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

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Title Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species
 
Creator Nayak, Spurthi N.
Balaji, Jayashree
Upadhyaya, Hari D.
Hash, C. Tom
Kavi Kishor, P.B.
Chattopadhyay, Debasis
Rodriquez, Lina Marıa
Blair, Matthew W.
Baum, Michael
McNally, Kenneth
This, Dominique
Hoisington, David A.
Varshney, Rajeev K.
 
Subject DREB
Candidate gene
Drought stress
SNP
Haplotype
 
Description 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.
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.
 
Date 2014-02-12T10:39:11Z
2014-02-12T10:39:11Z
2009
28 July 2009
 
Type Article
 
Identifier Plant Science, 177: 460-467
http://hdl.handle.net/123456789/125
 
Language en
 
Publisher Elsevier B.V.