Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis

Abstract

Plant disease resistance (R) genes confer race-specific resistance to pathogens and are genetically defined on the basis of intra-specific functional polymorphism. Little is known about the evolutionary mechanisms that generate this polymorphism. Most R loci examined to date contain alternate alleles and͞or linked homologs even in disease-susceptible plant genotypes. In contrast, the resistance to Pseudomonas syringae pathovar maculicola (RPM1) bacterial resistance gene is completely absent (rpm1-null) in 5͞5 Arabidopsis thaliana accessions that lack RPM1 function. The rpm1-null locus contains a 98-bp segment of unknown origin in place of the RPM1 gene. We undertook comparative mapping of RPM1 and f lanking genes in Brassica napus to determine the ancestral state of the RPM1 locus. We cloned two B. napus RPM1 homologs encoding hypothetical proteins with Ϸ81% amino acid identity to Arabidopsis RPM1. Collinearity of genes f lanking RPM1 is conserved between B. napus and Arabidopsis. Surprisingly, we found four additional B. napus loci in which the f lanking marker synteny is maintained but RPM1 is absent. These B. napus rpm1-null loci have no detectable nucleotide similarity to the Arabidopsis rpm1-null allele. We conclude that RPM1 evolved before the divergence of the Brassicaceae and has been deleted independently in the Brassica and Arabidopsis lineages. These results suggest that functional polymorphism at R gene loci can arise from gene deletions.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

“…1 A). Because these domains are common in plant diseaseresistance proteins, this finding is consistent with these proteins being particularly diverse because of pathogen pressure (7,(18)(19)(20).…”

Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

“…Comparing the genetic maps of Arabidopsis and different Brassica species also has revealed many colinear chromosome segments for species belonging to the Brassicaceae family (reviewed in Schmidt, 2000). The results of the first microsynteny studies using sequencelevel resolution in the Poaceae (Chen et al, 1997;Messing and Llaca, 1998;Tikhonov et al, 1999) and Brassicaceae families (Grant et al, 1998;Acarkan et al, 2000) support the view that genome colinearity can be observed at the level of genes.…”

“…Comparing the genetic maps of Arabidopsis and different Brassica species also has revealed many colinear chromosome segments for species belonging to the Brassicaceae family (reviewed in Schmidt, 2000). The results of the first microsynteny studies using sequencelevel resolution in the Poaceae (Chen et al, 1997;Messing and Llaca, 1998;Tikhonov et al, 1999) and Brassicaceae families (Grant et al, 1998;Acarkan et al, 2000) support the view that genome colinearity can be observed at the level of genes.Few attempts to analyze genome colinearity between more distantly related species have been reported (Paterson et al, 1996;Devos et al, 1999;van Dodeweerd et al, 1999;Ku et al, 2000). The low degree of sequence homology in distantly related species hampers the unambiguous 1 These authors contributed equally to this work.…”

Signature of balancing selection in Arabidopsis

“…The CR sequence encompasses the complete coding sequence of RFL1 (the 5Ј side of the DJ), a distantly related paralog of RPS5, and the partial sequence of the predicted gene encoding transaldolase (the 3Ј side of the DJ). The tandem arrangement of RPS5 and RFL1 is present in the sister species, Arabidopsis lyrata, indicating that the RPS5 polymorphism arose as a deletion, just as observed for RPM1 (31). The 5Ј-10kb and 3Ј-9kb sequences encompass partial sequence of ''T28K15.8, Hypothetical Protein'' and ␤-fructosidase, respectively, as illustrated in Fig.…”