| Reproductive traits of sows are important economic traits which largely determine the economic benefits of breeding farms.However,the reproductive traits are quantitative traits with low heritability(h2=0.05-0.15)controlled by multiple genes.The combination of molecular marker-assisted selection(MAS)and conventional breeding methods can improve the selection accuracy of reproductive traits and accelerate the progress of breeding.Therefore,it is important for breeders to screen out molecular markers related to litter size and nipple number of sows.In the present study,DNA samples from 485 Large white and 290 Bama-Xiang pig were used to screen SNP locus distributed in 13 candidate genes(ESR1,EPOR,VEGFA,DPPA5,RBP4,PRLR,OPN,PTGS2,IGFBP1,IGFBP2,FUT1,LIF,LEPR)and the correlation between SNP sites and reproductive traits of Bama Xiang pigs and large white pigs was analyzed.The results obtained were showed as follow:1.The average litter size of large white(LW)pigs(13.59 ± 3.15)was significantly higher than that of Bama Xiang(BX)pigs(9.60 ± 2.00)(P <0.001).2.A total of 50 SNP sites were screened from 13 candidate genes by using sequencing analysis of PCR products from sample DNA mixed pool.Furthermore,multiple PCR and next-generation sequencing technology was used to verify individuals genotype,and a total of 68 SNP sites were detected in two breeds.A total of 64 SNP loci were detected in the BX pig,including 35 low polymorphic SNPs and 29 moderate polymorphic SNPs;58 SNPs were in Hardy-Weinberg equilibrium and the other 6 SNPs were in unequilibrium state.A total of 36 SNP sites were detected in LW pigs,including 10 low polymorphic SNPs and 26 moderate polymorphic SNPs;29 SNPs were in Hardy-Weinberg equilibrium state,and the other 6 SNPs were in unequilibrium state.3.The association analysis results of SNP loci with the litter size and teat traits were showed as follow:(1)ESR1 rs14295786A>C locus was significantly correlated with litter size of the 2nd,4th,6th parity and average litter size of six parities(ALSP)in BX pigs(P<0.05),the litter size of AA genotype increased 0.860 compared with CC genotype.No significant association was found between the SNP and litter size in LW.(2)Five and three SNPs in DPPA5 gene were found in BX and LW,respectively.However,only g:52987170C>A locus was found to associate significantly with the litter size of the 3rd,4th,5th,6th and ALSP in BX pigs(P<0.05).(3)Eight and five SNP loci in EPOR gene had significant relation with the ALSP in BX and LW pig,respectively.(4)Two of three SNPs in LEPR gene were significantly related with the ALSP in BX P<0.05)and homozygous mutant pig had a trend to decrease the litter size in each parity.No significant association was found between the SNP and litter size in LW.(5)A total of 8 SNPs in VEGFA gene were detected in BX and LW pig,most of SNPs were significantly associated with litter size of each parity and ALSP(P<0.05)in BX pig,and only 4 SNPs were significantly associated with litter size of ALSP in LW.(6)Three and two SNPs in OPN gene were detected in BX and LW pig,respectively.The homozygous mutant of 3 SNPs had a decreased litter size in each parity,and the homozygous mutant pig of 2 SNPs showed significantly small ALSP in BX pig.No homozygous mutant pig was found in LW and the mutant heterozygote showed a trend to decrease the litter size in each parity.(7)PTGS2 rs81219156C>T locus was significantly correlated with the ALSP in LW(P<0.05)and TT genotype had 0.23 more teat number compared with CC genotype in BX pig(P<0.05).(8)No significant association between SNP locus in RBP4 gene and litter size in BX and LW pig(p>0.05).However,the RBP4 rs702101190C>A and s55618789 C>T loci were significantly related with the teat number in BX pig(P<0.05).(9)The IGFBP2 rs1112268627T>C locus was significantly associated with the litter size of 3rd,4th,6th and ALSP in BX pig,and the T locus was a favorable alleles in BX but a unfavorable alleles in LW pig.(10)Four SNPs in IGFBP1 gene detected in LW pig were formed a linkage module which showed relationship with the litter size.The homozygous mutant pig had a increased litter size in each parity and the 5th parity litter size of mutant homozygotes increased by 2.32 compared with wild homozygotes(P<0.05).4.The results of linkage disequilibrium and haplotype analysis showed that there were 9 haplotypes in BX pig,and the correlation between H1,H3,H4,H5,H6,H7,H8,H9 and litter size was significant(P < 0.05).H6 haplotype showed significant relationship with teat number in BX pig(P<0.05).Six haplotypes were found in LW pigs,and the correlation between H2,H3,H4 haplotypes and litter size was significant(P < 0.05). |
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