| Plant disease is one of the most limiting factors in crop production. The most effective approach for disease control is to use resistant crops. However, the resistance in cultivars is usually controlled by single resistance gene (R-gene), which is prone to be defeated by new strains of pathogen. For the resistance to be durable, an ideal resistant genotype should contain multiple resistance genes. To develop such resistant cultivars and properly use resistance genes requires a comprehensive understanding of their genomics and evolution.In this study, genes encoding nucleotide binding site and luncine rich repeat (NBS-LRR) domains in the genomes of rice, maize, sorghum and Brachypodium distachyon were analyzed comprehensively. Such genes are referred to as R-genes in this study. R-gene loci have ubiquitous presence/absence (P/A) polymorphism between different genomes. The absence of an R-gene could have resulted from unequal crossover, homologous repair, non-homologous repair and other unknown mechanisms. The P/A polymorphism of R-genes will impede their in silico mapping and cloning. To generate an integrated map of all R-genes in the grass family, R-gene loci identified from different genomes were mapped onto the chromosomes of rice cultivar Nipponbare by means of comparative genomics, resulting in an integrated map of495R-loci. Only few (3.23%) R-gene loci are present in all five genomes, indicating that R-genes are extremely dynamic in plant genomes. Furthermore, the flanking regions of the R-genes have poor synteny when compared with non R-gene loci. The R-genes with chimeric structure, termed Type I R-genes, only account for5.8%of all R-genes in rice cultivar Nipponbare, but their sequences are extremely diverse in different rice accessions. In contrast, the vast majority of R-genes in rice genome are Type â…¡.R-genes, which are highly conserved in different accessions. Surprisingly, pseudogene-causing mutations in some Type â…¡ lineages are often conserved, indicating that their conservations were not due to their functions. Functional R-genes cloned from rice so far have both Type â…¡ R-genes and Type â… R-genes. The NBS encoding gene Pi37cloned from rice has evolved in a pattern of Type I R-gene. It was generated by an unequal crossover between two neighboring paralogues followed by four point mutations. The Rpl-D is another functional R-gene in this gene family, and it encodes rust resistance in maize. At least two ancestral Rpl loci were found in Poaceae. These two Rpl loci experienced deletion and duplication in different species of Poceae. Different species in the grass family not only vary in locus number of Rpl homologues, but also in copy number. In wheat and maize, a large number of Rpl homologues are identified, while Oryza and Brachypodium have fewer than five Rpl genes. The diverse Rpl genes in Zea were generated by frequent sequence exchanges, but the frequent sequence exchanges between the Rpl genes within species did not cause concerted evolution between different species of Zea. Moreover, the Rpl genes in different species exhibit distinct evolutionary patterns. In maize and sorghum, the Rpl genes are extensive chimeras due to frequent sequence exchanges and have evolutionary patterns of Type â… R-genes. However, in wheat, barley and Brachypodium, the Rpl genes exhibit evolutionary patterns of Type â…¡ R-genes. The Rpl genes in Oryza have both Type â… and Type â…¡ evolutionary patterns.In summary, this study on the structural and molecular evolution of the R-genes in Poaceae demonstrated that most of the.R-genes are dynamic. Frequent deletions and translocations of R-genes result in prevalent P/A polymorphism between different accessions/species. In addition, this study showed that the same gene family may have had different evolutionary patterns in different species. The results from this study provide useful information for the proper use of R-genes in future and the integrated map of R-genes in the grass family can serve as an excellent reference for in silico mapping and cloning of functional R-genes. |
