Submitted to: Functional Plant Biology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 4/28/2006
Publication Date: 8/1/2006
Citation: Tesfaye, M., Silverstein, K.A., Bucciarelli, B., Samac, D.A., Vance, C.P. 2006. The Affymetrix Medicago Genechip Array is applicable for transcript analysis of alfalfa (Medicago sativa). Functional Plant Biology. 33:783-788. Interpretive Summary: Recently developed tools called gene chips allow researchers to measure the activity of all of the genes in an organism simultaneously. For plants in the bean family, the first gene chip that has been developed is based primarily on genes from the barrel medic, a plant closely related to the crop plant alfalfa. The gene chip was tested to determine its suitability for identifying active genes in barrel medic and alfalfa plants. An average of 54% of genes on the chip were shown to be active in barrel medic roots and 44% of genes were active in alfalfa roots. In leaves, 46% of genes were found to be active in barrel medic and 41% in alfalfa. In a comparison of the specific genes active in roots and leaves, a large overlap was found, indicating that the majority of genes are expressed in both parts of the plant. There was a small set of genes that were expressed only in roots or leaves. In a comparison of the genes active in the two species of plants, a small set of genes were found to be active in only barrel medic or alfalfa. These experiments showed that the gene chip is an effective tool for determining the genes active in two closely related plant species and for identifying genes that are specific to each plant and plant part. The gene chip will be of great utility for identifying genes for improving disease resistance, stand persistence, and forage quality in alfalfa, traits that are needed for increased utilization and continued economic vitality of the crop.
Technical Abstract: The recently released Affymetrix GeneChip® Medicago Genome Array contains approximately 52,700 probe sets representing genes in both the model legume Medicago truncatula and the closely related crop species M. sativa (alfalfa). We evaluated the utility of the Medicago GeneChip for monitoring genome-wide expression of M. truncatula and alfalfa seedlings grown to the first trifoliate stage. We found that approximately 40% - 54% of the Medicago probes were detected in leaf or root samples of alfalfa or M. truncatula. Approximately 45% - 59% of the detected Medicago probes were called present in all replicate GeneChips of Medicago species, indicating a considerable overlap in the number and type of Medicago probes detected between root and leaf organs. Nevertheless, gene expression differences between roots and leaf organs accounted for approximately 17% of the total variation, regardless of the Medicago species from which the tissues were harvested. The result shows that the Medicago GeneChip® is applicable for transcript analysis for both alfalfa and M. truncatula.