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.
Genet Sel Evol. 2020 Oct 9;52(1):59. doi: 10.1186/s12711-020-00579-x.
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.
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).
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.
基因表达水平的遗传分析是一种很有前途的方法，可用于鉴定与肉质等复杂经济性状相关的候选基因。本研究基于 189 头杜洛克×陆川杂交猪背最长肌的 RNA-seq 数据进行表达数量性状基因座 (eQTL) 和等位基因特异性表达 (ASE) 分析，以鉴定一些与肉质性状相关的候选基因。
我们使用基于混合线性模型的全基因组关联研究，鉴定到了 7192 个 cis-eQTL，对应 2098 个 cis-基因（p 值 ≤ 1.33e-3， FDR ≤ 0.05），以及 6400 个 trans-eQTL，对应 863 个 trans-基因（p 值 ≤ 1.13e-6， FDR ≤ 0.05）。利用 RNAseq SNPs 进行的 ASE 分析在 2253 个独特基因中鉴定到了 9815 个显著的 ASE-SNPs。cis-eQTL 和 ASE 靶基因的综合分析鉴定到了 540 个共同基因，其中 33 个基因的表达水平与至少一个肉质性状相关。在这 540 个共同基因中，有 63 个先前被报道为肉质性状的候选基因，如 cis-eQTL 分析中位于主导 SNP 的 PHKG1（q 值 = 1.67e-6）、NUDT7（q 值 = 5.67e-13）、FADS2（q 值 = 8.44e-5）和 DGAT2（q 值 = 1.24e-3）。
本研究通过 eQTL 和 ASE 分析，证实了几个先前发表的候选基因，并鉴定到了一些与肉质性状相关的新候选基因，这将有助于在进一步的研究中优先考虑候选基因。
