整合多群体全基因组关联分析、选择信号及多组学研究鉴别商品猪的新酸肉基因

The pH value is an important indicator of meat quality because it is closely related to pork color, water-holding capacity, processing yield and preservation period. So far, three causative genes for pH value have been identified. However, commercial pigs without the adverse effect of the three known genes still produce a high proportion of inferior meat with low ultimate pH (so called “acid meat”), which is obviously caused by undiscovered genes. In addition, the meat quality traits (especially ultimate pH of meat measured at postmortem 24h) of most Chinese native pig breeds (such as Erhualian) are much better than that of western commercial pig breeds, such as Duroc, Landrace and White. Using a 60K SNP beadchip, we have conducted genome-wide association studies (GWASs) for meat pH in four pig populations: a Duroc x Erhualian F2 cross, a Sutai half-sib family of boars, DLY hybrid pigs and Erhualian pigs. And we successfully identified a causative gene (PHKG1) leading to low pH in Duroc-related pigs. On the basis, this project will be carried out to identify new significant association signals (QTLs) for pH through meta-GWAS analysis with imputated whole-genome sequencing data of F2 and Sutai popualtions. Furthermore, this project will be conducted to reveal signatures of selection in Chinese and western pig breeds by whole-genome sequencing on animals with extreme phenotypes that are selected in the four populations. By Integrating the QTL mapping, signature of selection and the analyses of transcriptomics and metabolomics in muscle, we are able to identify causative genes and mutations underlying the QTLs. Therefore, the findings will provide new insights into genetic mechanism of the meat pH value and promote the molecular breeding of meat quality.

猪肉pH与其颜色、系水力、加工产量和保藏期密切相关，是很重要的肉品质指标之一。目前已确认三个影响猪肉pH的主效基因；但剔除其不利影响后，商品猪仍有较高比例的劣质偏酸肉产生，故还存在其他“酸肉”基因。另外，中国地方猪（如二花脸）的肉终pH明显高于杜洛克、长白和大白等引进品种，但其相关优良基因未知。本项目在我们前期对杜洛克X二花脸F2家系、苏太公猪半同胞家系、杜长大三元杂和二花脸4个群体60K芯片全基因组关联分析（GWAS）以及成功鉴别一个影响pH因果基因PHKG1基础上，拟利用F2和苏太家系开展基于亲本重测序及子代基因型填充的关联荟萃分析，鉴别新的显著关联信号（QTL）。再结合基于这4个种群极端表型个体重测序数据的全基因组选择信号检测以及其肌肉转录组和代谢组分析，鉴别QTL区域内关键基因及因果突变，阐明其作用机理，从而深入揭示中、外猪种pH复杂性状形成的遗传机制，促进肉质性状分子育种发展。

猪肉pH与其颜色、系水力、加工产量和保藏期密切相关，是很重要的肉品质指标之一。目前已确认三个影响猪肉pH的主效基因；但剔除其不利影响后，商品猪仍有较高比例的劣质偏酸肉产生，故还存在其他“酸肉”基因。另外，中国地方猪（如二花脸）的肉终pH明显高于杜洛克、长白和大白等引进品种，但其相关优良基因未知。本项目在我们前期对杜洛克X二花脸F2家系、苏太公猪半同胞家系、杜长大三元杂和二花脸4个群体60K芯片全基因组关联分析（GWAS）以及成功鉴别一个影响pH因果基因PHKG1基础上，拟利用F2和苏太家系开展基于亲本重测序及子代基因型填充的关联荟萃分析，鉴别新的显著关联信号（QTL）。再结合基于这4个种群极端表型个体重测序数据的全基因组选择信号检测以及其肌肉转录组和代谢组分析，鉴别QTL区域内关键基因及因果突变，阐明其作用机理，从而深入揭示中、外猪种pH复杂性状形成的遗传机制，促进肉质性状分子育种发展。

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