Genetic and physical localization of the root-knot nematode resistance locus Mi in tomato

Abstract

As part of a map-based cloning strategy designed to isolate the root-knot nematode resistance gene Mi, tomato F2 populations were analyzed in order to identify recombination points close to this economically important gene. A total of 21,089 F2 progeny plants were screened using morphological markers. An additional 1887 F2 were screened using PCR-based flanking markers. Fine-structure mapping of recombinants with newly developed AFLP markers, and RFLP markers derived from physically mapped cosmid subclones, localized Mi to a genomic region of about 550 kb. The low frequency of recombinants indicated that recombination was generally suppressed in these crosses and that crossovers were restricted to particular regions. To circumvent this problem, a population of Lycopersicon peruvianum, the species from which Mi was originally introgressed, that was segregating for resistance was developed. Screening of this population with PCR, RFLP and AFLP markers identified several plants with crossovers near Mi. Recombination frequency was approximately eight-fold higher in the Mi region of the L. peruvianum cross. However, even within the wild species cross, recombination sites were not uniformly distributed in the region. By combining data from the L. esculentum and L. peruvianum recombinant analyses, it was possible to localize Mi to a region of the genome spanning less than 65 kb.

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

“…The existence of a 70-kbp inversion between S. demissum and S. tuberosum in this genome segment has been demonstrated (Ballvora et al 2007). Suppression of recombination depending on the source and size of the introgression from wild species has been shown in tomato (Liharska et al 1996;Kaloshian et al 1998). Linkage disequilibrium extending over several centimorgan has also been observed by Simko et al (2006) and Li et al (2008) in diVerent populations of tetraploid and diploid potato genotypes.…”

TheMi-9Gene fromSolanum arcanumConferring Heat-Stable Resistance to Root-Knot Nematodes Is a Homolog ofMi-1

“…The short arm of tomato chromosome 6 is a rich source of disease R genes, and two distinct R gene groups have been cloned from this portion of the chromosome. These are Cf-2 and Cf-5 with LRR and transmembrane domains and Mi-1 with NBS-LRR domains (Dixon et al, 1996(Dixon et al, , 1998Kaloshian et al, 1998;Milligan et al, 1998). We considered the possibility that either a homolog of Cf or Mi-1 could confer the heat-stable nematode resistance.…”

“…The presence of this inversion partly explains the lack of recombination in this region in crosses between root-knot nematode susceptible tomato and resistant tomato that contains S. peruvianum-introgressed region Seah et al, 2004). Although the suppression of recombination is partly attributed to the presence of the S. peruvianum-introgressed genome, the suppression is more pronounced in the region spanning the inversion (Liharska et al, 1996;Kaloshian et al, 1998;Seah et al, 2004). While several recombination events were identified in close proximity to the Mi locus, no recombination between C264.2 and Rex-1 was previously reported .…”

“…For DNA-blot analysis, DNA was isolated, restricted with EcoRV restriction enzyme, and DNA blots prepared according to Kaloshian et al (1998). A 300-bp subclone of Mi-1 containing the NBS region (clone 3-3) was used as probe.…”

“…Two additional RFLP markers, C264.1 and C32.1, located on the short arm of chromosome 6, were used to further map the recombinants (Table I; Kaloshian et al, 1998). One recombinant from F 2 class 10, E27, had recombination between Rex-1 and C264.1 (Table I), and F 3 progeny of this family segregated in a 3:1 ratio for heat-stable resistance (Supplemental Table S2), indicating that Mi-9 is located below Rex-1 (e.g.…”