Genome-wide eQTL Reveals Novel Candidate Loci for Meat Quality Traits on Chromosome 11 in Pigs (Sus scrofa)
ZHENG Yun-Di1, RAN Xue-Qin2, NIU-Xi1, HUANG Shi-Hui2, LI Sheng1, WANG Jia-Fu1,*
1 College of Life Sciences/Institute of Agro-bioengineering/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China; 2 College of Animal Sciences/Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
Abstract：Genome-wide association study (GWAS) has detected a considerable amount of genetic variants associated with pork meat quality traits, however, the regulatory mechanism of numerous variants are generally unknown. Genetic variants mainly exert effects on complex traits by regulating gene expression levels. Thus, mapping expression quantitative trait locus (eQTL) has identified variants associated with gene expression levels, and will contribute to interpretate the association between variant loci and traits. In order to identify genetic variants/genes correlative with meat traits, this study used 19 hybrid Xiang pigs (Sus scrofa)(Large White pig ♂ × Congjiang Xiang pig ♀) of F2 generation as tested materials, whole genome sequencing (WGS) and high-throughput RNA sequencing (RNA-seq) data of the pork longissimus muscle tissues were integrated for eQTL analysis. The results showed a total of 1 332 cis-eQTL (PFDR<0.01) and 18 078 trans-eQTL (PFDR<1E-12) on chromosome 11. Subsequently, annotation and filtering were conducted on the eQTL-associated single nucleotide polymorphism (eSNP) which identified by cis-eQTL associations, and PCR-restriction fragment length polymorphism (RFLP) and Sanger sequencing were used to verify the candidate eSNP. An eSNP event rs319855910 c.-46C>G located in mitochondrial intermediate peptidase gene (MIPEP) 5'UTR was ultimately identified, and rs319855910 significantly associated with MIPEP gene expression (PFDR=8.81E-03). Statistical analysis combined with genotype and RNA-seq showed that rs319855910 genotypes significantly affected MIPEP gene expression (P<0.05), and it was observed that significant down-regulation (P<0.05) of MIPEP gene expression when the rs319855910 genotype was mutated from homozygote (CC) to homozygous mutant (GG). Furthermore, the transcription factor binding analysis revealed that rs319855910 was located in the region of transcription factor binding sequences, which could change the binding type or number of 5'UTR sequence with transcription factors. The above results suggested that rs319855910 was a novel candidate locus associated with pork meat quality traits, which could affect gene expression and regulate pork meat quality traits by changing the binding of transcription factors. This study provides basic data for pig breeding and genetic improvement.
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