浙江省3个地方猪种繁殖性状的全基因组关联分析  

Genome-Wide Association Study of Reproductive Traits in 3 Zhejiang Indigenous Pig Breeds

作　　者：阮鹏[1] 黄敏婕[1] 郭晓令[1] 徐宁迎 RUAN Peng;HUANG Min-jie;GUO Xiao-ling;XU Ning-ying(College of Animal Science,Zhejiang University,Zhejiang Hangzhou 315800,China)

机构地区：[1]浙江大学动物科学学院,浙江杭州310058

出　　处：《中国畜牧杂志》2018年第7期35-40,共6页Chinese Journal of Animal Science

基　　金：浙江省农业(畜禽)新品种选育重大科技专项(2016C02054-1)

摘　　要：本研究使用全基因组关联分析(GWAS)技术对嵊县花猪(SXHZ)、金华猪(JHZ)和淳安花猪(CAHZ)繁殖性状关联性强的SNP位点进行定位,寻找可能影响这些性状的基因。采集SXHZ 114头、JHZ 185头和CAHZ 31头血样制成干血斑样本,提取DNA将质检合格的样品用Illumina平台的GGP Porcine50K SNP芯片作基因型判定。繁殖性状数据来自各取样猪场。对SNP标记和样本进行质控,筛选合适数据作GWAS分析,定位出显著位点,在Ensembl和NCBI上寻找候选基因。结果表明:SXHZ独立GWAS有160个SNPs呈FDR校正水平显著;JHZ独立GWAS有124个SNPs呈FDR校正水平显著;经过META分析得到337个SNPs呈FDR校正水平显著,16个SNPs呈Bonferroni校正染色体水平显著;CAHZ的独立GWAS由于样本量小,初步分析的结果可靠性不高。初步筛选出SXHZ的候选基因为SEMA4D、EYA4、ZC3H12D、BANP、DIP2B和TUSC3;JHZ的候选基因为SPINK14、GRIP1和PPP3CA;META分析得出候选基因PACSIN2、ATP8A2、ZNF32、CTNNA2和FAT1,为进一步筛选繁殖性状的主效基因提供基础和参考。In this study,Single Nucleotide Polymorphism(SNP)sites of reproductive traits in Shengxian pigs(SXHZ),Jinhua pigs(JHZ)and Chun'an pigs(CAHZ)were analyzed by genome-wide association study(GWAS)to search for the genes which potentially affected these traits.114 SXHZ,185 JHZ and 31 CAHZ were genotyped using Illumina GGP Porcine SNP 50K BeadChip by dry blood spot.The data of reproductive traits was collected from pig farms.After quality control,the appropriate data were screen out for GWAS analysis and then significant loci were indentified to investigate candidate genes on Ensembl and NCBI.The results show that 160 SNPs were obtained significantly through FDR correction by SXHZ association analysis.124 SNPs were obtained significantly through FDR correction by JHZ association analysis.After META analysis,the results showed that 337 SNPs were detected significantly through FDR correction and 16 SNPs were detected significantly through Bonferroni correction at chromosome level.The independent GWAS analysis of CAHZ was not reliable because of small sample size.The candidate genes were determined preliminarily:SXHZ:SEMA4D,EYA4,ZC3H12D,BANP,DIP2B and TUSC3;JHZ:SPINK14,GRIP1 and PPP3CA;META:PACSIN2,ATP8A2,ZNF32,CTNNA2 and FAT1,the results provided the basis and reference for the subsequent work.

关 键 词：繁殖性状 GWAS META分析 FDR校正 Bonferroni校正 候选基因 

分 类 号：S828.2[农业科学—畜牧学]