Genome-Wide Identification of Cis-acting Expression QTLs in Large Yellow Croaker

The large yellow croaker is one of the largest marine economic fish in China with the farming yield about 30 tons per year. The genetic selection for growth and disease resistance has been performed in recent years. The identification of trait-associated molecular makers, causative variants, and causative genes is helpful for genetic selection in large yellow croaker. It has been discovered that most of polygenic traits are controlled with multiple genes via regulatory variant, and GWAS-identified loci are enriched in the regulatory variant. Cis-acting eQTL is a widespread regulatory variant that controls the expression of nearby gene. We herein take advantage of RNA-seq and whole genome sequencing technique to identify genome-wide eQTLs in liver tissue for large yellow croaker; a forward selection routine is applied for identification of multiple eQTLs. To fine map causative mutation for each eQTL, a credible set is built to confine causative variants. Totally, 2427 eQTLs have been identified, 69.7% (1,691/2,427) of them are primary eQTL signals, and the remaining are secondary signals, many functional important target genes have been discovered. We highlight several functional pivotal genes including SMC3, TUSC3, TITIN, MCPH1, and MDHC, in which the expression of MCPH1 is regulated by two eQTLs; the distance of these eQTLs from target genes is symmetrically distributed, 25.5% of them are within 1 Mb region from target genes, whereas 74.5% of them are between 1 and 2 Mb regions; most of the identified eQTL has been well resolved, and 19.3 (469/2427) of eQTL have the size of credible set (the number of variants in credible set) less than 50.