The rapid accumulation of genome sequence data sparked an array of functional genomics tools that are being employed to understand the complex pathways involved in host plant-pathogen interaction. Structural analysis of plant R proteins revealed that most R genes encode homologous proteins with similar domains. The existence of such conserved domain led to comparative genomics approach to discover candidate disease resistance genes in many plant species. The technique involves three major steps, 1) amplification of the RGA region, 2) cloning and sequencing, 3) sequence analysis and similarity search. Such homology-based identification of RGAs has been successfully utilized as short-cut method of resistance gene tagging and genome-wide survey for a complete set of genes containing NBS motif and other features. Furthermore, the RGA technique has applications in cloning, profiling, host-pathogen interaction. In IITA, RGA technique was used in cassava resulting in several novel sequences some of which were found to be similar to previously reported resistance gene analogs. Sequence specific primers derived from the two sequences were used to assess DNA sequence variation in several elite cassava clones. This information is expected to facilitate the identification of gene-targeted marker for molecular breeding and gene discovery in cassava.
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