Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa

PLoS One. 2015 Jul 14;10(7):e0132051. doi: 10.1371/journal.pone.0132051. eCollection 2015.

Abstract

Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in plants, controlling cell division, development, hormone signaling, and biotic and abiotic stress responses. Although MAPKs have been investigated in several plant species, a comprehensive analysis of the MAPK gene family has hitherto not been performed in Brassica rapa. In this study, we identified 32 MAPKs in the B. rapa genome by conducting BLASTP and syntenic block analyses, and screening for the essential signature motif (TDY or TEY) of plant MAPK proteins. Of the 32 BraMAPK genes retrieved from the Brassica Database, 13 exhibited exon splicing errors, excessive splicing of the 5' sequence, excessive retention of the 5' sequence, and sequencing errors of the 3' end. Phylogenetic trees of the 32 corrected MAPKs from B. rapa and of MAPKs from other plants generated by the neighbor-joining and maximum likelihood methods suggested that BraMAPKs could be divided into four groups (groups A, B, C, and D). Gene number expansion was observed for BraMAPK genes in groups A and D, which may have been caused by the tandem duplication and genome triplication of the ancestral genome of the Brassica progenitor. Except for five members of the BraMAPK10 subfamily, the identified BraMAPKs were expressed in most of the tissues examined, including callus, root, stem, leaf, flower, and silique. Quantitative real-time PCR demonstrated that at least six and five BraMAPKs were induced or repressed by various abiotic stresses and hormone treatments, respectively, suggesting their potential roles in the abiotic stress response and various hormone signal transduction pathways in B. rapa. This study provides valuable insight into the putative physiological and biochemical functions of MAPK genes in B. rapa.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Brassica / enzymology*
  • Brassica / genetics*
  • Chromosomes, Plant / genetics
  • Cloning, Molecular
  • Gene Expression Profiling*
  • Genome, Plant / genetics
  • Genomics*
  • Mitogen-Activated Protein Kinases / chemistry
  • Mitogen-Activated Protein Kinases / genetics*
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Organ Specificity
  • Phylogeny
  • Sequence Alignment

Substances

  • Mitogen-Activated Protein Kinases

Associated data

  • GEO/GSE43245

Grants and funding

This work was supported by grants from the 863 Project [2013AA102602, www.most.gov.cn], the National Science Foundation of China [31271756 and 31171619, http://www.nsfc.gov.cn], the 111 Project [B12006, http://www.moe.edu.cn], the 973 Project [2015CB250100, www.most.gov.cn], the Chongqing Project of Main Crop Variety Innovation [cstc2012ggB80008, http://www.cstc.gov.cn], and the Fundamental Research Funds for the Central Universities [XDJK2012A009 and XDJK2013C031, http://www.moe.edu.cn]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.