Identification Of The Genetic And Microbial Biomarkers Of Feed Efficiency Trait And The Interaction Between Host Genetics And Intestinal Microflora In Large White Pigs

Feed efficiency is an important trait in pig breeding and also an important factor affecting porcine feed costs,and feed intake behavior of pigs is closely related to the feed efficiency.A variety of complex traits in animals are affected by both the host genome and intestinal microorganisms,additionally,the host genome also affects the intestinal microbial community structure.There is a complex and close interaction among host genome,intestinal microbe and host phenotype.In this study,firstly,we analyzed the non-genetic factors and estimated the genetic parameters of feed efficiency,feed intake behavior and related traits of Large White pigs,including residual feed intake(RFI),feed conversion ratio(FCR),average daily gain(ADG),average daily feed intake(ADFI),100 kg backfat thickness(BF),number of visits to the feeder per day(NVD),time at the feeder per day(TFD),feed intake per visit to the feeder(FIV),time at the feeder per visit(TV),and feeding rate(FR).Secondly,we performed genome-wide association studies(GWAS)for RFI,FCR,ADG,BF,ADFI,NVD,FIV,TFD,TV,and FR by using reduced-representation genome sequencing.Thirdly,microbial16S rRNA gene sequencing combined with metagenomic sequencing technology was used to screen fecal microbial markers associated with RFI,FCR,ADG,BF,ADFI,NVD,FIV,TFD,TV,and FR.Finally,based on the above analysis,we preliminarily studied the interaction between the host genome and their fecal microbes of 80-day-old Larger White pigs.The main results of this study are as follows:(1)Non-genetic factor analysis and genetic parameter estimation were carried out on RFI,FCR,ADG,BF,ADFI,NVD,FIV,TFD,TV,and FR traits of 848 Large White pigs.The results showed that the year had significant effect on RFI,FCR,BF,ADFI,TFD,and FR(P<0.05 or P<0.01).The gender had significant effect on RFI,FCR,ADG,BF,ADFI,NVD,FIV,TFD,TV,and FR(P<0.05 or P<0.01).The parity only had significant effect on FCR(P<0.01)and ADFI(P<0.05).The season had significant effect on RFI,ADG,ADFI traits(P<0.01).The heritability of 10 traits were ranged from 0.3 to 0.54,which belonged to middle or high heritability traits.Among them,between RFI,FCR,ADFI,and TFD,and between FIV,ADFI and NVD,showed higher phenotypic correlation and genetic correlation.(2)Reduced-representation genome sequencing was used to performGWAS for RFI,FCR,ADG,BF,ADFI,NVD,FIV,TFD,TV,and FR traits in 349 Large White pigs.The results showed that,five traits,including RFI,FCR,ADG,TFD,and TV,had detected genome-wide significant association SNPs(-log10(P)>6).A total of 38SNPs significantly associated with RFI and FCR traits,11 SNPs significantly associated with ADG trait,and one SNP was genome-wide significantly associated with TFD and TV traits,were identified.According to the gene functions,combined with the analysis of haplotype,GO and KEGG enrichment,14 genes,including PIK3C3,CLCN3,CBR4,MFAP3L,DDX60,SH3RF1,AADAT,WWC3,RAB9A,OFD,EGFL6,Gl RA2,TLR7,and TLR8 were considered as important candidates for RFI and FCR traits.Immunity(such as toll-like receptor signaling),inflammation(such as measles),and metabolism(such as2-Oxocarboxylic acid and tryptophan metabolism)may be involved in regulating the RFI and FCR traits.One unknown functional gene was annotated associated with ADG:LOC110255823.Five genes,including ELAC2,COX10,ARHGAP44,HS3ST3A1,and HS3ST3B1,were identified significantly associated with TFD and TV traits.