A Solanum lycopersicum x Solanum pimpinellifolium linkage map of tomato displaying genomic locations of R-genes, RGAs, and candidate resistance/defense-response ESTs

Abstract

We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F(2) population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4 cM of the 12 tomato chromosomes with an average marker distance of 4.0 cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and other S. pimpinellifolium accessions, and possibly for utilization of genetic variation within S. lycopersicum.

Figure 1

Distribution of percent Solanum lycopersicum genome in the F₂ population, estimated based on 220 codominant markers.

Figure 2

A genetic linkage map of tomato constructed based on an F₂ population of a cross between a tomato (S. lycopersicum) breeding line (NCEBR-1) and an accession (LA2093) of tomato wild species S. pimpinellifolium and 250 RFLP, EST, and RGA markers. RFLP markers are shown in blue, ESTs in green, and RGAs in red fonts. The names of the markers are shown at the right and the map distances between them (in cM, using Kosambi function) are shown at the left of the chromosomes. The approximate chromosomal locations of disease-resistance genes (R-genes) and quantitative resistance loci (QRL), as inferred from other published researches, are shown in parentheses to the right of chromosomes. The descriptions of the R-genes and QRL are as follows: Asc: resistance to Alternaria stem canker (Alternaria alternata f. sp. lycopersici) [54, 55]; Bw (1–5) or Rrs (3–12): QLRs for resistance to bacterial wilt (Ralstonia solanacearum) [–59]; Cf (1–9, ECP2): resistance to leaf mould (Cladosporium fulvum) [–65]; Cmr: cucumber mosaic virus [66]; Fen: sensitivity to herbicide fenthion [67]; Frl: resistance to Fusarium crown and root rot (Fusarium oxysporum f. sp. radicis-lycopersici) [68]; Hero: resistance to potato cyst namatode (Globodera rostochiensis) [69]; I (I, 1, 2, 2C, 3): resistance to different races of Fusarium wild (Fusarium oxysporum f. sp. lycopersici) [–78]; Lv: resistance to powdery mildew (Leveuillula taurica) [79]; Meu-1: resistance to potato aphid [–82]; Mi (Mi, 1, 2, 3, 9): resistance to root knot nematodes (Meloidogyne spp.) [, –89]; Ol (1, 2, 3): resistance to powdery mildew (Oidium lycopersicum) [90, 91]; Ph (1, 2, 3): resistance to late blight (Phytophthora infestans) in tomato [–94]; Pot-1: resistance to potyvirus [95]; Pto and Prf: resistance to bacterial speck (Pseudomonase syringae pv tomato) [96, 97]; Py-1: resistance to corky root rot (Pyrenochaeta lycopersici) [98]; Rcm (1–10): QRL for resistance to bacterial canker (Clavibacter michiganensis) [99, 100]; Rrs (3–12) or Bw (1–5): QLRs for resistance to bacterial wilt (Ralstonia solanacearum) [–59]; Rx (1, 2, 3, 4): resistance to bacterial spot (Xanthomonas campestris) [–103]; Sm: resistance to Stemphilium [104]; Sw-5: resistance to tomato-spotted wilt virus [105, 106]; Tm-1 and Tm-2^a: resistance to tobacco mosaic virus [, –110]; Ty (1, 2, 3): resistance to tomato yellow leaf curl virus [–113]; Ve: resistance to Verticillium dahliae [114, 115].