农业生物技术学报2024，Vol.32Issue(4)：807-819,13.DOI:10.3969/j.issn.1674-7968.2024.04.007
全基因组eQTL揭示猪11号染色体肉质性状新候选位点
Genome-wide eQTL Reveals Novel Candidate Loci for Meat Quality Traits on Chromosome 11 in Pigs(Sus scrofa)
摘要
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.关键词
猪/全基因组测序(WGS)/转录组测序/表达数量性状位点(eQTL)/SNP/肉质性状Key words
Pig/Whole genome sequencing(WGS)/RNA-seq/Expression quantitative trait locus(eQTL)/SNP/Meat quality trait分类
农业科技引用本文复制引用
郑韵頔,冉雪琴,牛熙,黄世会,李升,王嘉福..全基因组eQTL揭示猪11号染色体肉质性状新候选位点[J].农业生物技术学报,2024,32(4):807-819,13.基金项目
国家自然科学基金(31960641) （31960641）
贵州省科技创新人才团队项目(黔科合平台人才[2019]5615) （黔科合平台人才[2019]5615）
贵州省"百"层次创新型人才培养项目(黔科合人才[2016]4012) （黔科合人才[2016]4012）
贵州省科技支撑计划(黔科合支撑[2017]2585 （）
黔科合支撑[2017]2987) （）
贵州省农业农村厅生猪产业高质量发展计划[202208-5] （）
