Abstract
BackgroundMADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. Studies on stress resistance-related functions of MADS-box genes are very limited and no such functional studies in Brassica rapa have been reported. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa.ResultsWhole-genome survey of B. rapa revealed 167 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (MIKCc and MIKC*) based on phylogeny, protein motif structure and exon-intron organization. Expression analysis of 89 MIKCc and 11 MIKC* genes was then carried out. In addition to those with floral and vegetative tissue expression, we identified MADS-box genes with constitutive expression patterns at different stages of flower development. More importantly, from a low temperature-treated whole-genome microarray data set, 19 BrMADS genes were found to show variable transcript abundance in two contrasting inbred lines of B. rapa. Among these, 13 BrMADS genes were further validated and their differential expression was monitored in response to cold stress in the same two lines via qPCR expression analysis. Additionally, the set of 19 BrMADS genes was analyzed under drought and salt stress, and 8 and 6 genes were found to be induced by drought and salt, respectively.ConclusionThe extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MADS-box genes in stress resistance in addition to their growth and developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1349-z) contains supplementary material, which is available to authorized users.
Highlights
MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development
Identification and sequence analysis of MADS-box genes in B. rapa A set of 167 candidate MADS-box genes from the B. rapa genome was recovered using key word ‘MADS-box’ to search Swissprot annotations at the Brassica database (BRAD) [37]
We designated the 167 annotated MADSbox genes of B. rapa as BrMADS followed by Arabic numbers 1–167, consecutively following the five classes (MIKCc, MIKC*, Mα, Mβ and Mγ)
Summary
MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa. MADS-box genes play important roles in many aspects of plant development [1]. They are the major components in the well-known ‘ABC’ model that describes their roles in floral organ development [2]. The M-type MADSbox genes are grouped into Mα, Mβ and Mγ based on phylogenetic relationships within their MADS-box regions [4]. The MIKCc genes are further partitioned into 14 clades based on phylogeny [9]
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