Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.)

Abstract

BackgroundMitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. Although this family has been systematically studied in many plant species, little is known about MAPKKK genes in wheat (Triticum aestivum L.), especially those involved in the regulatory network of stress processes.ResultsIn this study, we identified 155 wheat MAPKKK genes through a genome-wide search method based on the latest available wheat genome information, of which 29 belonged to MEKK, 11 to ZIK and 115 to Raf subfamily, respectively. Then, chromosome localization, gene structure and conserved protein motifs and phylogenetic relationship as well as regulatory network of these TaMAPKKKs were systematically investigated and results supported the prediction. Furthermore, a total of 11 homologous groups between A, B and D sub-genome and 24 duplication pairs among them were detected, which contributed to the expansion of wheat MAPKKK gene family. Finally, the expression profiles of these MAPKKKs during development and under different abiotic stresses were investigated using the RNA-seq data. Additionally, 10 tissue-specific and 4 salt-responsive TaMAPKKK genes were selected to validate their expression level through qRT-PCR analysis.ConclusionsThis study for the first time reported the genome organization, evolutionary features and expression profiles of the wheat MAPKKK gene family, which laid the foundation for further functional analysis of wheat MAPKKK genes, and contributed to better understanding the roles and regulatory mechanism of MAPKKKs in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2993-7) contains supplementary material, which is available to authorized users.

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-Like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

“…In addition, SBP genes were mapped to corresponding chromosomes to determine their physical position, and we found that SBP genes were widely but not evenly distributed on chromosomes. Similar findings have been reported in other wheat transcription factor families, such as MADS [81], AP2/ERF [82], and MAPKKK [83]. The number of genes on chromosome 7 (23 genes) was the most, whereas the number of genes on chromosome 4 (1 gene) was the least in wheat.…”

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

“…A phosphoproteomic analysis in maize identified hundreds of male sterility-associated proteins which were assumed to form protein complexes with kinases [50]. Regarding the regulation of phosphorylation, the protein kinase gene family as well as the protein phosphatase gene family have been widely studied in model plants and agronomically important crops such as wheat and maize [51,52,53]. It was revealed that plants do not possess typical protein tyrosine kinase genes [51].…”

“…Regarding the regulation of phosphorylation, the protein kinase gene family as well as the protein phosphatase gene family have been widely studied in model plants and agronomically important crops such as wheat and maize [51,52,53]. It was revealed that plants do not possess typical protein tyrosine kinase genes [51]. However, protein tyrosine phosphatases were discovered in crops like tomato [54].…”

Genome-Wide Identification and Expression Analysis of Heat Shock Transcription Factor Family in Chenopodium quinoa Willd

“…Gene expression patterns are usually closely related to their functions [25]. To gain insight into the temporal and spatial expression patterns of CqHsf genes, RNA-seq data of different organs, including seedling, stem, leaf, inflorescence, and dry seeds were downloaded from the NCBI Sequence Read Archive (SRA) database, and then were used to analyze the expression profiles in tissues.…”

“…The potential members of the quinoa Hsf gene family were identified following the method described by Wang et al [25] with some modifications. Firstly, all the available quinoa protein sequences were obtained from the Ensembl Plants database as a local protein database [26].…”