Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat

BMC Genomics

Xinyi Zhang¹  Lizhu Niu¹  Huan Long¹  Mufeng Wang¹  Lianni Wang¹  Tingting Ma¹  Yu Lei¹  Simin Feng¹  Qiankun Wang¹  Yilong Chen¹  Yan Liu²  Xuewen Xu² 

[1] Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China;The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China;Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China;The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, China;Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, 430070, Wuhan, China;

关键词: Pig;    IMF;    eQTL;    ASE;    GWAS;    AMPK/PPAR;   

DOI  :  10.1186/s12864-021-08141-9

来源: Springer

【 摘 要 】

BackgroundIntramuscular 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.ResultsIn 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.ConclusionsThe 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.

【 授权许可】

CC BY