Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato

Abstract

SummaryComparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race-specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co-evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown.

The Fractionated Orthology of Bs2 and Rx/Gpa2 Supports Shared Synteny of Disease Resistance in the Solanaceae

“…Approaches to understanding and utilizing R-gene macrosynteny in the Solanaceae are certainly viable. The cloning of the late blight resistance gene R3a from potato based on I2 in tomato illustrates the potential of these comparative approaches (Huang et al 2005). Extensions of our model provide for the a priori localization of cloned R-gene sequences in one species on the basis of the genomic location of its fractionated ortholog in a model species and a selection criterion for candidate sequences where resistances align in comparative maps.…”

Allele mining in Solanum: conserved homologues of Rpi-blb1 are identified in Solanum stoloniferum

“…To date, four late blight R-genes have been cloned: R1 (Ballvora et al 2002), R3a (Huang et al 2005), RB or Rpiblb1 (Song et al 2003;van der Vossen et al 2003) and Rpiblb2 (van der Vossen et al 2005). The latter two genes were cloned from S. bulbocastanum and confer resistance to all P. infestans isolates tested so far.…”

Potato chromosomes IX and XI carry genes for resistance to potato virus M

“…The co-linear region of tomato chromosome 11 harbors the I2 locus conferring resistance to race 2 of F. oxysporum f. sp. lycopersici (Ori et al 1997;Simons et al 1998;Huang et al 2005). The Rm locus reported here was at a close genetic distances of 0.8 cM from the marker GP250.…”

“…Such a resistance hotspot is the distal end of the short arm of chromosome XI where genes for resistance to various pathogens have been located. The marker GP250 co-segregated with the R3a gene for resistance to P. infestans (Huang et al 2004) and is tightly linked to four other R genes with distinct specificities to the late blight disease caused by Phytophthora infestans (El Kharbotly et al 1996;Huang et al 2005). QTL for resistance to late blight and Erwinia carotovora ssp atroseptica have also been mapped to the same region Collins et al 1999;Zimnoch-Guzowska et al 2000).…”

“…The PVM resistance gene Rm is therefore a new member of this resistance gene cluster located on potato chromosome XI and the first one conferring resistance to a virus. Sequence analysis of the I2 locus in tomato (Ori et al 1997;Simons et al 1998) and the R3a locus in potato (Huang et al 2005) revealed a complex structure of clustered resistance gene homologs. Based on its position, the gene Rm could be another member of these gene families.…”