杜洛克猪饲料利用效率相关性状的全基因组关联分析及mRNA表达谱研究

发布时间：2018-03-25 06:03

  本文选题：猪　切入点：饲料利用效率　出处：《中国农业科学院》2016年博士论文

【摘要】：饲料成本占养猪成本的60%以上,尤其在集约化大群饲养的情况下,效率利用效率是饲养成本高低的决定性因素之一。所以通过遗传学手段,获得重要的候选基因,对饲料利用效率指标进行遗传改良,是我们尚待解决的重要问题。由于饲料利用效率的主效基因及调控机制研究还尚不清楚,本研究对已报道的候选基因进行分析,确定主要的候选基因及因果突变位点;再利用全基因组关联分析的方法筛选杜洛克群体饲料利用效率相关性状的候选基因;并通过RNA-seq手段对RFI高低组的垂体组织进行转录本表达量分析,获得重要的调控通路及网络。主要的研究如下:1.对已报道的RFI性状候选基因MAP3K5和GPX2进行深入研究。由于MAP3K5基因还没有全长,所以我们首先扩增获得了MAP3K5基因的mRNA 5451bp全长,分析了基因结构及组织表达情况。并发现RFI高低组中,MAP3K5基因的拷贝数也存在显著的差异。MAP3K5基因的2个SNP位点与RFI性状显著相关,1个SNP位点与FCR性状显著相关,1个SNP位点与ADG性状显著相关。扩增发现了GPX2基因外显子及5’flank区的7个SNP位点,这些位点在本杜洛克群体中与RFI性状并无显著的关联,但与猪100kgBF等生长性状显著相关,且分型个体的背部脂肪中表达差异显著。2.利用TASSEL软件对613头杜洛克猪6种计算方法的RFI性状进行GWAS,发现6种算法对RFI的GWAS分析结果有一定影响,但是大部分位点均一致。RFI性状全基因组关联显著的SNP位点有1个,位于4号染色体。发现与RFI1-6关联显著的SNP位点(P5×10-5)9个,共定位到MTERF3等6个候选基因。GWAS分析FCR性状,发现5个全基因组关联显著的SNP位点,共定位到PLA1A等7个候选基因。3.利用TASSEL软件对613头杜洛克猪ADFI、LEA等8个饲料利用其他相关性状进行GWAS。发现了LEA性状发现全基因组关联显著的SNP位点6个,集中位于9号和12号染色体上且呈现连锁平衡关系,在3号染色体上分布了1个SNP位点,共定位到HLF等候选基因6个。其他7个性状并未发现全基因组关联显著的SNP位点。4.本研究通过RNA-seq技术对RFI高低组的垂体组织中的转录本进行深度测序,发现了1万2千多个新的转录本,在RFI高低组的垂体组织中共筛选出了112个差异表达基因。低RFI组与高RFI组相比有37个上调基因,75个下调基因。差异表达的基因富集在磷酸肌醇、神经信号调节、钙离子调剂、肾上腺激素调控等生物学过程及信号通路中。而GWAS定位到的候选基因在垂体组织中有部分表达,且有一部分基因也与磷脂代谢及神经调节有关。通过基因功能验证发现MAP3K5可能为本杜洛克群体饲料利用效率相关性状的候选基因。本研究对杜洛克的饲料利用效率相关性状进行GWAS,分析确定MTERF3、PLA1A和HLF等与RFI、FCR和LEA关联的可能候选基因。RFI高低组垂体组织中磷脂代谢和神经调节是影响RFI性状的重要调控通路。
[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.
【学位授予单位】：中国农业科学院
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S828
，

本文编号：1661839