Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping

Abstract

The model plant Arabidopsis thaliana exhibits extensive natural variation in resistance to parasites. Immunity is often conferred by resistance (R) genes that permit recognition of specific races of a disease. The number of such R genes and their distribution are poorly understood. In this study, we investigated the basis for resistance to the downy mildew agent Hyaloperonospora arabidopsidis ex parasitica (Hpa) in a global sample of A. thaliana. We implemented a combined genome-wide mapping of resistance using populations of recombinant inbred lines and a collection of wild A. thaliana accessions. We tested the interaction between 96 host genotypes collected worldwide and five strains of Hpa. Then, a fraction of the species-wide resistance was genetically dissected using six recently constructed populations of recombinant inbred lines. We found that resistance is usually governed by single dominant R genes that are concentrated in four genomic regions only. We show that association genetics of resistance to diseases such as downy mildew enables increased mapping resolution from quantitative trait loci interval to candidate gene level. Association patterns in quantitative trait loci intervals indicate that the pool of A. thaliana resistance sources against the tested Hpa isolates may be predominantly confined to six RPP (Resistance to Hpa) loci isolated in previous studies. Our results suggest that combining association and linkage mapping could accelerate resistance gene discovery in plants.plant | quantitative trait loci | gene discovery

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes inArabidopsis

“…To obtain additional insights into within-and between-species NB-LRR gene evolution, we shotgun sequenced a bacterial artificial chromosome (BAC) containing the RPP7 cluster from the A. thaliana accession Cape Verde Islands (Cvi-0). Specific alleles of RPP7 are linked to resistance of Hyaloperonospora arabidopsidis ex parasitica in accessions Columbia (Col-0) and Landsberg erecta of A. thaliana (Speulman et al, 1998;Nemri et al, 2010). The Cvi-0 BAC contains a tandem cluster of NB-LRR genes residing in contig 1 (AT1G58370-AT1G59530; hereafter Cvi1), separated from another NB-LRR gene, AT1G59620, by five intervening genes residing in contig 2 (AT1G59590-AT1G59630; hereafter Cvi2; Fig.…”

Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4

“…R proteins of the TIR-NB-LRR (TNL) subclass carry a Toll/Interleukin-1 receptor/Resistance (TIR) protein domain at their N-termini, with homology to cytoplasmic domains of mammalian and Drosophila transmembrane immune receptors 6,7 . Examples include the tobacco N gene for virus resistance 8 , flax L and M genes for flax rust resistance 9 , several Arabidopsis RPP genes for downy mildew resistance 10 , Arabidopsis RPS4 (originally defined as conferring recognition of Pseudomonas syringae pathovar pisi effector AvrRps4) 11 and Arabidopsis RRS1-R that confers resistance to Ralstonia solanacearum via recognition of effector PopP2 (refs 12,13). The RRS1-R allele in accession Nd-1 confers PopP2 recognition, whereas the Col-0 RRS1-S allele does not.…”

Association Mapping in Plant Genomes

“…In Arabidopsis, new studies have been carried out aiming to dissect downy mildew resistance genes and climate-sensitive QTL, with special efforts focused on the understanding of adaptative variation Nemri et al, 2010). The first applied a CG approach, and the second a GWAS based on no fewer than 213,497 SNPs.…”