USDA-ARS Crop Production and Pest Control Research Unit, 915 West State Street, West Lafayette, IN 47907, USA.
Department of Crop Sciences, University of Illinois, 1101 W. Peabody Drive, Urbana, IL 61801, USA.
Int J Genomics. 2015;2015:603182. doi: 10.1155/2015/603182. Epub 2015 Feb 11.
The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.
大豆的全基因组序列为发现控制重要性状的基因提供了前所未有的机会。特别是，调控基因的潜在功能是分析的重点。已知转录因子的基本螺旋-环-螺旋（bHLH）家族参与控制作物适应和品质的广泛系统，包括光合作用、光信号、色素生物合成和种子荚发育。使用隐马尔可夫模型搜索算法，在大豆基因组序列中鉴定出 319 个具有基本螺旋-环-螺旋转录因子结构域的基因。根据其预测的 DNA 结合潜力、内含子/外显子结构以及 bHLH 结构域的系统发育对这些基因进行了分类。有证据表明，这些 319 个大豆 bHLH 基因中的绝大多数（281 个）在 mRNA 水平上表达。在这些大豆 bHLH 基因中，有 67%被发现存在于两个或更多的同源拷贝中。该数据集为今后研究大豆 bHLH 基因功能提供了框架。未来研究的挑战仍然是定义大豆基因组中编码的 bHLH 因子的功能，这可能为在这种广泛种植的作物中进行生长和环境适应性的遗传选择提供更大的灵活性。
