GWAS-based Identification Of Molecular Markers And Candidate Genes For Growth Traits In Large White Pigs

Growth trait is one of the most important economic traits of pigs.It is important for promoting genetic improvement of pigs to reveal the molecular genetic basis of growth trait.To date,the genetic basis of pig growth traits remains unclear.In order to identify the single nucleotide polymorphisms(SNPs)and candidate genes for growth traits in Large White pigs,the whole genome SNPs of 499 pigs were examined by using the Illumina 50 K SNP Bead Chip.Genome-wide association study(GWAS)was conducted using the mixed linear model(MLM)method for six growth traits,age to 30 kg body weight(D30),age to 100 kg body weight(D100),average daily gain from 30 to 100 kg(ADG30-100),live backfat thickness at 100 kg(BFL),live loin muscle area at 100 kg(LMA),and live loin muscle depth at 100 kg(LMD).Gene annotation and candidate gene enrichment analysis were also performed for SNP loci that significantly associated with the target traits.The main results were as follows:(1)Genome-wide SNP detection in Large White pigs based on DNA chip technique.After genotyping and quality control,a total of 41,311 valid SNPs were detected in Large White pigs with an average spacing of 55.71-65.66 kb between the adjacent SNPs.(2)Detection of SNP markers for growth traits in Large White pigs based on GWAS.A total of 29 SNP loci significantly associated with growth traits were detected on six chromosomes,by conducting GWAS for six growth traits in Large White pigs using MLM.Among them,one SNP on chromosome 8 was significantly associated with ADG30-100;25 SNPs were significantly associated with BFL,which 24 SNPs detected on chromosomes 5 and 1 on chomosome 12;and 3 SNPs located separately on chromosomes7,13 and 16 were significantly associated with LMA,which the SNP on chromosome 16 also significantly associated with LMD.(3)Discovery of candidate genes for growth traits in Large White pigs.Through gene annotation and candidate gene enrichment analysis of SNPs that significantly associated with target traits,it indicated that NDST3 was a candidate gene for ADG30-100,thirteen genes,LMO3,PIK3C2 G,PDE3A,SLCO1C1,SLCO1B3,SLCO1A2,KCNJ8,ABCC9,GYS2,SLC15A5,PLEKHA5,LDHB,MYO19 were the candidate genes for BFL,6genes,PROX2,FOS,AREL1,DLST,NEK9 and EBF1(also affecting LMD)were the candidate genes for LMA.These SNPs and candidate genes related to growth traits in Large White pigs identified in this study further enriched the molecular markers for pig growth traits and provided a scientific basis for the application of molecular breeding technology to promote genetic improvement of pig growth traits.