Isolation and sequence analysis of wheat NBS-LRR type disease resistance gene analogs using degenerate PCR primers

Isolation of disease resistance gene analogs (RGAs) using the conserved motifs of the resistance genes has attracted considerable attention since it was first reported more than a decade ago. In this study, RGAs are isolated using homology-based PCR to target the nucleotide binding site (NBS) conser...

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Bibliographic Details
Published in:Biochemical genetics 2007-06, Vol.45 (5-6), p.469-486
Main Authors: Bozkurt, O, Hakki, E. E, Akkaya, M. S
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Analogs
Avena sativa
Binding sites
Binding Sites - genetics
Cloning
Conserved sequence
Crop diseases
Disease resistance
DNA Primers - chemistry
DNA, Plant - genetics
DNA, Plant - metabolism
Domains
Genes
Genetic Markers
Genetics
Genomics
Homology
Immunity, Innate - genetics
Introns
Kinase2 and kinase3 motifs
Kinases
Molecular Sequence Data
Nucleotide binding site (NBS)
Nucleotides
Oryza sativa
Plant Diseases - microbiology
Plant Proteins - genetics
Plant Proteins - isolation & purification
Polymerase Chain Reaction
Primers
Resistance gene analog (RGA)
Sequence analysis
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Triticum - genetics
Triticum - microbiology
Triticum aestivum
Wheat
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Summary:Isolation of disease resistance gene analogs (RGAs) using the conserved motifs of the resistance genes has attracted considerable attention since it was first reported more than a decade ago. In this study, RGAs are isolated using homology-based PCR to target the nucleotide binding site (NBS) conserved regions from hexaploid wheat varieties and a few accessions of wild types. Based on sequence similarity analysis, 83 of the sequenced clones were clustered as groups. Of these RGAs, 40 were in the NBS-LLR class, containing kinase-1a (GGVGKTT or GGVGKTA), kinase-2 (KRFLIVLDDXW), kinase-3a (GSXIVVITTR or GCXVLATTR), and the GLPL motif of the NBS-spanning region. Among these, 15 contained possible intron regions, similar to Avena sativa O2 NBS-LLR type disease resistance gene (AF078874), and one to Rpm1 of rice and Yr10 and Lr10 of wheat. To our knowledge, this is the first observation of an intronic site within the P-loop domain of wheat RGAs. We detected an unspecified motif (VMVCVS) between the kinase-1a and kinase-2 domains within our clones. Additionally, one of the clones showed replacement with the kinase-3a motif with an undefined sequence.
ISSN:0006-2928
1573-4927
DOI:10.1007/s10528-007-9089-7