Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America.
PLoS One. 2011 Feb 24;6(2):e14726. doi: 10.1371/journal.pone.0014726.
The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs.
METHODOLOGY/PRINCIPAL FINDINGS: Using Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages.
CONCLUSIONS/SIGNIFICANCE: This study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection.
最近完成的猪基因组测序项目和高密度猪 SNP 芯片的开发，使得在猪中进行全基因组关联（GWA）研究成为可能。
方法/主要发现：我们使用 Illumina 的 PorcineSNP60 BeadChip，在 820 头商业母猪中进行了一项先导性 GWA 研究，这些母猪的表型特征包括背膘、腰肉面积、身体结构以及脚部和腿部（FL）结构的健全性。使用贝叶斯技术，总共联合拟合了 51,385 个 SNP，这些 SNP 作为随机效应在混合模型中拟合，该模型假设 99.5%的 SNP 具有零效应。SNP 注释是通过猪 Ensembl 提供的 Sus scrofa Build 9 来实现的。我们发现了一些候选染色体区域，其中一些与先前报道的 QTL 区域相对应。我们不仅鉴定了一些与感兴趣性状相关的已知候选基因，如 MC4R（用于背膘）和 IGF2（用于腰肉面积），还获得了一些有前途的新基因，包括 CHCHD3（用于背膘）、BMP2（用于腰肉面积、体型和几个 FL 结构性状），以及一些 HOXA 家族基因（用于整体腿部动作）。负责身体结构和 FL 结构健全性的候选区域没有很大的重叠，这表明这些性状是由不同的基因控制的。功能聚类分析将这些基因分为与骨骼和软骨发育、肌肉生长和发育或胰岛素途径相关的类别，表明这些性状受共同途径或基因网络的调控，这些途径或基因网络在不同的时空阶段发挥作用。
结论/意义：本研究是猪重要数量性状的最早 GWA 报告之一，研究结果将有助于进一步分析鉴定的候选基因的生物学功能，并有可能在标记辅助选择中利用它们。
