Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits.
Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits.
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对猪肌肉中表达 QTL (eQTL) 和等位基因特异性表达 (ASE) 进行全基因组分析，确定肉质性状的候选基因
DOI：
10.1186/s12711-020-00579-x
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发表时间：
2020-10-09
期刊：
影响因子：
--
通讯作者：
Xu X
中科院分区：
文献类型：
--
作者：
Liu Y;Liu X;Zheng Z;Ma T;Liu Y;Long H;Cheng H;Fang M;Gong J;Li X;Zhao S;Xu X
基因表达水平的遗传分析是一种很有前途的方法，用于表征参与复杂经济性状（如肉品质）的候选基因。本研究基于rna测序（RNAseq）数据，对189头杜鲁猪最长肌进行了表达数量性状位点（eQTL）和等位基因特异性表达（ASE）分析，以鉴定肉质性状的候选基因。基于混合线性模型的全基因组关联研究，共鉴定出2098个顺式基因对应的顺式- eqtl 7192个（p≤1.33e-3, FDR≤0.05），863个反式基因对应的反式- eqtl 6400个（p≤1.13e-6, FDR≤0.05）。使用RNAseq snp进行ASE分析，在2253个独特基因中鉴定出9815个显著的ASE snp。顺式eqtl与ASE靶基因的整合分析鉴定出540个常见基因，其中33个基因的表达水平与至少一种肉质性状相关。在这540个常见基因中，有63个已被报道为肉质性状的候选基因，如PHKG1（顺式- eqtl分析中先导SNP的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，确认了几个已发表的候选基因，并鉴定了一些新的肉质性状候选基因，为进一步研究确定候选基因的优先级提供了依据。
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.