Identification Of Imprinting Effect Expression Quantitative Trait Loci(ieQTL) In A White Duroc×Erhualian F2 Pig Resource Population

The economic traits of agricultural animal were not only affected by the additive effect of genetic loci,but also the non-additive genetic effects,including the imprinting effects.For example,the muscle and growth related traits in pigs and sheep,are affected by large effect imprinting loci in IGF2 and MSTN gene regions.The discovery of these loci provides important markers for the genetic improvement of related traits.However,in recent years,studies on imprinting QTL mapping in agricultural animal populations are rare.The main reason is that most of the current researches are based on high-throughput SNP data without pedigree information,which is hard to infer haplotypes from parental origin.Besides,there is no one-stop software to carry out imprinting effect QTL mapping research.In this study,we integrate LINKPHASE3 and GEMMA software to develop a computational workflow for whole-genome imprinting effect locus mapping based on SNP data from pedigree resources.This workflow was applied to liver digital gene expression traits and 60K SNP data of 499 F2 individuals from a White Duroc×Erhualian F2 resource population designed and constructed by Prof.Lusheng Huang,to identify imprinting effect loci that affect liver gene expression traits.These loci were then integrated with complex trait-associated loci for further analysis,with the goal of identifying and screening for new genes that are regulated by imprinting effects and associated with complex trait loci.The main results are detailed as follow:（1）To verify the reliability of the imprinting effect locus analysis workflow proposed in this paper,we analyzed the longissimus dorsi area trait within the same population and identified a known imprinting effect locus that affects the longissimus dorsi area in the IGF2gene region on chromosome 2,thus confirming the reliability of our computational workflow.（2）SNP satisfying the following three conditions were considered as imprinting effect expression QTL（ieQTL）:1)The P-value of paternal or maternal effect QTL corresponding to the significance threshold(2.4×10^-5),and the significance was no less than a two-unit decrease in the-log10（P-value）value compared to the most significant SNP on the corresponding chromosome.2)Within the 5 Mb region upstream and downstream of the candidate ieQTL site,at least three SNP sites had P-values that reached the significance level.3)The P-values of ieQTLs reached the significance level.Under these criteria,a total of 1055liver ieQTLs were identified,including 125 Cis and 784 Trans ieQTLs.The significance of the cis-ieQTLs effect was higher than that of the trans-ieQTLs,involving genes related to liver function,such as innate immunity（TAX1BP1,C4BPB,FCN2,MPEG1,HLA-DRA,OLR1 and TRIM26）,nucleic acid metabolism（DPYD,UPB1）,and lipid biosynthesis（ABHD5,HSD17B7,CDIPT）.The number of trans-ieQTLs was much higher than that of cis-ieQTLs.At the same time,we detected 19 one-to-many effects where the same ieQTL affected multiple expression of genes.（3）By analyzing the additive effects of ieQTL region sites,we found that out of the1055 detected ieQTLs,906 had additive effects on SNP sites within 2 Mb upstream and downstream of the corresponding SNP but did not reach the significance threshold.This suggests that most of the ieQTLs identified in this study cannot be identified by classic additive effect models and are new discoveries.Based on these results,we can expect that using imprinting effect models can detect new loci that affect gene expression or complex phenotypes,further enriching our understanding of the mechanism of imprinting effect regulation of complex traits.（4）We downloaded 23,614 GWAS loci from Animal QTLdb and matched them with the ieQTLs detected in this study.A total of 150 loci from 65 traits overlapped with the identified ieQTLs,including 41 genes whose ieQTLs were associated with liver function,production,and meat quality traits.These results provide candidate genes for further analysis of the genetic mechanisms underlying complex trait loci.The imprinting effect eQTL analysis workflow constructed in this study provides a reference framework for studying the imprinting effects on complex traits.The results are helpful for deepening our understanding of the molecular mechanisms underlying the imprinting regulation of complex traits,and lay a foundation for further considering imprinting effects in molecular breeding practices.