Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development

Abstract

BackgroundWheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction.ResultsA NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile.ConclusionsThe differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.

Signal transduction during wheat grain development

“…As of date, some crucial and important signaling pathways in the developing grain have never been explored in wheat (Capron et al 2012). Much work remains to be done before the precise roles of signals in grain development and the roles of signal transduction pathways that coordinate the response to the environment are understood.…”

“…The differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up-or downregulated during the early and late stages of the grain development (Capron et al 2012).…”

dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

“…Transcription factor UniGenes were retrieved from the wDBTF database (34). E3 ligase and hormone-responsive UniGenes were recovered from the NCBI and TAIR databases using all A. thaliana and O. sativa E3 ligase and hormone-responsive sequences as the query in homology searches using the BLASTn, BLASTx and tBLASTx programs (36). The BLAST hits were filtered using an e-value threshold of 10 − 5 and an alignment length exceeding 80 bp.…”

“…A total of 39 029 transcripts from the UniGene set (build #55) and 1613 transcription factors from the wDBTF database not present in the UniGene set are spotted on the custom T. aestivum NimbleGen 40 k microarray (36). Previous studies have shown that 18 140 (44.6%) of these transcripts are expressed during T. aestivum grain development (47).…”

“…To fill this gap, we developed dbWFA, an open-access database relating the T. aestivum UniGene set and the full-length cDNA sequences from TriFLDB to A. thaliana (TAIR10) (32) and O. sativa (pseudomolecules version 7.0) (33) annotation through BLAST (34) results. dbWFA also includes the inventory database of T. aestivum transcription factors (wDBTF) (35) and hand-curated gene families (36). As an all-in-one interface for the annotation of T. aestivum sequences, dbWFA will be useful to the researchers working on T. aestivum and more generally on cereals, particularly for comparative cereal genomics and functional genomics.…”