Department of Agro-Food Science and Technology, Sezione di Allevamenti Zootecnici, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.
J Anim Sci. 2012 Aug;90(8):2450-64. doi: 10.2527/jas.2011-4797. Epub 2012 Feb 24.
Combining different approaches (resequencing of portions of 54 obesity candidate genes, literature mining for pig markers associated with fat deposition or related traits in 77 genes, and in silico mining of porcine expressed sequence tags and other sequences available in databases), we identified and analyzed 736 SNP within candidate genes to identify markers associated with back fat thickness (BFT) in Italian Large White sows. Animals were chosen using a selective genotyping approach according to their EBV for BFT (276 with most negative and 279 with most positive EBV) within a population of ≈ 12,000 pigs. Association analysis between the SNP and BFT has been carried out using the MAX test proposed for case-control studies. The designed assays were successful for 656 SNP: 370 were excluded (low call rate or minor allele frequency <5%), whereas the remaining 286 in 212 genes were taken for subsequent analyses, among which 64 showed a P(nominal) value <0.1. To deal with the multiple testing problem in a candidate gene approach, we applied the proportion of false positives (PFP) method. Thirty-eight SNP were significant (P(PFP) < 0.20). The most significant SNP was the IGF2 intron3-g.3072G>A polymorphism (P(nominal) < 1.0E-50). The second most significant SNP was the MC4R c.1426A>G polymorphism (P(nominal) = 8.0E-05). The third top SNP (P(nominal) = 6.2E-04) was the intronic TBC1D1 g.219G>A polymorphic site, in agreement with our previous results obtained in an independent study. The list of significant markers also included SNP in additional genes (ABHD16A, ABHD5, ACP2, ALMS1, APOA2, ATP1A2, CALR, COL14A1, CTSF, DARS, DECR1, ENPP1, ESR1, GH1, GHRL, GNMT, IKBKB, JAK3, MTTP, NFKBIA, NT5E, PLAT, PPARG, PPP2R5D, PRLR, RRAGD, RFC2, SDHD, SERPINF1, UBE2H, VCAM1, and WAT). Functional relationships between genes were obtained using the Ingenuity Pathway Analysis (IPA) Knowledge Base. The top scoring pathway included 19 genes with a P(nominal) < 0.1, 2 of which (IKBKB and NFKBIA) are involved in the hypothalamic IKKβ/NFκB program that could represent a key axis to affect fat deposition traits in pigs. These results represent a starting point to plan marker-assisted selection in Italian Large White nuclei for BFT. Because of similarities between humans and pigs, this study might also provide useful clues to investigate genetic factors affecting human obesity.
我们综合采用了多种方法（对 54 个肥胖候选基因的部分序列进行重测序、对与脂肪沉积或 77 个基因相关性状相关的猪标记进行文献挖掘、对猪表达序列标签和数据库中其他序列进行计算机挖掘），鉴定并分析了候选基因中的 736 个 SNP，以鉴定与意大利大白母猪背部脂肪厚度（BFT）相关的标记。根据其背部脂肪厚度的 EBV（276 个最负向 EBV，279 个最正向 EBV），在约 12000 头猪的群体中，我们使用选择性基因分型方法选择了动物。利用 MAX 检验对 SNP 与 BFT 之间的关联进行了分析，该检验专为病例对照研究而设计。设计的检测方法在 656 个 SNP 中取得了成功：370 个 SNP 被排除（低呼叫率或次要等位基因频率<5%），而其余 286 个 SNP 位于 212 个基因中，用于后续分析，其中 64 个 SNP 的 P(nominal)值<0.1。为了处理候选基因方法中的多重检验问题，我们应用了假阳性比例（PFP）方法。38 个 SNP 具有统计学意义（P(PFP)<0.20）。最显著的 SNP 是 IGF2 内含子 3-g.3072G>A 多态性（P(nominal)<1.0E-50）。第二个最显著的 SNP 是 MC4R c.1426A>G 多态性（P(nominal)=8.0E-05）。第三个最显著的 SNP（P(nominal)=6.2E-04）是位于内含子的 TBC1D1 g.219G>A 多态性位点，与我们之前在独立研究中获得的结果一致。显著标记的列表还包括其他基因中的 SNP（ABHD16A、ABHD5、ACP2、ALMS1、APOA2、ATP1A2、CALR、COL14A1、CTSF、DARS、DECR1、ENPP1、ESR1、GH1、GHRL、GNMT、IKBKB、JAK3、MTTP、NFKBIA、NT5E、PLAT、PPARG、PPP2R5D、PRLR、RRAGD、RFC2、SDHD、SERPINF1、UBE2H、VCAM1 和 WAT）。使用 IPA 知识库（Ingenuity Pathway Analysis）获得了基因之间的功能关系。得分最高的途径包括 19 个 P(nominal)<0.1 的基因，其中 2 个（IKBKB 和 NFKBIA）参与了下丘脑 IKKβ/NFκB 程序，这可能代表了影响猪脂肪沉积性状的关键轴。这些结果为计划在意大利大白猪核心群体中进行 BFT 的标记辅助选择提供了一个起点。由于人类和猪之间的相似性，这项研究也可能为研究影响人类肥胖的遗传因素提供有用的线索。
