Screening Genes Related To Reproductive Trait Based On SNP Of Whole Genome Of Pig

The swine reproductive performance is of great significance to the improvement of PSY and the economic benefit.The heritability of sow reproductive performance is about 0.1.And the sow reproductive performance is a quantitative trait of low heritability.It is hard to acquire genetic progress for quantitative trait with low heritability through traditional genetic methods.Conducting marker assisted selection with the utilization of SNP can improve the genetic progress of quantitative trait with low heritability.Resequencing data is consisted of SNPs of 31 pigs which is produced by our own lab.Pig Var data is consisted of SNPs of whole genome of 60 pigs downloaded from Pig Var database.SNPs with significant difference are detected through Chi square test and T test.Gene names of SNPs with significant difference are acquired through gene annotation.GO,KEGG pathway and Gene network analyses are conducted for the genes.NCBI is used to analysis the function of genes.Then the genes possibly related to fertility is acquired.There are 9,156,138 SNPs in resequencing data.43,072 SNPs with extremely significant difference(P <0.01)are acquired through Chi square test.2,412 genes are acquired through gene name annotation for the 43,072 SNPs.95,040 SNPs with extremely significant difference(P <0.01)are acquired through T test.4,132 genes are acquired through gene name annotation for the 95,040 SNPs.13 genes possibly related to reproductive performance are acquired in the resequencing data after the analyses of Chi square test and T test.BMP7,ESR1,PRLR and BMPR1 B are genes related to fertility and covered in literature in the 13 genes.ITPR1,EGFR,ROCK2,FOXO3,LEP,JAK2,MAPK3,PIK3 CA and SMAD3 are novel genes possibly related to reproductive performance in the 13 genes.5.77 Gb SNPs are acquired in Pig Var data.1,505,016 SNPs with significantdifference(P <0.05)are acquired through Chi square test.11,121 genes are acquired through gene name annotation for the 1,505,016 SNPs.488,155 SNPs with extremely significant difference(P <0.01)are acquired through T test.7,897 genes are acquired through gene name annotation for the 488,155 SNPs.26 genes possibly related to reproductive performance are acquired in Pig Var data.ESR1,PRLR,BMP7,RARG,NCOA1,ADAMTS1,ITGB1 and BMPR1 B are genes covered in literature in the 26 genes.SMAD4,ITPR1,IGF1,MAPK1,MMP2,PIK3 CG,PRKACA,ROCK2,BMPR1 A,SMAD2,EP300,SHH,FOXO3,CDK2,FLT1,GHRL,LEP and SRC are novel genes possibly related to reproductive performance in the 26 genes.31 genes possibly related to reproductive performance are acquired in this research after the analyses of resequencing data and Pig Var data.RARG,ESR1,PRLR,NCOA1,BMPR1 B,BMP7,ADAMTS1 and ITGB1 are genes covered in literature in the 31 genes.SMAD4,ITPR1,IGF1,MAPK1,MMP2,PIK3 CG,PRKACA,ROCK2,BMPR1 A,SMAD2,EP300,SHH,FOXO3,CDK2,FLT1,GHRL,LEP,SRC,EGFR,JAK2,MAPK3,PIK3 CA and SMAD3 are novel genes possibly related to reproductive performance in the 31 genes.SMAD4,PIK3 CG,MAPK1,ITPR1,MMP2,IGF1,CDK2,FLT1,GHRL,SHH,ROCK2,LEP and EGFR are the genes which may have the potential to improve litter size.PRKACA and FOXO3 are the genes which may reduce litter size.Gn RH signaling pathway,Estrogen signaling pathway,Oxytocin signaling pathway,Prolactin signaling pathway,Progesterone-mediated oocyte maturation,Oocyte meiosis and Ovarian steroidogenesis are pathways possibly related to reproductive performance.JAK2,PRLR,LEP,PRL and LEPR have interaction relationship.BMPR1 B,BMP7 and SMAD3 have interaction relationship.MAPK3,PIK3 CA and ESR1 have interaction relationship.SMAD2,SMAD4,BMPR1 B and BMPR1 A have interaction relationship.