Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
BMC Genomics. 2021 Nov 8;22(1):805. doi: 10.1186/s12864-021-08141-9.
Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat quality, and the reason remains unknown.
In the present study, we identified 212 IMF-correlated genes (FDR ≤ 0.01) using correlation analysis between gene expression level and the value of IMF content. The IMF-correlated genes were significantly enriched in the processes of lipid metabolism and mitochondrial energy metabolism, as well as the AMPK/PPAR signaling pathway. From the IMF-correlated genes, we identified 99 genes associated with expression quantitative trait locus (eQTL) or allele-specific expression (ASE) signals, including 21 genes identified by both cis-eQTL and ASE analyses and 12 genes identified by trans-eQTL analysis. Genome-wide association study (GWAS) of IMF identified a significant QTL on SSC14 (p-value = 2.51E), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E) was proposed as the candidate gene. Furthermore, we highlighted another three novel IMF candidate genes, namely AGT, EMG1, and PCTP, by integrated analysis of GWAS, eQTL, and IMF-gene correlation analysis.
The AMPK/PPAR signaling pathway together with the processes of lipid and mitochondrial energy metabolism plays a vital role in regulating porcine IMF content. Trait correlated expression combined with eQTL and ASE analysis highlighted a priority list of genes, which compensated for the shortcoming of GWAS, thereby accelerating the mining of causal genes of IMF.
肌肉内脂肪（IMF）含量是决定肉质的一个决定因素。陆川猪是中国南方的一个脂肪型地方品种，因其高 IMF 而具有理想的肉质，但陆川母猪与杜洛克公猪的杂交后代在肉质方面表现出群体内的变异，其原因尚不清楚。
本研究通过基因表达水平与 IMF 含量值之间的相关性分析，鉴定出 212 个与 IMF 相关的基因（FDR≤0.01）。与 IMF 相关的基因显著富集在脂质代谢和线粒体能量代谢过程中，以及 AMPK/PPAR 信号通路中。从与 IMF 相关的基因中，我们鉴定出 99 个与表达数量性状基因座（eQTL）或等位基因特异性表达（ASE）信号相关的基因，包括 21 个通过 cis-eQTL 和 ASE 分析鉴定的基因和 12 个通过 trans-eQTL 分析鉴定的基因。IMF 的全基因组关联研究（GWAS）在 SSC14 上鉴定出一个显著的 QTL（p 值=2.51E），并提出与 IMF 相关的基因 SFXN4（r=0.28，FDR=4.00E）为候选基因。此外，我们通过 GWAS、eQTL 和 IMF 基因相关性分析的综合分析，突出了另外三个新的 IMF 候选基因，即 AGT、EMG1 和 PCTP。
AMPK/PPAR 信号通路以及脂质和线粒体能量代谢过程在调节猪的 IMF 含量方面起着至关重要的作用。性状相关表达与 eQTL 和 ASE 分析相结合，突出了一个基因的优先列表，弥补了 GWAS 的不足，从而加速了 IMF 因果基因的挖掘。
