Genome-Wide Discovery of Tissue-Specific Genes in Maize

Abstract

Analysis of spatial and temporal gene expression pattern is instrumental to elucidation of gene networks and molecular mechanisms of tissue development. It also holds great value to applied research by providing tissue-specific (TS) promoter candidates for transgenic studies. Here, we present a large-scale systematic discovery of tissue-specific genes in maize. Profiles of TS genes were generated from a maize transcriptome atlas, with 71, 539, 23, 352, 51, and 287 genes showing expression specificity in the root, leaf, cob, endosperm, silk, and anther. Functional annotations and enrichment analysis of these TS genes identified pathways overrepresented for each tissue. Tissue specificity was experimentally confirmed by RT-PCR, mRNA in situ hybridization, and transgenic expression of promoter-fluorescent proteins. Two significantly enriched binding motifs, CATTGYCG and KGGTATCA, were identified from the promoter analysis of the anther- and endosperm-specifically expressed genes. Further, co-expression analysis on a broader set of maize germplasms identified molecular networks of TS genes and revealed a number of novel transcripts including non-coding RNA expressing the same pattern with the TS genes from B73. Our global analysis of maize TS transcriptomes could shed light on the molecular mechanisms of tissue specificity and facilitate transgenic studies by providing a valuable resource of TS promoter candidates.