USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA.
BMC Plant Biol. 2010 May 7;10:85. doi: 10.1186/1471-2229-10-85.
Common bean (Phaseolus vulgaris L.) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean.
To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR) analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent.
The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In addition to transcript profiling, CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
普通菜豆（Phaseolus vulgaris L.）和大豆（Glycine max）都属于菜豆族，具有显著的编码序列同源性。这表明大豆基因芯片（GeneChip® Soybean Genome Array，大豆基因芯片）可用于普通菜豆的基因表达研究。
为了评估大豆基因芯片用于普通菜豆转录谱分析的适用性，我们将普通菜豆根、叶和根的 cRNA 分别与大豆基因芯片进行了三次杂交。初步数据分析表明，与大豆相比，普通菜豆的杂交基因芯片数据在测量差异基因表达方面的灵敏度和准确性降低。我们采用了一种方法，对针对普通菜豆和大豆之间物种可变（ISV）区域的探针进行掩蔽。选择了一个掩蔽信号强度阈值，该阈值优化了测量差异基因表达的灵敏度和准确性。对 ISV 区域进行掩蔽后，普通菜豆中差异表达基因的数量增加了 2.8 倍，反映了灵敏度的提高。对 20 个随机选择的基因和嘌呤脲途径基因进行定量 RT-PCR（qRT-PCR）分析表明，ISV 区域掩蔽后，差异基因表达的测量准确性提高。我们还评估了每个探针组的掩蔽探针频率，以深入了解普通菜豆和大豆之间的序列分化模式。序列分化模式分析表明，大豆和普通菜豆之间基本细胞功能和代谢的基因高度保守。此外，我们的结果表明，某些类别的基因，特别是与环境适应相关的基因，高度分化。
当与所描述的掩蔽方案结合使用时，大豆基因芯片是普通菜豆转录谱分析的合适的跨物种平台。除了转录谱分析之外，基因芯片的杂交结合 ISV 区域中的掩蔽探针可用于比较生态和/或进化基因组学研究。
