Rice Genetics IV - IRRI books - International Rice Research Institute

ConclusionsThese analyses must be considered preliminary because of the limited number oftranscripts that are included. Another limitation is the experimental setup that relieson salt shock, which does not simulate natural conditions. With the shock treatments,however, we hope to define the model systems and to derive a set of transcripts withmicroarrays of selected ESTs to which ESTs for functionally unknown yet stressregulatedtranscripts are added, which should then be used under more natural stressconditions. Such experiments have not yet been reported with plants. Irrespective ofthe limited set of transcripts included in the experiments, a list of regulated transcriptsis included (Table 5) because the nature of the regulated ESTs is informative. Includedin the list are many transcripts that have previously been associated with salinitystress responses (Bohnert et al 1999, Hasegawa et al 2000). Table 5 also includesseveral functionally unknown or novel transcripts. The latter category seems to includetranscripts that are only expressed in (salt) stressed plants and they are notrepresented in the large collection of rice ESTs deposited in GenBank. Among theapproximately 4,000 rice ESTs that we have obtained so far, mainly from stressedplants, more than 300 are in the category “novel” after a comparison of our sequencesagainst the 67,000 rice ESTs (October 2000; www.ncbi.nih.gov/dbEST/dbEST_summary.html).The rapid development of microarray technologies has brought about a betterunderstanding of handling, experimental setup, and statistical data analysis (Eisen etal 1998, Kehoe et al 1999, Deyholos and Galbraith 2001). The inclusion of larger setsof genes for comparisons is possible but equally valuable data will come from smallarrays for selected pathways (e.g., nitrogen or one-carbon metabolisms), groups offunctionally related genes (mitogen-activated protein kinases, P450), or conditionallyor developmentally related genes (drought-induced unknown transcripts, cellcycle). We have not yet included other abiotic stress factors such as drought or lowtemperature in the analysis of rice ESTs, but such experiments are in progress (drought)or in the planning stage. The time-dependent progression of upregulation in highsalinity in various categories of genes seems to indicate the temporal operation ofdifferent programs and several regulated transcripts. Based on these results, a challengingnext step will be the analysis of the many functionally unknown genes thatare regulated when plants experience abiotic stress.358 Bohnert et al