【作者】 程笃学；

【导师】 王立贤；

【作者基本信息】 中国农业科学院 ， 动物遗传育种与繁殖， 2012， 博士

【摘要】 猪肉品质是猪的重要经济性状，也是现阶段种猪育种工作中的关键指标。近年来，随着高密度SNP芯片的不断出现和基因分型技术平台的不断发展，使对猪开展全基因组关联分析（Genome-wide Association Study，GWAS）研究成为现实。因此，本研究以大白猪×民猪F2设计资源群体的455头F2个体为研究对象，利用Illumina PorcineSNP60BeadChip（包含62,163个SNPs位点）技术，采用GRAMMAR-GC (Genome-wideRapid Association using the Mixed Model and Regression-Genomic Control)方法，使用DMU软件和R统计环境下的GenABEL软件包对猪背最长肌的IMF、肉色、嫩度、酸度、水分、失水率、瘦肉率、瘦肉量、后腿瘦肉量等共计9个性状的16个指标进行了GWAS分析，以寻找与猪肉质性状相关的遗传变异。主要实验结果如下：1、完成了对455头大白猪×民猪资源群体F2代个体的屠宰分割和16个猪肉质相关性状指标的准确测定与详细记录。描述性统计表明，各性状数据分布符合资源家系分离群体的特征。KF与NF间，WLR24、WLR48、WLR72相互间，IMF与MS，IMF与MC，L*与MS性状间均为高度相关，且均达到极显著水平（P <0.01）。2、利用GWAS研究，在IMF、大理石纹评分、水分含量、肉色评分、a*、后腿瘦肉量和瘦肉率共7个指标中检测到了基因组水平显著SNPs，显著位点个数依次分别为40、37、6、6、4、23和5个,其中达极显著水平位点数依次分别是27、27、5、1、3、12和2个；在肉色L*、b*、pH24、嫩度、失水率和瘦肉量性状未检测到与其相关的显著SNPs。3、根据芯片SNP序列信息，利用Sus scrofa Build9版本猪基因组数据库和NCBI数据库信息，对不同肉质性状显著SNPs位点进行注释发现：在IMF、MS、MC、CS、a*五个性状中共有45个SNPs与其1个或多个性状显著关联，且除9个未定位到染色体上SNPs外，其余36个显著位点均落在猪12号染色体上；与后腿瘦肉量和瘦肉率性状中1个或2个性状显著关联的SNPs共有24个，其中19个分布在猪2号染色体上。4、根据NCBI、Ensembl、KEGG、Uniprot、GeneCards等数据库信息，利用生物信息学和比较基因组学方法，对显著SNPs周围基因进行功能注释后发现，这些基因功能主要涉及DNA修复、转录调节和翻译调控，细胞骨架或基质成分，调节机体营养成分代谢和平衡，细胞增殖再生与凋亡，具有激酶活性，参与细胞信号转导和不同离子通道构成等8个方面。5、利用HAPLOVIEW3.1软件开展单倍型分析，结果表明，在12号染色体上存在2个与猪肉品质性状紧密相关的单倍型块，分别是由5个位点组成的约325Kb区域和由2个位点组成的0.99Kb区域。单倍型1中的AGAAG单倍型和CAGGA单倍型均同IMF、大理石纹、肉色a*和肉色评分性状显著关联（P <0.001）。利用单倍型分析在缩小重点研究区域范围的同时，单倍型块1中包含的GAS7, MYH1, MYH2, MYH3和MYH4共5个基因也被初步筛为肉质性状相关的重要候选基因。6、综合所有研究信息，MYH、SLC和GAS家族可作为猪肉质性状的重要候选基因或候选家族。更多还原

【Abstract】 Pork quality is an economically important trait and the key index for pig breeding at present. Thecontinuous appearance of high density SNP chips and the sustainable development of genotypingtechnique make it possible to implement the Genome-wide Association Study(GWAS) in pigs.455pigsof F2generation from a porcine Large White×Minzhu intercross resource population were used as theexperimental animals. The Illumina PorcineSNP60BeadChip（including62,163SNPs）technology, theGenome-wide Rapid Association using the Mixed Model and Regression-GenomicControl(GRAMMAR-GC) method, DMU software and GenABEL software package under the Rstatistical environment were used to carry out the GWAS analysis on the intramuscular fat content(IMF), meat color(MC), tenderness, acidity, moisture, water loss rate, lean meat percentage, lean meatyield, ham lean weight such as a total of16indexes of9traits in longissimus muscle in order to searchfor the genetic variation related to the pork quality traits. The results showed that:1.455pigs were slaughtered and cutted and16indexes related to pork quality were measured andrecorded. The descriptive statistics indicated that the distribution of phenotype values of all traits werein accordance with the character of resource family segregating population. The relationship betweenKF and NF, among WLR24, WLR48, WLR72, between IMF and MS, MC, between L*and MS weresignificant(P <0.01).2. The significant SNPs related to IMF, marbling score, moisture content, meat color score, a*value, ham lean weight were detected using GWAS analysis. The number of significant SNPs at genomelevel were40,37,6,6,4,25and5, respectively. The number of very significant SNPs among themwere27,27,5,1,3,12and2, respectively. The SNPs related to meat color, L*value, b*value, pH24,tenderness, water loss rate and lean meat weight were not detected.3. According to the sequence information of SNP chip, the significant SNPs related to meatquality traits were annotated using Sus scrofa Build9genome database and NCBI database. The resultsindicated that, for IMF, MS, MC, CS and a*value, a total of45SNPs showed significant associationwith one or multiple traits of them. Of the45SNPs,36were located on SSC12. A tatal of24SNPsshowed significant association with one or two traits for ham lean weight and lean meat percentage,19of them located on SSC2.4. According the database information from NCBI, Ensembl, KEGG, Uniprot, and GeneCards, thefunction of genes in the vicinity of the significant SNPs were annotated using bioinformatics andcomparative genomics. The results showed that the gene functions mainly involved in DNA repair,transcriptional regulation and translational control, cytoskeleton and matrix components, adjusting thebody’s metabolism of nutrients and balance, cell proliferation, regeneration and apoptosis, kinaseactivity, participating in cellular signal transduction and ion channels constitute, and so on.5. The HAPLOVIEW V3.1program was used to detect the haplotype blocks in this work. Theresults showed that two haplotype blocks associated with pork quality traits were identified on SSC12,and block1was ASGA0100525-ASGA0055225-ALGA0067099-MARC0004712-DIAS0000861for325kb and block2was ASGA0085522-H3GA0056170for0.99kb. For block1, the AGAAG (47.7%and positive effect) and CAGGA (37.0%and negative effect) haplotypes were significantly associated (P <0.001) with IMF, marbling, color a*and color score. Narrowed the scope of the study, MYH1,MYH2, MYH3and MYH4genes contained in haplotype block1were preliminary screened as theimportant candidate genes for meat quality traits.6. In summary, MYH, SLC and GAS gene family were preliminary identified as the key candidategenes and candidate family for meat quality traits in the study.更多还原