Shen Yu, Wang Haiyan, Xie Jiahao, Wang Zixuan, Ma Yunlong
Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.
Front Genet. 2021 Nov 16;12:761252. doi: 10.3389/fgene.2021.761252. eCollection 2021.
In past decades, meat quality traits have been shaped by human-driven selection in the process of genetic improvement programs. Exploring the potential genetic basis of artificial selection and mapping functional candidate genes for economic traits are of great significance in genetic improvement of pigs. In this study, we focus on investigating the genetic basis of five meat quality traits, including intramuscular fat content (IMF), drip loss, water binding capacity, pH at 45 min (pH45min), and ultimate pH (pH24h). Through making phenotypic gradient differential population pairs, Wright's fixation index (F) and the cross-population extended haplotype homozogysity (XPEHH) were applied to detect selection signatures for these five traits. Finally, a total of 427 and 307 trait-specific selection signatures were revealed by F and XPEHH, respectively. Further bioinformatics analysis indicates that some genes, such as , , , , , and , overlapping with the trait-specific selection signatures are responsible for the phenotypes including fat metabolism and muscle development. Among them, a series of promising trait-specific selection signatures that were detected in the high IMF subpopulation are located in the region of 93544042-95179724bp on SSC4, and the genes harboring in this region are all related to lipids and muscle development. Overall, these candidate genes of meat quality traits identified in this analysis may provide some fundamental information for further exploring the genetic basis of this complex trait.
在过去几十年里，肉质性状在遗传改良计划过程中受到人类驱动选择的影响。探索人工选择的潜在遗传基础并绘制经济性状的功能候选基因图谱，对猪的遗传改良具有重要意义。在本研究中，我们着重研究五个肉质性状的遗传基础，包括肌内脂肪含量（IMF）、滴水损失、水结合能力、45分钟时的pH值（pH45min）和最终pH值（pH24h）。通过构建表型梯度差异种群对，应用赖特固定指数（F）和跨种群扩展单倍型纯合性（XPEHH）来检测这五个性状的选择信号。最终，F和XPEHH分别揭示了427个和307个特定性状的选择信号。进一步的生物信息学分析表明，一些与特定性状选择信号重叠的基因，如 、 、 、 、 和 ，与包括脂肪代谢和肌肉发育在内的表型有关。其中，在高IMF亚群中检测到的一系列有前景的特定性状选择信号位于SSC4上93544042 - 95179724bp区域，该区域内的基因均与脂质和肌肉发育相关。总体而言，本分析中鉴定出的这些肉质性状候选基因可能为进一步探索这一复杂性状的遗传基础提供一些基础信息。