(3)The 16S rRNA gene sequencing of fecal microbes was performed on 349 80-day-old Large White pigs.Gender,season,birth weight,parity,and litter size were significantly correlated with the composition of the intestinal microbial community by analyzing the genetic and environmental factors(P<0.05).The results of enterotypes identification showed that there were two enterotypes,Lactobacillus and Gemmiger,in the feces of 80-day Large White pigs.The results revealed significant effects of enterotypes on RFI,FCR and alpha diversity,while no significant effect on ADG,BF,ADFI,NVD,FIV,TFD,TV,or FR.We found some intestinal microflora were significantly related to RFI(e.g.,unidentified?Lachnospiraceae,and Lactobacillus),FCR(Prevotella and Lactobacillus),ADG(Roseburia),BF(unidentified?CoriobacteriaceaeandPrevotella),ADFI(unidentified?Coriobacteriaceae and Corynebacterium),NVD(unidentified?Rikenellaceae),TFD(unidentified?Acidimicrobiales),TV(SMB53),and FR(Corynebacterium and Faecalibacterium)by analyzing the different grouping of phenotypic extreme values,and these microbes may could be used as microbial markers related to the phenotypes.(4)Based on the results of 16S rRNA gene sequencing,fecal microbes of 12 high/low feed efficiency(RFI/FCR)Large White pigs were performed metagenome sequencing.The results showed that there were significant differences in fecal microorganisms of 80-day-old Large White pigs with different feed efficiency.Compared with the low feed efficiency group,the abundance of bacteria(e.g.Lachnospiraceae,Ruminococcaceae and Clostridiaceae)producing short-chain fatty acids in feces of the high feed efficiency group was higher.The enrichment of metabolic pathways of microbes in high feed efficiency pigs were amino acid metabolic pathways(e.g.glycine,serine,threonine,and phenylalanine metabolism),nitrogen metabolic pathways,and carbohydrate metabolic pathways(e.g.tricarboxylic acid cycle,glyoxylic acid,and dicarboxylic acid metabolism).Compared with the high feed efficiency group,low feed efficiency pigs have higher abundance of Lactobacillus(such as Lactobacillus?reuteri and Lactobacillus?johnsonii),and the enrichment of metabolic pathways were lipid-like compound metabolism,phosphatase system,and unclassified genetic information processing process.(5)The comparison of the similarity of gut microbial composition among full-sibs,half-sibs,and unrelated members showed a higher similarity of beta-diversity between full-sib members than half-sibs and unrelated members.Further correlation analysis showed some relationships between host genetics and the gut microbiome.We identified 34 host SNPs significantly associated with microbial beta-diversity,and their cumulative interpretation rate for microbial beta-diversity was 5.07%.By evaluating the correlation between microbial abundance and host genetic variations,6 genera,73 KOs,and58 Meta Cyc metabolic pathways were identified significantly associated with host genetic variations.Moreover,we identified 82 microbial genera with heritability in the feces(h~2>0.1),including SMB53(h~2=0.56),Lactobacillus(h~2=0.52)and Oscillospira(h~2=0.47).Finally,the microbial genome-wide association studies(mGWAS)were used to identify the host genetic variations and genes that influence the relative abundance of the five microbial genera,including SMB53,Turicibacter,Clostridium,[Ruminococcus],and 02d06,and found that the functions of these genes were mainly involved in inflammatory,immune,and metabolic pathways.In conclusion,based on the host genome sequencing and microbiome sequencing technology,we identified the candidate host genes and fecal microorganisms affecting RFI,FCR,ADG,BF,ADFI,NVD,FIV,TFD,TV,and FR traits by using various analysis methods and analyzing the biological functions of candidate genes and microorganisms.In addition,the interaction between the host genetics and fecal microorganisms at the stage of early performance test was analyzed by combing host genome sequencing and fecal microbiome sequencing,and identified some genes associated with intestinal microbes and their possible interaction pathways.The results of this study provided a new research idea and some genetic markers for future molecular breeding of Large White pigs.