Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species

Nayak, S N and Balaji, J and Upadhyaya, H D and Hash, C T and Kishor, P B K and Chattopadhyay, D and Rodriquez, L M and Blair, M W and Baum, M and McNally, K and This, D and Hoisington, D A and Varshney, R K (2009) Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species. Plant Science, 177 (5). pp. 460-467.

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The transcription factor, DREB2A, is one of the promising candidate genes involved in dehydration tolerance in crop plants. In order to isolate DREB2A homologues across cereals (rice, barley and sorghum) and legumes (common bean and chickpea), specific or degenerate primers were used. Gene/phylogenetic trees were constructed using a non-redundant set of 19 DREB1A and 27 DREB2A amino acid sequences and were combined with taxonomic/species tree to prepare reconciled phylogenetic trees. In total, 86 degenerate primers were designed for different clades and 295 degenerate primer combinations were used to amplify DREB homologues in targeted crop species. Successful amplification of DREB2A was obtained in case of sorghum. In parallel, gene-specific primers were used to amplify DREB2A homologues in rice, barley, common bean and chickpea. Seven to eight diverse genotypes from targeted species were used for sequence analysis at DREB2A locus identified/isolated. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, three SNPs with five haplotypes were observed in barley whereas a single SNP was observed in rice, sorghum and chickpea. Parsimony based phylogenetic tree revealed distinct clustering of cereals and legumes. Furthermore, alignment of corresponding amino acid sequences showed conservation of AP2 domain across the targeted species.

Item Type: Article
Subjects: Others > Agriculture-Farming, Production, Technology, Economics
Depositing User: Library ICRISAT
Date Deposited: 27 Aug 2011 06:40
Last Modified: 02 Jan 2012 09:27
Official URL:
Funders: Generation Challenge Programme, Council of Scientific and Industrial Research(India)
Acknowledgement: Financial support from Generation Challenge Programme (GCP) to the ADOC (Allelic Diversity at Orthologous Candidate Genes in GCP Crops) project is gratefully acknowledged. SNN is thankful to Council of Scientific and Industrial Research (CSIR) for sponsoring fellowship.
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