ARS | Publication request: UTILIZATION OF TOMATO MICROARRAYS FOR COMPARATIVE GENE EXPRESSION ANALYSIS IN THE SOLANCEAE

Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 12, 2005
Publication Date: October 20, 2005
Citation: Moore, S., Payton, P.R., Wright, M., Tanksley, S., Giovannoni, J.J. 2005. Utilization of tomato microarrays for comparative gene expression analysis in the solanceae. Journal of Experimental Botany. 56:2885-2895.

Interpretive Summary: In the current era of genomics biology, availability of genome DNA sequence information is becoming a limiting factor in biological research. In the plant community, extensive DNA sequence information is currently available only for Arabidopsis and rice though international efforts have been recently initiated for Medicago, lotus, and tomato. As available research funding is limited, it is imperative to investigate the degree to which available sequence resources can be exploited for discovery in species for which less information and resources are currently available. Here we present data describing a tomato cDNA microarray and its utility as a tool for characterizing gene expression in species related to tomato but for which substantial genomic resources are either currently unavailable (eggplant) or are limited (pepper, potato). We identify genes that are uniquely expressed in the fruit of tomato versus pepper versus eggplant and show that at least some of these genes encode activities which trace back to characteristics that differentiate the fruit of the examined species. Members of the plant family Solanaceae include tomato, pepper, eggplant and potato and represent the most important family of vegetable species in the US and much of the world. We show that the tomato microarray can be used for meaningful characterizing of gene expression in all four of these species.

Technical Abstract: Transcriptional profiling allows for the assessment and comparison of cross-species gene activity and function on a comprehensive scale. The Solanaceae is a large, diverse dicot family with well-established genetic relationships between major crop species (tomato, potato, pepper, eggplant, and tobacco). Although, Arabidopsis thaliana is often the model of choice for anchoring comparative studies, certain biological processes are better examined in other plants. The ripening of fleshy fruits is not tractable in Arabidopsis; however it has received considerable attention in tomato. As a member of the Solanaceae, tomato provides a well-characterized system to anchor transcriptional profiles of fruit ripening and development in related species. By utilizing different stages of tomato, pepper, and eggplant fruit, we have both demonstrated the utility of tomato microarrays for expression analysis in closely-related heterologous species and identified groups of candidate ESTs useful both as orthologous markers as well as genes implicated in fruit ripening and development in the Solanaceae.