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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING ALFALFA AND OTHER FORAGE CROPS FOR BIOENERGY, LIVESTOCK PRODUCTION, AND ENVIRONMENTAL PROTECTION Title: Transcript Profiling of Common Bean (Phaseolus vulgaris) Using the GeneChip Soybean Genome Array: Optimizing Analysis by Masking Biased Probes

Authors
item Yang, Suk
item Valdes-Lopez, Oswaldo -
item Xu, Wayne -
item Bucciarelli, Bruna
item Gronwald, John
item Hernandez, Georgina -
item Vance, Carroll

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 9, 2009
Publication Date: January 9, 2010
Citation: Yang, S.H., Valdes-Lopez, O., Xu, W.W., Bucciarelli, B., Gronwald, J.W., Hernandez, G., Vance, C.P. 2010. Transcript Profiling of Common Bean (Phaseolus vulgaris) Using the GeneChip Soybean Genome Array: Optimizing Analysis by Masking Biased Probes [abstract]. XVIII Plant and Animal Genome Conference Proceedings, January 9-13, 2010, San Diego, California. Abstract P724.

Technical Abstract: Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. 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 specificity 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 specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity 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 results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. 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.

Last Modified: 12/22/2014
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