Identification Of QTL Affecting Chest And Abdominal Circumference Of Duroc Breed Pig Based On Genome Resequencing

Chest circumference(CC)and abdominal circumference(AC)are the important factor for the selection and breeding of lean type pigs,which directly determines the breeding goals of improving the carcass lean ratio of pigs.In the actual production,the pig with large CC and small AC have a higher score in the live grading system,which has better economic benefits.However,the measurement of body size traits,such as CC and AC,usually needs to be conducted in a certain age.Thus,the traditional selection method can’t make a judgement on whether to keep or not at the early age,which makes the breeding process slowly.With the development of genotyping technologies including gene chips and next-generation sequencing,more and more single nucleotide polymorphisms(SNP)related to phenotype have been found,and the molecular marker-assisted selection technology developed based on it can effectively promote the selection of these traits in an early stage and greatly accelerate the breeding process.Therefore,we conducted a genome-wide association study(GWAS)for CC and AC based on the 50 K gene chip and phenotype data of 2206 S21(American origin)and 2082 S22(Canadian origin)Duroc pigs preliminarily.And the whole genome resequencing was performed on 152 S21 and 151 S22 Duroc pigs,the resequencing data was imputed into the individuals sequenced by gene chip.GWAS was conducted again to identify the significant locus and candidate gene associated with CC and AC of Duroc pigs.The main results are as follows:(1)After analyzing the genetic parameters of the phenotypes in S21 and S22 Duroc pigs,the heritability of CC and AC was between 0.12 and 0.15,which was a medium to low heritability.The coefficient of phenotypic variation between CC and AC ranged from3.13% to 4.06%,indicating that there is still room for genetic improvement.(2)According to the data of 50 K gene chip,we detected 6 suggestive SNP were associated with CC,4 suggestive SNP were associated with AC,all of them located on Sus scrofa chromosome(SSC)1.Among them,3 SNP were significantly associated with CC and AC.In S22 Duroc pigs,21 SNP were detected to be significantly associated with CC on SSC1,and 2 SNP were significantly associated AC on SSC17.(3)After imputation with resequencing data,a total of 53 suggestive SNP were identified to be associated with CC and AC in S21 Duroc pig population.Among them,50 SNP significantly associated with CC were distributed on SSC1,SSC7 and SSC15,3 SNP significantly associated with AC were distributed on SSC1 and SSC6.In S22 Duroc pigs,55 suggestive SNP were detected to be associated with CC,which distributed on SSC1,SSC4 and SSC8.Only 1 suggestive SNP was identified to be associated with AC,which located on SSC17.This study also found that there is a SNP that is significantly related to the phenotype of CC and AC,which is located in the ALPK2 gene.We speculate that this gene may have multiple effects as an important candidate gene.(4)According to the detected SNP site information,we determine the QTL interval associated with the trait,and search for candidate genes in the interval.According to gene function and literature review,we identified ten candidate genes(OR13C3、OR13C4、OR13C8、ENPP5、NOX5、KIF23、ABLIM2、AFAP1、RPLP1)associated with CC and AC.In this study,we performed GWAS on S21 and S22 two Duroc pig populations based on gene chip and resequencing data,SNP and QTL associated with CC and AC were found on SSC1,SSC4,SSC6,SSC7,SSC8 and SSC15,which provided a new theoretical basis for genetic analysis of CC and AC.It’s helpful for genetic improvement of CC and AC by using molecular breeding technology and speeding up the breeding of lean type pigs,improving the production efficiency.