Microarray analysis of developing Arabidopsis seeds

To provide a broad analysis of gene expression in developing Arabidopsis se eds, microarrays have been produced that display approximately 2,600 seed-e xpressed genes. DNA for genes spotted on the arrays were selected from >10, 000 clones partially sequenced from a cDNA library of developing seeds. Bas ed on a series of controls, sensitivity of the arrays was estimated at one to two copies of mRNA per cell and cross hybridization was estimated to occ ur if closely related genes have >70% to 80% sequence identity. These array s have been hybridized in a series of experiments with probes derived from seeds, leaves, and roots of Arabidopsis. Analysis of expression ratios betw een the different tissues has allowed the tissue-specific expression patter ns of many hundreds of genes to be described for the first time. Approximat ely 25% of the 2,600 genes were expressed at ratios greater than or equal t o 2-fold higher in seeds than leaves or roots and 10% at ratios greater tha n or equal to 10. Included in this list are a large number of proteins of u nknown function, and potential regulatory factors such as protein kinases, phosphatases, and transcription factors. The Arabidopsis arrays were also f ound to be useful for transcriptional profiling of mRNA isolated from devel oping oilseed rape (Brassica napus) seeds and expression patterns correlate d well between the two species.