Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat.
Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat.
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性状相关表达结合 eQTL 和 ASE 分析确定了影响肌内脂肪的新候选基因
DOI：
10.1186/s12864-021-08141-9
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发表时间：
2021-11-08
期刊：
影响因子：
4.4
通讯作者：
Xu X
中科院分区：
文献类型：
--
作者：
Liu Y;Long H;Feng S;Ma T;Wang M;Niu L;Zhang X;Wang L;Lei Y;Chen Y;Wang Q;Xu X
肌内脂肪（IMF）含量是决定肉的味道的一个因素。陆川猪是我国南方的一个脂肪型地方猪种，因其高肌内脂肪（IMF）而具有良好的肉质品质，但陆川母猪与杜洛克公猪杂交后代的肉质性状存在群体内变异，其原因尚不清楚。在本研究中，我们确定了212个IMF相关基因（FDR ≤ 0.01），通过基因表达水平和IMF含量的值之间的相关性分析。与IMF相关的基因在脂质代谢、线粒体能量代谢以及AMPK/PPAR信号通路中显著富集。从与IMF相关的基因中，我们鉴定了99个与表达数量性状位点（eQTL）或等位基因特异性表达（ASE）信号相关的基因，其中21个基因通过顺式eQTL和ASE分析鉴定，12个基因通过反式eQTL分析鉴定。IMF的全基因组关联研究（GWAS）在SSC 14上发现了一个显著的QTL（p值= 2.51E−7），并提出了与IMF相关的最近基因SFXN 4（r = 0.28，FDR = 4.00E−4）作为候选基因。此外，通过GWAS、eQTL和IMF基因相关分析，我们还发现了另外3个新的IMF候选基因，即AGT、EMG 1和PCTP。AMPK/PPAR信号通路与脂质和线粒体能量代谢过程一起对猪IMF含量的调节起着至关重要的作用。性状相关表达结合eQTL和ASE分析突出了基因的优先级列表，弥补了GWAS的不足，从而加快了IMF致病基因的挖掘。在线版本包含补充材料，可通过10.1186/s12864-021-08141-9获得。
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−7), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E−4) 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. The online version contains supplementary material available at 10.1186/s12864-021-08141-9.