Genome-wide Association Studies For Important Economic Traits In Pure Lines Of Xushan Chickens

Carcasses and egg production are important economic traits in poultry production.Exploring genetic variation sites and candidate functional genes related to target traits,and implementing precise molecular breeding can improve the breeding efficiency.In this study,genetic parameter estimation and genome-wide association study(GWAS)were performed on the carcass traits of Xushan chicken D line and egg laying traits of Xushan chicken F line.(1)Analysis of genetic parameters and GWAS of carcass traits of Xushan chicken D lineThe study was conducted on the Xushan chicken D line,Jiangsu Lihua Animal Husbandry Company,with 150 males and 150 females,and collected 90-day-old carcasses and internal organ-related phenotypes.The resequencing technology was used for genotyping and quality control on experimental individuals.A total of 298 valid individuals,7882695 SNPs loci were involved in subsequent genetic parameter estimation and GWAS analysis.The DMU software was used to estimate the genetic parameters of 11 external carcass traits.The results showed that the weight(BW),carcass weight(CW),carcass weight percentage(CWP),total eviscerated weight(EW),and total eviscerated weight percentage(EWP),breast muscle weight(BMW),breast muscle weight percentage(BMWP).leg muscle weight(LMW),leg muscle weight percentage(LMWP),paw weight(PW),and paw weight percentage(PWP)were 0.40,0.40,0.42,0.37,0.36,0.29,0.33,0.31 and 0.34 respectively.There were high genetic correlations between BW,CW,EW.BMW,LMW and PW,with a correlation coefficient between 0.31 and 0.98.The heritability of liver rate(LP),heart rate(HP),spleen rate(SP),lung rate(LuP),muscle stomach rate(GsP),and glandular stomach rate(PsP)were 0.27,0.33,0.32,0.29,0.38 and 0.44 respectively.GWAS analysis was performed on the above 17 traits by using GEMMA software.A total of 41 significant SNP loci were found to correlate with external slaughter traits.And these loci explained 1.64 to 3.23%of the phenotypic variation respectively.The annotation of significant SNP loci revealed that SLIT2,KCNIP4,PHF14,NDUFA4,M6PR,and SLITRK6 may be related to external slaughter traits.A total of 11 significant SNP loci were found to be related to the aforementioned organ indexes.These loci explained 0.98 to 3.28%of the phenotypic variation respectively.It was found by annotated that FAM105A,DEUP1,HEPHL1,PP4R1,TRIM,LGR6 and STX19 were related to the immune and Metabolic,which is worthy of further study.(Ⅱ)Analysis of genetic parameters and egg production traits of F-line egg laying traits in Xushan chickensThe research object of this experiment is the Xueshan Chicken F line from Jiangsu Lihua Animal Husbandry Co.，Ltd.The phenotypes of 60-week-old egg-laying traits of three generations were collected.We used 50K chip technology for genotyping and quality control in 2,000 individuals from 3 generations.And there were a total of 1996 valid individuals,and 37,838 SNPs loci were involved in subsequent genetic parameter estimation and GWAS analysis.The DMU software was used to estimate the genetic parameters of the eight egg-laying traits.The results showed that the heritability based on genealogy of malformed eggs(ME),broken eggs(BK),soft-shell eggs(SS),sand-shell eggs(CD),defective eggs(DE),age at start of egg(AFE),number of qualified eggs(QE),and total number of eggs(EN)were 0.013,0.0056,0.015,NA,0.016,0.11,0.027,0.033 respectively;the genomic-based heritability of them were 0.0085,NA,0.030,NA,0.030,0.14,0.11,0.14 respectively.There were extremely significant genetic correlations among ME,BK,SS,CD,and DE traits and the correlation coefficient is 0.076～0.72.There were weakly negative genetic correlations between AFE,QE and EN,the correlation coefficients were-0.058 and-0.061;and there was an extremely significant positive genetic correlation between QE and EN,with a correlation coefficient of 0.97.GWAS analysis was performed on the above eight traits using GEMMA software.40 significant SNP loci were found to be associated with egg laying traits,which explained 0.89 to 3.12% of the phenotypic variation,respectively.Annotation of significant SNP loci revealed that multiple candidate genes including ENTPD3,NOD1 and PRL14 may be related to egg production traits.These genes are involved in biological pathways such as immunity,reproduction and growth of the body.It is worth of further research.The above research results provide valuable theoretical basis for further identifying the key genes of carcass and egg-laying traits and improving the accuracy of chicken genome selection and breeding.