Abstract
We analyzed the nucleotide variability and the expression profile of DREB genes from common bean, a crop of high economic and nutritional value throughout the world but constantly affected by abiotic stresses in cultivation areas. As DREB genes have been constantly associated with abiotic stress tolerance, we systematically categorized 54 putative PvDREB genes distributed in the common bean genome. It involved from AP2 domain location and amino acid conservation analysis (valine at the 14th position) to the identification of conserved motifs within peptide sequences representing six subgroups (A-1 to A-6) of PvDREB proteins. Four genes (PvDREB1F, PvDREB2A, PvDREB5A, and PvDREB6B) were cloned and analyzed for their expression profiles under abiotic stresses and their nucleotide and amino acid diversity in genotypes of Andean and Mesoamerican origin, showing distinct patterns of expression and nucleotide variability. PvDREB1F and PvDREB5A showed high relative inducibilities when genotypes of common bean were submitted to stresses by drought, salt, cold, and ABA. PvDREB2A inducibility was predominantly localized to the stem under drought. PvDREB6B was previously described as an A-2 (DREB2) gene, but a detailed phylogenetic analysis and its expression profile clearly indicated it belongs to group A-6. PvDREB6B was found as a cold- and dehydration-responsive gene, mainly in leaves. Interestingly, PvDREB6B also showed a high nucleotide and amino acid diversity within its coding region, in comparison to the others, implicating in several nonsynonymous amino acid substitutions between Andean and Mesoamerican genotypes. The expression patterns and nucleotide diversity of each DREB found in this study revealed fundamental characteristics for further research aimed at understanding the molecular mechanisms associated with drought, salt, and cold tolerance in common bean, which could be performed based on association mapping and functional analyses.
Highlights
Abiotic stresses have a negative impact on plants, limiting their growth and survival
The remaining 157 sequences had only one AP2 domain. These 157 putative ERF genes were distributed among the 11 chromosomes of common bean. Their annotation with an e-value cutoff of 1 × 10−5 provided an initial assessment of the putative DREB gene sequences in the common bean genome, but further phylogenetic analyses strengthened the categorization
The number of DREB genes categorized for common bean was similar to A. thaliana, which has 57 AtDREB separated into four main subgroups in the AP2/ERF superfamily [5], or 56 within six subgroups, from Arabidopsis is that DREB1/CBF (A-1) to A-6 [6]
Summary
Abiotic stresses have a negative impact on plants, limiting their growth and survival. One category of genes primarily works for mechanic and osmotic adjustment, while another set is involved in a series of regulation processes for overcoming the stress conditions [3]. The latter group comprises several stress-inducible genes such as NAC, bZIP, leucine-rich repeats (LRR), and EREBP/AP2 [4]. ERF proteins are primarily involved in responses to biotic stresses, such as pathogenesis, by recognizing the AGCCGCC cis-regulatory element, known as GCC box [7]. DREB proteins have a crucial role in the response of plants to abiotic stresses by recognizing the dehydration responsive element (DRE), which consists on the conserved motif A/GCCGAC [8]. DRE has been found essential for gene regulation due to dehydration [8], but since it has been found in the promoter region of other drought-, salinity-, and cold-inducible genes [5, 6, 9]
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