Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site.

Abstract

The tobacco N and Arabidopsis RPS2 genes, among several recently cloned disease-resistance genes, share a highly conserved structure, a nucleotide-binding site (NBS). Using degenerate oligonucleotide primers for the NBS region of N and RPS2, we have amplified and cloned the NBS sequences from soybean. Each of these PCR-derived NBS clones detected low-or moderate-copy soybean DNA sequences and belongs to 1 of 11 different classes. Sequence analysis showed that all PCR clones encode three motifs (P-loop, kinase-2, and kinase-3a) of NBS nearly identical to those in N and RPS2. The intervening region between P-loop and kinase-3a of the 11 classes has high (26% average) amino acid sequence similarity to the N gene although not as high (19% average) to RPS2. These 11 classes represent a superfamily of NBS-containing soybean genes that are homologous to N and RPS2. Each class or subfamily was assessed for its positional association with known soybean disease-resistance genes through near-isogenic line assays, followed by linkage analysis in F2 populations using restriction fragment length polymorphisms. Five of the 11 subfamilies have thus far been mapped to the vicinity of known soybean genes for resistance to potyviruses (Rsvl and Rpv), Phytophthora root rot (Rpsl, Rps2, and Rps3), and powdery mildew (rmd). The conserved N-or RPS2-homologous NBS sequences and their positional associations with mapped soybean-resistance genes suggest that a number of the soybean disease-resistance genes may belong to this superfamily. The candidate subfamilies of NBScontaining genes identified by genetic mapping should greatly facilitate the molecular cloning of disease-resistance genes.Over the past few years, we have witnessed a breakthrough in the molecular cloning of disease-resistance genes (for review, see ref.

Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling

“…Conservation of several structural motifs within the NBS domain encoded by plant R genes has prompted the development of homology-based approaches aimed at identiWcation of structurally related sequences, termed R gene analogues (RGAs) (Kanazin et al 1996;Yu et al 1996;Leister et al 1996;Aarts et al 1998;Shen et al 1998;Pan et al 2000;van der Linden et al 2004). Cosegregation of speciWc RGAs and R loci and/or quantitative trait loci (QTL) involved in disease resistance has been reported (Hunger et al 2002;Kuhn et al 2003), suggesting that NBS proWling can be a powerful tool for the development of markers linked to resistance loci.…”

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

“…The PCR products were placed into distinct groups and a member of each group was mapped genetically. Altogether, 19 soybean (Kanazin etaL, 1996;Yu et al, 1996) and 12 potato (Leister et al, 1996) sequences were identified and mapped. In each of the three projects, several resistance gene-related fragments mapped near known disease resistance loci.…”

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

“…avenae. Yu et al (1996) identified homologous regions for resistance to obligate biotrophs in Avena, Hordeum and Zea mays on the homologous group 1. The group 1 chromosomes of the Triticeae and the group A chromosomes of oat are homologous to the LG1 of Lolium; on this LG, we also found two QTLs (LpPc2 and LpPc4) linked with crown rust resistance.…”