A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on aLycopersicon esculentum×Lycopersicon hirsutumcross

Abstract

A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); 01-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, 1-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with other molecular linkage maps of tomato, including the high density L. esculentum x Lycopersicon pennellii map, indicated that the lengths of the maps and linear order of RFLP markers were in good agreement, though certain chromosomal regions were less consistent than others in terms of the frequency of recombination. The present map provides a basis for identification and mapping of genes and QTLs for disease resistance and other desirable traits in PI126445 and other L. hirsutum accessions, and will be useful for marker-assisted selection and map-based gene cloning in tomato.

Quantitative resistance to Botrytis cinerea from Solanum neorickii

“…Two plants contained both pQTL4 and pQTL9 (group abb) and the additional reduction in DI of these lines suggests a fully additive model, showing the potential of pyramiding these two pQTLs. Figure 1 shows a comparison between (p)QTL positions identified in this study and previously mapped QTLs conferring resistance to B. cinerea (Finkers et al 2007b), mapped positions of resistance genes (R-genes), R-gene analogs mapped by Zhang et al (2002) and QTLs conferring resistance to other diseases (Tables 7, 8). The positions of B. cinerea QTLs may be homologous with the positions of R-genes or QTLs conferring resistance to Phytophtora infestans and Xanthomonas campestris (Chromosome 3); Ralstonia solanacearum, P. infestans, and O. neolycopersici (Chromosome 4); Alternaria solani, Fusarium oxysporum, and TMV (Chromosome 9).…”

Isolation and characterization of NBS-LRR- resistance gene candidates in turmeric(Curcuma longa cv. surama)

“…The structural specificity has made it possible to isolate potential resistance gene analogs (RGAs) by homology-based techniques in different plant species such as soybean (Kanazin et al, 1996;He et al, 2003), maize (Collins et al, 1998), lettuce (Shen et al, 1998), rice (Mago et al, 1999), common bean (Rivkin et al, 1999), citrus (Deng et al, 2000), wheat (Lacock et al, 2003), sorghum (Totad et al, 2005), and ginger (Nair and Thomas, 2007). The RGA fragments were also used as molecular markers for tagging the disease resistance loci in Arabidopsis (Aarts et al, 1998), rice (Ilag et al, 2000), tomato (Zhang et al, 2002), etc. Some RGAs have been demonstrated to be linked with known R-genes, and the wheat Lr10 gene has been successfully cloned by this method (Feuillet et al, 1997).…”

Targeting and genotyping RGAs in a mappingpopulation of the AA genome of wild Arachis

“…Resistance Gene Analogs are often clustered in the genome and are frequently part of resistance genes (Zhang et al 2002). However, since RGAs belong to a complex gene family, their use as molecular markers is complicated as it requires the use of techniques that are sensitive enough to distinguish similar sequence regions, such as PCR followed by PAGE.…”

“…The tagging of resistance genes together with marker-assisted selection should minimize the problems with linkage drag. In a number of reports, RGAs (Resistance Gene Analogs) were found to be clustered on chromosomes near to resistance genes or to be part of them (Zhang et al 2002). With the aim of understanding the diversity of resistance genes in Arachis, we scanned the genome of several wild and cultivated species in search for RGAs , using degenerate primers designed for resistance gene regions described elsewhere for other species (Kanazin et al 1996, Leister et al 1996, Yu et al 1996.…”