母猪初情期全基因组关联分析和位置候选基因研究

Genome-Wide Association Study and Positional Candidate Gene Analysis on Age at Puberty of Gilts

【目的】分离影响母猪初情期的主效基因或分子标记。【方法】以白色杜洛克×二花脸资源群体F2代母猪为研究材料,利用Illumina猪60K SNP芯片分别对F0和F1及316头有初情期表型记录的F2代母猪进行基因型判定,通过单标记全基因组关联分析(GWAS)和连锁-连锁不平衡(LDLA)分析检测与母猪初情期显著关联的SNP位点或单倍型。采用标准关联分析、标记辅助关联分析和F值下降检验分析lin-28同源B基因(LIN28B)和跨膜蛋白38B基因(TMEM38B)3个SNP位点与母猪初情期的关联性。【结果】①与母猪初情期关联性最强的SNP为ASGA0032316,位于7号染色体(SSC7)33.07 Mb处RAB23基因内含子中,同时在1、6、12、15和17号染色体也检测到与母猪初情期显著关联的SNP;②达基因组显著水平的单倍型均位于SSC7,其中关联性最强的单倍型位于SSC7的38.39-38.47 Mb处F1RVR7和ZFAND3基因之间的基因间隔区;③LIN28B和TMEM38B基因的3个SNP与母猪初情期均未达到显著相关(P>0.05)。【结论】在白色杜洛克×二花脸资源群体中,与母猪初情期关联性最强的SNP位点和单倍型均定位于7号染色体,1、6、12、15和17号染色体也定位到与母猪初情期显著关联的SNP,LIN28B和TMEM38B基因不是1号染色体QTL区间内的因果基因或需要搜寻更多的SNP进行分析验证。

[Objective] Isolation and characterization of the causative gene or molecular marker for age at puberty will contribute to the selection and breeding of sows. [Method] The materials used in this study were F2 gilts from a white Duroc x Erhualian F2 resource population. F0, F1 and 316 well phenotyped F2 gilts were genotyped with Illumina porcine 60K SNP chip. Genome-wide association study （GWAS） and linkage and linkage-disequilibrium analysis （LDLA） were carried out to detect SNPs or haplotypes that were significantly associated with age at puberty of gilts. The associations of 3 SNPs within two candidate genes of Lin-28 Homolog B （LIN28B） and Trans-membrane Protein 38B （TMEM38B） with age at puberty of gilts were evaluated by standard association test, marker-assisted association test and F-drop test. [Result] The results from GWAS showed that the ASGA0032316 was the most significant SNP that was associated with age at puberty. It is located at 33.07 Mb of pig chromosome 7 （SSC7） and exactly within the intron region of RAB23. At the same instant, several significant ShiPs were also detected on chromosomes 1, 6, 12, 15 and 17. The results from LDLA analysis showed that all haplotypes that were associated with age at puberty at genome-wide significance level were located on SSC7. The most significant haplotype was located at 38.39-38.47 Mb and within the intergenic region of F1RVR7 and ZFAND3. In association analyses of positional candidate genes, although 3 SNPs from LIN28B and TMEM38B were significantly associated with age at puberty in standard association test （P〈0.05）, it was not achieved significance level both in the marker-assisted association test and F-drop test （P〉0.05）. [Conclusion] The SNP and haplotype that were most significantly associated with age at puberty of gilts was detected on SSC7. Several other significantly associated SNPs were also detected on chromosomes 1, 6, 12, 15 and 17. The results from association tests suggested that LIN28B or TMEM38B gene on SSC1 is not the quantitative trait gene for age at puberty, or more SNPs from two genes need to be fiLrther analyzed.