Full-genome analysis of resistance gene homologues in rice

Abstract

The availability of the rice genome sequence enabled the global characterization of nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes, the largest class of plant disease resistance genes. The rice genome carries approximately 500 NBS-LRR genes that are very similar to the non-Toll/interleukin-1 receptor homology region (TIR) class (class 2) genes of Arabidopsis but none that are homologous to the TIR class genes. Over 100 of these genes were predicted to be pseudogenes in the rice cultivar Nipponbare, but some of these are functional in other rice lines. Over 80 other NBS-encoding genes were identified that belonged to four different classes, only two of which are present in dicotyledonous plant sequences present in databases. Map positions of the identified genes show that these genes occur in clusters, many of which included members from distantly related groups. Members of phylogenetic subgroups of the class 2 NBS-LRR genes mapped to as many as ten different chromosomes. The patterns of duplication of the NBS-LRR genes indicate that they were duplicated by many independent genetic events that have occurred continuously through the expansion of the NBS-LRR superfamily and the evolution of the modern rice genome. Genetic events, such as inversions, that inhibit the ability of recently duplicated genes to recombine promote the divergence of their sequences by inhibiting concerted evolution.

A maize resistance gene functions against bacterial streak disease in rice

“…Paralog 1 was predicted to code for a 905-aa protein typical of cereal (non-TIR class; ref. 30), NBS-LRR proteins (Fig. 2B).…”

“…If other R genes function in heterologous cereal backgrounds, it will have a significant impact on strategies to improve disease resistance in our most important crops. Considering that the NBS-LRR genes account for Ϸ1% of genes in the rice genome (30,42) and the thousands of different species of grasses, this could provide a deep resource of R genes to control different phytopathogens. In the case of Rxo1, the maize gene confers broad resistance to a diverse group of X. o. pv.…”

Complex genetic networks underlying the defensive system of rice ( Oryza sativa L.) to Xanthomonas oryzae pv. oryzae

“…The correspondence between major R genes and QRL in genomic locations has been reported in several studies involving rice blast (11)(12)(13). Because of the low resolution in QTL mapping, this association between CR genes and QRL for PR could result from differentiated functions of different members in the R gene families (14), from the secondary functions of the same alleles of the R genes that can activate pathways leading to PR, or from both. This uncertainty will be resolved when all rice R genes are cloned in the future.…”

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

“…The RGA marker (NBS-1) mapped in the proximity of QTL2. Given the abundance of RGA sequences in plant genomes, many of which are not functional (Leister, 2004;Monosi et al, 2004), the colocation of this RGA marker with QTL2 is not sufficient to conclude that the identified RGA is involved in crown rust resistance. A more detailed study of the identified RGA sequence is necessary before it can be determined whether it is part of a functional gene and whether this gene is involved in crown rust resistance.…”