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Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants

DOI: 10.1186/1471-2229-9-29

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Affymetrix microarrays were used for expression-based gene discovery to identify sets of genes expressed in either or both integuments. The genes were identified by comparison of pistil mRNA from wild type with mRNA from two mutants; inner no outer (ino, which lacks the outer integument), and aintegumenta (ant, which lacks both integuments). Pools of pistils representing early and late stages of ovule development were evaluated and data from the three genotypes were used to designate genes that were predominantly expressed in the integuments using pair-wise and cluster analyses. Approximately two hundred genes were found to have a high probability of preferential expression in these structures, and the predictive nature of the expression classes was confirmed with reverse transcriptase polymerase chain reaction and in situ hybridization.The results showed that it was possible to use a mutant, ant, with broad effects on plant phenotype to identify genes expressed specifically in ovules, when coupled with predictions from known gene expression patterns, or in combination with a more specific mutant, ino. Robust microarray averaging (RMA) analysis of array data provided the most reliable comparisons, especially for weakly expressed genes. The studies yielded an over-abundance of transcriptional regulators in the identified genes, and these form a set of candidate genes for evaluation of roles in ovule development using reverse genetics.Ovules, the precursors to seeds, are an important focus of study to better understand plant development within a unique reproductive context. Ovules are highly specialized for reproductive function, but the typical angiosperm ovule, as found in Arabidopsis, is relatively simple morphologically. Development of the ovule within the carpel is well described, [1-5], beginning with primordia emergence from the marginal placentas of the carpels (floral stage 9, ovule stage 1). The primordia have three regions, the distal region or nucellus, ma


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