Detection And Analysis Of Eight Structural Variations In Indigenous Pig Breeds

Guizhou has a wealth of indigenous pig breed resources,and the low fecundity seriously affects the development of breeding industry.However,the molecular mechanism of how to regulate reproductive traits is not clear.In this study,eight structural variations which screened out from the resequencing results based on platform Hiseq 2000 were taken as the research object.To confirm the structural variations,the genotypes were detected by PCR method in seven pig breeds?Xiang,Kele,Nuogu,Jiangkouluobo,Qianbei black,Rongchang and Yorkshire pigs?.In addition,the Xiang pig litter size of different genotypes in the eight SVs and transcript preference of four SVs in heterozygous individuals were analyzed.The main conclusions were as follows:1. The deletion of IBSP-I₄-sv227 was 227 bp,which located in intron 4 of IBSP gene.DD,ID and II genotypes were found in seven pig breeds.The highest frequency of D allele was in Xiang pig?0.939?and the lowest in Yorkshire pig?0.291?,and which in six indigenous pig breeds was significantly higher than that in Yorkshire pig?P<0.01?.What's more,there was no II genotype in the high production group of Xiang pigs,and the distribution of genotypes was significant difference between high and low production groups?P=0.037?,but no difference in allele frequency?P=0.783?.Furthermore,the three litter sizes of DD and ID samples were more 0.58 to 1.06 and 0.88 to 1.90 than NN,respectively.2.The deletion of NBEA-I₃₂-sv366 was 366 bp,and located in intron 32 of NBEA gene.The dominant genotype was II in seven pig breeds,However,the three genotypes only found in Xiang pig,Nuogu pigs were detected by II,and other five pig breeds were ID and II genotypes.The allele frequency in high and low production groups of Xiang pigs showed no significant difference?P>0.05?.Aditional,in the third litter size of Xiang pig,the ID and II were more 1.04 and 0.85 than DD,respectively.There were two transcripts in heterozygous ID genotype pigs.3.The D allele of MCU-I₁-sv433 was deleted 433 bp,which located in the intron 1 of the MCU gene.DD and ID genotypes were mainly in Xiang pig,but ID and II were dominant among the other six pig breeds.The highest frequency of D allele was Xiang pigs,Which was significantly higher than that of the other six pig breeds?P<0.01?.However,there were no significant differences in allele frequencies between high and low production groups and in the three litter sizes of Xiang pigs among different genotypes.But the major transcript in the heterozygous ID genotype pigs was from D allele.4.The D allele of MELK-I₁₄-sv252 was deleted 252 bp,and located in intron 14 of MELK gene.There were no NN genotype in Xiang and Nuogu pig breeds.The ID genotype was dominant in Xiang,Nuogu and Rongchang pig breeds,but in Qianbei black pig was ID.The highest frequency of D allele was in Xiang pig?0.966?.However,the genotype and allele frequency distribution of the high and low production groups of Xiang pigs were similar,and the three litter sizes was no difference among different genotypes.5.The MSH4-I₆-sv313 was deleted 313 bp,which located in intron of MSH4 gene,only DD and ID genotypes were detected in Rongchang pigs,and the other six pig breeds were found three genotypes.The frequency of D allele in Rongchang pig was the highest?0.976?,and the lowest in Kele pig?0.472?.The allele frequency among high and low production groups showed no significant difference?P>0.05?.But in the second litter size,DD was more0.06 than II,and in third,the ID and II were more 1.04 and 0.85 than DD,respectively.Furthermore,the major transcript in the heterozygous ID genotype pigs was from D allele.6.The deletion of MMP15-I₅-sv155,155 bp,was located in intron 5 of MMP-15 gene.The mainly geneotypes in six indigenous pig breeds were DD and ID,but in Yorkshire pig were ID and II.In addition to Qianbei black pigs,the deletion?D allele?frequency in other five breeds was significantly higher than Yorkshire pig?P<0.01?.Nevertheless,the allele frequency among high and low production groups of Xiang pig was no difference,and the litter size between different genotypes also showed no difference.7.The deletion 106 bp of PICK1-I₄-sv106 was located in intron 4 of PICK1 gene,of which the D allele frequency in Rongchang pig was significantly higher than the other six Pig breeds?P<0.01?,but among high and low production groups of Xiang pig had no difference,and the three litter sizes is consistent between the three genotypes.8.The deletion 294 bp of BMP6-I₁-sv294 was located in intron 1 of BMP-6 gene.The lowest frequency of D allele was in Yorkshire pig?0.104?,which was significantly lower than that of the other six breeds?P<0.01?.And the genotypes distribution between high and low-yield groups of Xiang pigs was significant difference?P=0.003?,but allele frequency was no difference?P=0.561?.In the second litter size of Xiang pig,genotype ID was more 0.07 than DD.What's more,There were two transcripts in heterozygous individuals.In summary,IBSP-I₄-sv227 and NBEA-I₃₂-sv366 could be used as breeding molecular markers for Xiang pig;MCU-I₁-sv433 can be used as a auxiliary molecular marker to identify Xiang pig.Except for Qianbei black pigs,MMP15-I₅-sv155 and IBSP-I₄-sv227 could be taken as molecular markers to distinguish the five indigenous pig breeds from Yorkshire pig.In addition,it was confirmed that the major transceipt in the heterozygous pigs of MCU-I₁-sv433 and MSH4-I₆-sv313 was from D allele but not detected from I allele.And this data inferred that the deletions positively regulated the expression of MCU and MSH4 genes.