Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate ge
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RESEARCH ARTICLE
Ge n e t i c s Se l e c t i o n Ev o l u t i o n
Open Access
Genome‑wide analysis of expression QTL (eQTL) and allele‑specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits Yan Liu1,2,3, Xiaolei Liu1,2,3, Zhiwei Zheng1,2,3, Tingting Ma1,2,3, Ying Liu1,2,3, Huan Long1,2,3, Huijun Cheng1,2,3, Ming Fang5, Jing Gong4, Xinyun Li1,2,3, Shuhong Zhao1,2,3 and Xuewen Xu1,2,3*
Abstract Background: Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Results: Using a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3). Conclusions: The present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies. Background In the past 10 years, genome-wide association studies (GWAS) have dramatically accelerated the forward genetic dissection of complex traits in various species. For example, according to the release (as of 2019 *Correspondence: [email protected] 1 Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China Full list of author information is available at the end of the article
September 30) of the animal quantitative trait loci (QTL) database (https://www.animalgenome.org/), 16,085 QTL or associations for pork quality and carcass traits have been reported. However, previous reported GWAS results revealed that most of the leading single nucleotide polymorphisms (SNPs) for complex traits were located in noncoding regions [1], which suggests that variants located in regulatory elements contribute to phenotypic variation by regulating gene expression. Thus, prioritizing the functional genes and related causal variants that underlie QTL, espec
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