He Hua, Tian Xinyang, Kang Zhe, Wang Guozhi, Jia Xianbo, Sun Wenqiang, Lai Song-Jia, Chen Shi-Yi
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China.
Front Vet Sci. 2024 Dec 6;11:1453196. doi: 10.3389/fvets.2024.1453196. eCollection 2024.
Meat rabbits are a small herbivorous livestock and have been popularly raised in China for producing high-quality meat. Therefore, it is economically important to genetically improve both carcass performance and meat quality in meat rabbits. However, we still know less about the underlying candidate genes that may determine phenotypic variation on carcass and meat traits of meat rabbits. The main objective of this study was to identify candidate genes whose mRNA expression levels may be significantly involved in regulating carcass and meat traits of meat rabbits based on the transcriptome-wide association studies (TWAS). Five carcass traits of the carcass weight (CW), dressing out percentage (DP), cut weight of hind legs (LW), weight ratio of cut hind legs to carcass (RLW), and weight of visceral and interscapular fat (WF), as well as two meat traits of the drip loss (DL) and cooking loss (CL) were phenotyped in a F1 crossbred population ( = 119) between Zika rabbits and Sichuan White rabbits. The effects of mRNA expression levels of a total of 10,288 genome-wide genes on these seven traits were statistically estimated using the mixed linear model, in which the polygenic background effects were accounted for. Our results revealed two candidate genes ( and ) that were statistically significantly associated with LW trait (the adjusted values <0.05), whereas no gene reached the statistically significant threshold for all the remaining six traits. Because of the relatively small sample size analyzed, we alternatively selected 20 candidate genes with the lowest values for every trait and subjected them to functional enrichment analyses, which identified three Gene Ontology (GO) terms that were significantly enriched by the candidate genes of CW and RLW traits. In conclusion, this study used TWAS approach to successfully reveal several candidate genes whose mRNA expression levels may be involved in regulating carcass and meat traits in meat rabbits, which are helpful to explore the underlying molecular mechanism in the future studies.
肉兔是一种小型草食性家畜，在中国因生产优质肉而被广泛养殖。因此，从基因层面改善肉兔的胴体性能和肉质在经济上具有重要意义。然而，我们对可能决定肉兔胴体和肉质表型变异的潜在候选基因仍知之甚少。本研究的主要目的是基于全转录组关联研究（TWAS），鉴定其mRNA表达水平可能显著参与调控肉兔胴体和肉质性状的候选基因。在齐卡兔和四川白兔的F1杂交群体（n = 119）中，对五个胴体性状（胴体重（CW）、屠宰率（DP）、后腿切割重量（LW）、后腿切割重量与胴体的重量比（RLW）以及内脏和肩胛间脂肪重量（WF））以及两个肉质性状（滴水损失（DL）和蒸煮损失（CL））进行了表型分析。使用混合线性模型统计估计了总共10288个全基因组基因的mRNA表达水平对这七个性状的影响，其中考虑了多基因背景效应。我们的结果揭示了两个与LW性状显著相关的候选基因（和）（校正P值<0.05），而其余六个性状均未发现基因达到统计学显著阈值。由于分析的样本量相对较小，我们另外为每个性状选择了20个P值最低的候选基因，并对其进行功能富集分析，确定了三个基因本体（GO）术语，它们在CW和RLW性状的候选基因中显著富集。总之，本研究采用TWAS方法成功揭示了几个候选基因，其mRNA表达水平可能参与调控肉兔的胴体和肉质性状，这有助于在未来研究中探索潜在的分子机制。
