Early Effect And Association Analysis Of Genomic Selection For Growth Traits In Duroc

Compared with traditional breeding methods,genomic selection(GS)has many advantages,such as improving selection accuracy and shortening generation interval.Since the commercialization of pig 60 K SNP genotyping chip in 2009,many foreign well-known breeding companies had started genomic selection breeding and applied it as a conventional breeding method.However,the breeding system in most Chinese companies has not been established and perfected,the application of genomic selection technology is not widespread.To research the application effect of genomic selection technology in Duroc breeding work and use GWAS to mine the SNP markers and candidate genes that are significantly related to Duroc growth traits,it is of great significance to research the genetic progress and genetic mechanism of Duroc growth traits.In this study,we first collected phenotypic data with age at 100kg(AGE100)and backfat thickness at 100kg(BT100)traits and pedigree data of Duroc pigs.Then established a genomic selection reference population to study the early selection effect of the Duroc growth traits using different selection strategies.At the same time,the GWAS of the Duroc population was conducted to find the possible functional loci and candidate genes related to population growth traits.The results of this study are as follows:(1)The reference group for genomic selection of Duroc growth traits was established.48,475 pieces of pedigree data,17,013 pieces of AGE100 data,16,837 pieces of BT100 data,and 1644 pieces of genotype information of the experimental population were collected.The genetic parameters of the reference population were estimated,the heritability of AGE100 and BT100 by BLUP method was 0.195 and0.334,respectively,and the genetic correlation between the two traits was-0.228.The heritability of two traits by the ss GBLUP method was 0.193 and 0.329,respectively,and the genetic correlation was-0.223.The heritability of growth traits estimated by the two methods was roughly equal,but the heritability estimated by the ss GBLUP method was slightly lower than that estimated by the traditional BLUP method.(2)Different calculation models were used to study the early selection effect of genomic selection in the Duroc candidate population,in terms of the accuracy of breeding value prediction,the ss GBLUP method with phenotypic value information had the highest accuracy,the prediction accuracy of the AGE100 and BT100 were0.153 and 0.342,respectively.Compared with the ss GBLUP method without phenotypic value information,the prediction accuracy of the ss GBLUP method with phenotypic value information were increased by 4.1% and 2.4%.Compared with the traditional BLUP method with phenotypic value information,the prediction accuracy were increased by 1.3% and 1.8%.Compared with the traditional BLUP method without phenotypic value information,the prediction accuracy were increased by15.9% and 8.2%.And the accuracy of any prediction models to BT100 was higher than that of AGE100.In terms of predicting unbiasedness,the traditional BLUP method with phenotypic value information had the best unbiased performance in the estimation of breeding value of growth traits of candidate population.Compared the correlation between the results of different calculation methods,the correlation between the two methods using genomic selection was the highest in all groups.The paternity index results of different prediction models of the candidate groups were ranked,and the ranking interval distribution of the top 20% individuals(i.e.the best individuals)in the genomic selection method with phenotypic value information in the other three estimation models was observed,in the genomic selection models,the results showed that after the performance test,all the excellent individuals reserved with the genomic selection index were in the top 50% of the index ranking in the model before the performance test,while some of the top performers in the traditional BLUP group were missing out of the top 50%.(3)Genome-wide association analysis was conducted for the growth traits of Duroc pig populations.A total of 13 candidate SNPs were located on SSC3,SSC5,SSC8 and SSC11,which were associated with the AGE100.And 10 candidate SNPs related to BT100 were located on SSC1,SSC7 and SSC13.By comparing,querying and analyzing the association loci,a total of 8 candidate genes that may be related to Duroc’s AGE100 traits were identified,including INPP4 B,TBC1D19,PLAC8,TSPAN9,ZFP36L2,KCTD8,ENSSSCG00000045684 and ENSSSCG00000048820.A total of 10 candidate genes that may be related to Duroc’s BT100 traits were identified,including ACAD9,CHCHD6,CHGA,PLAGL1,DOCK3,ABCG1,TEX264,RAD54L2,CACNA2D2 and ENSSSCG00000039042.In conclusion,two growth traits of Duroc pigs were selected as the research objects in this study.Firstly,a reference population for growth traits of Duroc pigs was established by using genomic selection techniques.Then different methods were used to estimate the genetic parameters of the population,and the selection effects of different calculation models on Duroc growth traits were evaluated.Finally,GWAS was studied for the growth traits and the associated SNP sites and candidate genes were found.This study not only contributes to the research on genetic progress and genetic mechanism of Duroc growth traits,but also has important reference value for the establishment of demutualization genomic selection breeding system in China.