GENOMIC ORGANIZATION OF RESISTANCE GENES AND EXPLOITING GERMPLASM RESOURCES
Department of Vegetable Crops, University of California, Davis, California 95616, USA
Classical genetics has demonstrated that resistance genes tend to be clustered in the genome. This led to the hypothesis that resistance genes are members of multigene families encoding receptors with individual members of these families having diverged to acquire novel recognition specificities. The cloning of resistance genes for a variety of diseases from diverse plant species is providing increasing support for this hypothesis. The similarities between resistance genes have allowed the identification of resistance gene candidates (RGCs) from several species using PCR with degenerate oligonucleotide primers to conserved domains. However, it is becoming evident that there are hundreds of RGCs in all plant species and these RGCs tend to be organized in clusters. Therefore it remains difficult to identify sequences that encode an individual recognition specificity . Transgenic complementation and mutant analysis are still required. A significant proportion of plant genes are involved in defense. It is currently unknown how many distinct types of resistance genes there are in plants. The most common types are receptor-like sequences containing a nueleotide binding domain and leucine rich region (NBS-LRR). Sequence analysis indicates the presence of several sub-families of varying complexity within the NBS-LRR type. However, insufficient numbers have been characterized to identify the total number of subfamilies that exist.
Classical genetics also indicated that clusters of resistance genes were unstable. This led to the idea that clusters of resistance genes are dynamic regions of the genome in which new specificities are frequently being generated by unequal crossing over. Characterization of resistance gene clusters at the molecular level confirms that unequal crossing-over can occur. However, the rate of unequal crossing over at resistance loci seems too low to allow the rapid generation of new specificities because orthologs are more similar than paralogs and there is little evidence for gene conversion homogenizing these multigene families. Clusters of resistance genes seem to be storehouses of variation rather than dynamic, rapidly-evolving pools of sequences. Genome rearrangements may be instrumental in expressing cryptic recognition specificities as well as generating specificities de novo. However, the primary evolutionary force seems to be divergent evolution on orthologs with a birth and death process responsible for changes in copy number.
The availability of cloned resistance genes allows germplasm resources and wild populations to be assayed for variation at these clusters. Preliminary studies have revealed extensive polymorphism in lines with similar wide spectrum resistance phenotypes indicating the presence of many new resistance genes. The sequences of resistance genes allow the development of gene-specific PCR-based markers for introgression, combining resistance genes with wide efficacy and minimizing linkage drag . The presence of many new resistance genes, particularly if they are in species with restricted sexual compatibility with the cultivated species, presents the challenge of how to access them transgenically.