香猪基因组外显子SNPs检测及繁殖和体型性状候选基因分析

为从基因组水平上探究香猪性成熟早、产仔数少、体型小的分子机理，本研究下载与香猪在繁殖和体型性状方面有明显差异的梅山猪、杜洛克猪的重测序数据作为参照，对26头香猪、24头梅山猪和24头杜洛克猪的重测序数据进行SNPs检测和等位基因频率差值分析，筛选香猪基因组外显子上与梅山猪、杜洛克猪高度分化的SNPs位点，并使用AS-PCR方法和Sanger测序方法统计其中8个SNPs位点的群体等位基因频率。最后，对含有高度分化SNPs位点的基因进行GO功能富集和KEGG通路分析。结果显示，SNPs检测获得香猪基因组外显子上SNPs共236 710个，包括193个终止密码子丢失、1 238个终止密码子获得、90 945个错义SNPs和144 334个同义SNPs。得到1 046个香猪高度分化SNPs，包括429个错义SNPs、2个终止子丢失、6个终止子获得和609个同义SNPs，影响524个蛋白质编码基因；并发现X染色体上44-58 Mb的一段富含高度分化SNPs的热点区域。群体等位基因频率验证结果与重测序结果一致，鉴定了8个位点均为香猪与梅山猪、杜洛克猪高度分化的SNPs。对524个含有高度分化SNPs的基因进行GO和KEGG分析，富集到卵母细胞减数分裂、雌激素信号途径等繁殖相关通路；GO功能注释到细胞内雌激素受体信号、纤毛运动等繁殖相关条目，骨骼系统形态发生、骨骼发育、成骨细胞分化等体型相关条目。得到含有香猪高度分化SNPs的18个繁殖性状候选基因PTGFR、TRO、DNAH17、PKDREJ、KAT8、DNAI2、VDR、TEX14、QSOX1、AR、WNK3、ADCY3、SPEF1、MIGA2、SLC2A8、PSMF1、TBC1D20、IFT172和7个体型相关基因IBSP、NR6A1、HSPG2、TARS、PDZD2、FGF4、AMER1，可能是决定香猪性成熟早、产仔数少、体型小的关键基因。

Detection of Genome Exon SNPs and Analysis of Candidate Genes for Reproduction and Body Type Traits in Xiang Pig

In order to explore the molecular mechanism of early sexual maturity,low litter size and small body size of Xiang pig at the genomic level,we downloaded the re-sequencing data of Meishan pig and Duroc pig,which had obviously differences in reproduction and body-size as references.SNPs detection and allele frequency difference analysis were carried out on the re-sequencing data of 26 Xiang pigs,24 Meishan pigs and 24 Duroc pigs.The SNPs highly differentiated from Meishan pig and Duroc pig were detected by AS-PCR and Sanger sequencing.Finally,GO enrichment and KEGG pathway analysis were performed for genes with highly differentiated SNPs.The results showed that there were 236710 SNPs in exons of Xiang pig genome,including 193 of stoplosses,1238 of stopgains,90945 of nonsynonymous SNPs and 144334 synonymous SNPs.A total of 1046 highly differentiated SNPs were obtained,including 429 of nonsynonymous SNPs,2 of stoplosses,6 of stopgains and 609 of synonymous SNPs,which affected 524 protein coding genes,and a hotspot rich in highly differentiated SNPs in 44-58 Mb of X chromosome was found.The results of allele frequency verification in populations were consistent with the re-sequencing results.8 loci were identified as highly differentiated SNPs in Xiang pig from Meishan pig and Duroc pig.Analysis for the 524 affected genes through GO and KEGG classification,it enriched in the oocyte meiosis,estrogen signaling pathway,estrogen signaling pathway together with other reproduction-related pathways.GO terms were annotated to intracellular estrogen receptor signaling,cilia movement and other reproduction-related items,skeletal system morphogenesis,bone development,osteoblast differentiation and other body-related items.The 18 reproduction-related genes PTGFR,TRO,DNAH17,PKDREJ,KAT8,DNAI2,VDR,TEX14,QSOX1,AR,WNK3,ADCY3,SPEF1,MIGA2,SLC2A8,PSMF1,TBC1D20,IFT172 and 7 size-related genes IBSP,NR6A1,HSPG2,TARS,PDZD2,FGF4,AMER1 with highly differentiated SNPs of Xiang pigs were identified,which might be the key genes to regulate the early sexual maturity,small litter size and small body size of Xiang pigs.