Study On The Polymorphisms Of SNPs And The Relationships With The Growth Traits Of Xiang Pig

Congjiang Xiang pig is a rare miniature pig breed in China. Compared with other breeds, it is not only slow in growth, but also small in length. However, the mechanism of slow growth trait is still remained to be clear. The present paper focused on the genetic polymorphism investigation in Congjiang Xiang pig using Allele specific amplification PC R method(AS-PCR) and Illumina Porcine SNP60(60K) chips. The results were as following:1. The single nucleotide polymorphisms in genome wide of Xiang pig were detected by Illumina Porcine SNP60 chips. After strict quality control, 13 SNPs were deduced to be correlated with the body length trait of Xiang pig by genome-wide association analysis(GWAS) approach. Six SNPs, which were ALGA0105966, ALGA0059836, ASGA0106099, ASGA0016323, MARC0036889 and ASGA0084095, were verificated by AS-PCR method. It demonstrated that the AS-PCR method could be used for further SNP detection in a large pig populations.2. All of 6 SNP sites were genotyped in six different pig breeds, including Xiang, Q ianbei black, Kele, Nuogu, Rongchang, and Yorkshire pig breeds, by AS-PCR method. The correlation between the SNPs polymorphism and the body measurement sizes of Xiang pig were further analyzed. The results indicated that the SNP site ALGA0105966 located in podocalyxin(PODXL) gene and possessed polymorphism in six pig breeds. Homozygous AA genotypes were dominant in Xiang, Kele and Rongchang pigs with a higher frequency in allele A(P<0.01). Heterozygous AG genotypes were higher in Q ianbei black, N uogu and Yorkshire pig breeds without difference between frequencies of allele A and G(P>0.05). Based on correlation analysis, it revealed that the genotypes of locus ALGA0105966 showed a weak negative correlationship with the eight body measurement indexes, body height, body length, and abdominal girth in Large Xiang, 12 month old Xiang, and 24 month old Xiang pigs. ALGA0059836 is located in intergenic and possessed polymorphism. Homozygous CC genotypes were dominant in six pig breeds with a higher frequency in allele C(P<0.01). Based on correlation analysis, it revealed that the genotypes of locus ALGA0059836 showed a weak positive or negative correlationship with the body height, body length, body width, chest, tube circumference, weight, and the abdominal girth in Large Xiang, 12 month old Xiang, and 18 month old Xiang pigs. ASGA0106099 is located in intergenic and possessed polymorphism in six pig breeds. Homozygous GG genotypes were dominant in Xiang, Nuogu and Rongchang pigs with a higher frequency in allele G(P<0.01). Heterozygous AG genotypes were higher in Kele, Q ianbei black and Yorkshire pig breeds without difference between frequencies of allele A and G(P>0.05). Based on correlation analysis, it revealed that the genotypes of locus ASGA0106099 showed a weak positive correlationship with the weight and body width in Large Xiang and 18 month old Xiang pigs. A SNP site MARC0036889 located in intergenic and possessed polymorphism in six pig breeds. Heterozygous AG genotypes were higher in Xiang, Kele, and Rongchang pig breeds without difference between frequencies of allele A and G(P>0.05). Homozygous GG genotypes were dominant in Nuogu, Q ianbei black, and Yorkshire pigs with a higher frequency in allele G(P<0.01). Based on correlation analysis, the genotypes of MARC0036889 showed no correlation with the body measurements indexes in Xiang pig. ASGA0016323 is located in intergenic and possessed polymorphism in six pig breeds. Homozygous CC genotypes were dominant in 18 month old, 24 month old Xiang pigs,and other five pig breeds with a higher frequency in allele C(P<0.01). It showed no correlationship with the body measurements indexes. A SNP site ASGA0084095 located in FAT3 gene in six pig breeds. Heterozygous AG genotypes were higher in six pig breeds without difference between frequencies of allele A and G(P>0.05).3. The mi RNA expression level of ssc- mi R-4331 was detected by RT-q PCR method, which is predicted at 18000 bp upstream of ASGA0106099 locus. The results infered that ssc- mi R-4331 did express in muscle of Xiang pig, but it might not transcripted from the upstream of ASGA0106099 locus on the chromosome 2 of Xiang pig.All of the SNP sites were worth for further investigation for the function and would be helpful for the protection and usage for native pig breeds.