Research On The Polymorphisms Of SNPs And Relationship With The Reproductive Traits Of Xiang Pig

Xiang pig is a rare miniature pig breed in C hina. Compared with the Large White and Rongchang pigs, Xiang pig presents specific physiology characteristics in reproduction, such as low litter size and early sexual maturity. However, the regulatory mechanism of low reproduction rate in Xiang pig is still remained to be clear. Based on the data of porcine 60 K SNP chip, the present paper focused on candidate single nucleotide polymorphism(SNP) loci related to reproductive traits in Xiang pig using the whole genome association analysis( GWAS). The six candidate SNP loci of reproductive traits(ASGA0076852, M1GA0008617, ASGA0020493, DIAS0003365, H3GA0056106, ALGA0115838) were validated by allele-specific PCR(AS-PCR) method in a large sample groups. The results obtained are as following:1. ASGA0076852 polymorphic loci ASGA0076852(rs80839320) is located in the third intron of glutathione synthetase(GSS) gene. Genotype frequencies of Rs80839320 site was significantly different in Xiang pigs with large and small litter size(P<0.01). The genotypes of rs80839320 were weak negative correlated with the litter sizes of Xiang pig at the second and third parities. The results revealed that the genotypes of rs80839320 were much diverse in six pig breeds. Compared with the six pig breeds: the frequencies were significantly higher in allele A of Xiang pig than that of Nuogu, Q ianbei black and Large White pigs(P<0.01). The frequencies were significantly lower in allele A of Kele pig than that of N uogu pig(P<0.01), Q ianbei black pig(P<0.05). The frequencies were significantly higher in allele A of Nuogu, Q ianbei black pigs than that of Rongchuang and N uogu pigs(P<0.01).2. M1GA0008617 polymorphic loci M1GA0008617(rs81388211) is located in intergenic. It was significantly higherfor the frequencies of allele D in Xiang pigs with large litter size than that in small litter size(P<0.01). The genotypes of rs81388211 were weak positive correlated with the litter sizes at the second and third parities. It revealed that the genotypes of rs81388211 were much diverse in six pig breeds. Compared with the six pig breeds, the frequencies were significantly higher in allele C of Large White pig than that of other five pig breeds(P<0.01). The frequencies were significantly lower in allele D of Rongchuang pig than that of Kele, Xiang pigs(P<0.01) and Q ianbei black pig breeds(P<0.05). The difference was not distinct between the other breeds besides Large White and Rongchang pig(P>0.05).3. ASGA0020493 polymorphic loci ASGA0020493(rs80951600) is located in the third exon of T-box 19(TBX19) gene. single nucleotide mutation C/T at site Rs80951600 resulted in missense mutation with residues substitution from Thr to Ala. Rs80951600 genotypes were different between Xiang pig with large and samll litter sizes(P = 0.073, closed to 0.05). The genotypes of rs80951600 showed weak positive correlation with the litter sizes at the second and third partities. It revealed that diverse genotype at site rs80951600 distributed among six pig breeds. Compared with the six pig breeds, the frequencies were significantly higher in allele E of Large White pig than that of other five pig breeds(P<0.01). The frequencies were distinctly lower in allele E of Rongchang pig than that of N uogu and Q ianbei black pigs(P<0.01). The frequencies were distinctly higher in allele E of Kele pig than that of N uogu and Q ianbei black pigs(P<0.01). The frequencies were distinctly lower in allele E of Xiang pig than that of N uogu pig(P<0.05).4. DIAS0003365 polymorphic loci Site DIAS0003365(rs81213998) located at exon18 of muskelin 1( intracellular mediator containing kelch motifs,MK LN1) gene. There was not different between the frequencies of allele E in in Xiang pigs with large and small litter size(P>0.05). The genotypes of site rs80951600 showed no correlation with the litter sizes at the secondand third birthes. The results showed that the genotypes of rs81213998 were much different among four pig breeds. The frequencies were significantly higher in allele C and lower in allele H of Xiang pig than that of Kele, N uogu and Q ianbei black pigs(P<0.01). The difference was not distinct between the other breeds besides Xiang pig(P>0.05).5. H3GA0056106 and ALGA0115838 loci Both of H3GA0056106(rs81320066) and ALGA0115838(rs81345180) are located in intergenic regions. It was much close each other between the frequencies of allele J and K in Xiang pig with large and small litter size groups(P>0.05).In summary, both of sites ASGA0076852 and M1GA0008617 might be the minor SNP site related to the reproduction of Xiang pig, site ASGA0020493 might contain some information of evolution for pig breeds, and site DIAS0003365 might related to the growth performance of pig breeds.