Genome-wide Association Analysis Of Traits Related To Growth And Feed Efficiency Of Duroc Boars

Feed cost has always been the largest production cost that affects the economic efficiency of pig production,accounting for 50 to 85% of the total cost.The key to reducing feed cost is to increase feed efficiency.FCR and RFI are two important indicators for evaluating feed efficiency.In this study,animal models combined with mean information maximum likelihood(AI-REML)was used to estimate the genetic parameters of growth and feed efficiency traits in the Duroc population in southern China,revealing the phenotype and genetic correlation of RFI and FCR with other important economic traits,Which provides a genetic basis for the application of RFI in pig breeding.Using wssGWAS to identify QTL regions and candidate genes related to growth and feed efficiency in the Duroc boar population,and to identify the biological processes and functions of the candidate genes through KEGG pathway analysis and GO enrichment analysis.Test 1: To explore the genetic basis of feed efficiency-related traits in Duroc boar populations,this study used the DMU program to estimate the variance components of370 Duroc boars and calculate their heritability,including the average daily feed intake(ADFI),Daily weight gain(ADG),feed conversion rate(FCR),residual feed intake(RFI),birth weight(BW),age corrected to 100 kg or 115 kg body weight(Day100,Day115),and backfat thickness corrected to 100 kg or 115 kg body weight(BF100,BF115).The coefficient of variation of 9 traits ranged from 6.44 to 21.79%.The additive genetic variance was larger than the environmental variance,and the heritability range was 0.32 to 0.63,which belonged to the moderately strong heritability.The phenotypic correlation coefficients of FCR between with ADFI,ADG,BF100 and BF115 were 0.27,-0.85,0.01 and 0.04,respectively;the genetic correlation coefficients of FCR between with ADG,BF100 and BF115 were-0.80,0.15 and 0.19,respectively.The phenotypic correlation coefficients of RFI between with FCR,ADFI,ADG,BF100,and BF115 was 0.40,0.98,0.11,0.06,and 0.07,respectively;the genetic correlation coefficients of RFI between with ADFI,ADG,FCR,BF100,and BF115 were 0.99,-0.36,0.81,0.22,and 0.25,respectively.FCR and RFI are currently the main selection indicators for improving feed efficiency.Due to the strong correlation between ADFI and RFI,ADFI has the potential to be an early selection indicator for selecting RFI.Test 2: In order to identify genetic variation of traits related to growth and feed efficiency of Duroc boar populations,SNPs,QTLs and candidate genes that were significantly related to the traits were Identified.This study used the BLUPF90 program to perform weighted single step genome-wide association study(wssGWAS)on feed efficiency traits of 370 Duroc boar,including the average daily feed intake(ADFI),residual feed intake(RFI),feed conversion rate(FCR),average daily weight gain(ADG),age corrected to 100 kg or 115 kg body weight(Day100,Day115),backfat thickness corrected to 100 kg or 115 kg body weight(BF100,BF115)and birth weight(BW).Cytoscape 3.6.1 software was used to perform KEGG pathway(Kyoto Encyclopedia of Genes and Genomes)and GO(Gene Ontology)enrichment analysis on genes with significant SNP sequences.This study identified 138 to 211 SNP loci that were significantly related to feed efficiency traits.A total of 20 significant SNPs were located on the gene exon sequence,and the variance of genetic interpretation of each SNP was 1.02 to 14.49%.Polymorphisms at rs343914250,rs336768928,and rs345879479 loci significantly affected the average daily feed intake(ADFI),feed conversion rate(FCR),and residual feed intake(RFI)of Duroc boars.The 9 most important QTLs for 9 traits contain 4 to 29 significant SNP loci and the 3 most important QTLs for each trait explain 13.95 ～ 30.10% genetic variance,and the most important QTL explains 6.51 ～ 15.00% genetic variance.ADFI,RFI,FCR,ADG,Day100,Day115,BF100,BF115 and BW identified out 6,9,8,8,3,3,3,3 and 5 candidate genes,respectively.The candidate genes identified in this study have been reported in the literature on functions and physiological processes related to growth and feed efficiency,but the functions of candidate genes on pig growth and feed efficiency need to be functionally verified.