂肪中表達(dá)差異顯著。2.利用TASSEL軟件對(duì)613頭杜洛克豬6種計(jì)算方法的RFI性狀進(jìn)行GWAS,發(fā)現(xiàn)6種算法對(duì)RFI的GWAS分析結(jié)果有一定影響,但是大部分位點(diǎn)均一致。RFI性狀全基因組關(guān)聯(lián)顯著的SNP位點(diǎn)有1個(gè),位于4號(hào)染色體。發(fā)現(xiàn)與RFI1-6關(guān)聯(lián)顯著的SNP位點(diǎn)(P5×10-5)9個(gè),共定位到MTERF3等6個(gè)候選基因。GWAS分析FCR性狀,發(fā)現(xiàn)5個(gè)全基因組關(guān)聯(lián)顯著的SNP位點(diǎn),共定位到PLA1A等7個(gè)候選基因。3.利用TASSEL軟件對(duì)613頭杜洛克豬ADFI、LEA等8個(gè)飼料利用其他相關(guān)性狀進(jìn)行GWAS。發(fā)現(xiàn)了LEA性狀發(fā)現(xiàn)全基因組關(guān)聯(lián)顯著的SNP位點(diǎn)6個(gè),集中位于9號(hào)和12號(hào)染色體上且呈現(xiàn)連鎖平衡關(guān)系,在3號(hào)染色體上分布了1個(gè)SNP位點(diǎn),共定位到HLF等候選基因6個(gè)。其他7個(gè)性狀并未發(fā)現(xiàn)全基因組關(guān)聯(lián)顯著的SNP位點(diǎn)。4.本研究通過RNA-seq技術(shù)對(duì)RFI高低組的垂體組織中的轉(zhuǎn)錄本進(jìn)行深度測(cè)序,發(fā)現(xiàn)了1萬(wàn)2千多個(gè)新的轉(zhuǎn)錄本,在RFI高低組的垂體組織中共篩選出了112個(gè)差異表達(dá)基因。低RFI組與高RFI組相比有37個(gè)上調(diào)基因,75個(gè)下調(diào)基因。差異表達(dá)的基因富集在磷酸肌醇、神經(jīng)信號(hào)調(diào)節(jié)、鈣離子調(diào)劑、腎上腺激素調(diào)控等生物學(xué)過程及信號(hào)通路中。而GWAS定位到的候選基因在垂體組織中有部分表達(dá),且有一部分基因也與磷脂代謝及神經(jīng)調(diào)節(jié)有關(guān)。通過基因功能驗(yàn)證發(fā)現(xiàn)MAP3K5可能為本杜洛克群體飼料利用效率相關(guān)性狀的候選基因。本研究對(duì)杜洛克的飼料利用效率相關(guān)性狀進(jìn)行GWAS,分析確定MTERF3、PLA1A和HLF等與RFI、FCR和LEA關(guān)聯(lián)的可能候選基因。RFI高低組垂體組織中磷脂代謝和神經(jīng)調(diào)節(jié)是影響RFI性狀的重要調(diào)控通路。
[Abstract]:Feed cost accounts for more than 60% of the cost of pig raising. Efficiency is one of the decisive factors of feeding cost, especially in intensive large group feeding. Therefore, important candidate genes are obtained by means of genetics. Genetic improvement of feed utilization efficiency index is an important problem that remains to be solved. Since the main genes and regulation mechanisms of feed use efficiency are not clear, the reported candidate genes are analyzed in this study. The main candidate genes and causal mutation sites were identified, and the candidate genes of feed efficiency related traits of Duroc population were screened by genome-wide association analysis. The transcriptional expression of pituitary tissue in high and low RFI group was analyzed by RNA-seq. Important regulatory pathways and networks were obtained. The main studies were as follows: 1.The reported candidate genes for RFI traits, MAP3K5 and GPX2, were studied in depth. Since the MAP3K5 gene is not yet full-length, we first amplified the mRNA 5451bp full length of the MAP3K5 gene. The gene structure and tissue expression were analyzed, and it was found that there were significant differences in copy number of MAP3K5 gene between high and low RFI groups. Two SNP loci of MAP3K5 gene were significantly correlated with RFI traits, one SNP locus was significantly related to FCR traits, and one was SNP locus. SNP loci were significantly correlated with ADG traits. Seven SNP loci of GPX2 gene exon and 5'flank region were found by amplification. These loci were not significantly associated with RFI traits, but significantly correlated with growth traits such as pig 100kgBF in Bendolock population. The expression of RFI in the back fat of 613 Duroc pigs was analyzed by using TASSEL software. It was found that the six algorithms had a certain influence on the results of GWAS analysis of RFI. However, there was one SNP locus with a significant genomic association with .RFI, which was located on chromosome 4. Nine SNP loci were found to be significantly associated with RFI1-6. MTERF3 and other 6 candidate genes. Gwas was used to analyze FCR traits. Five SNP loci with significant genome-wide association were found. 7 candidate genes, such as PLA1A, were located. GWASs were used to detect 8 other related traits in 613 Duroc pigs, including ADFILEA, using TASSEL software. Six SNP loci with significant genomic association of LEA traits were found. It was located on chromosomes 9 and 12 and showed a linkage equilibrium relationship. A SNP locus was distributed on chromosome 3. 6 candidate genes such as HLF were located. No significant SNP loci were found in the other 7 traits. In this study, the transcripts in the pituitary tissues of high and low RFI groups were deeply sequenced by RNA-seq technique. More than 12,000 new transcripts were found. A total of 112 differentially expressed genes were screened in pituitary tissues of high and low RFI groups. There were 37 up-regulated genes and 75 down-regulated genes in low RFI group compared with high RFI group. The differentially expressed genes were enriched in inositol phosphate, neural signal regulation and calcium modulator. Adrenal hormone regulation and other biological processes and signaling pathways. The candidate genes identified by GWAS are partially expressed in pituitary tissues. Some genes were also related to phospholipid metabolism and neuroregulation. MAP3K5 was found to be a candidate gene related to feed efficiency. By GWAS-based analysis, it was determined that phospholipid metabolism and neuroregulation in pituitary tissues of patients with high and low RFI genes, such as MTERF3, PLA1A and HLF, were important regulatory pathways affecting RFI traits.
【學(xué)位授予單位】：中國(guó)農(nóng)業(yè)科學(xué)院
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：S828
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本文編號(hào)：1661839