Presence of disease resistance genes in tomato germplasm revealed by gene-based or gene-linked molecular markers

Tomato (Solanum lycopersicum L.) is a worldwide economically important vegetable crop, but the production is severely threatened by diseases and pests. Clarifying the presence of disease resistant genes in tomato germplasm is helpful for the development and deployment of resistant cultivars. In this study, 21 genes for resistance to 10 diseases were examined in a collection of 401 tomato accessions using gene-associated molecular markers. The results showed that the presence of the 21 genes in the 401 tomato accessions ranged from 0.2% to 66.1%. Frequencies (27.9–66.1%) of I-1, I-2, Sm, Tm-2a, and Ph-3 genes were higher than other genes, while frequencies (0.2–1.2%) of Ty-2, Ty-4, Mi-HT, I-3, and Tm-2 genes were very low. Based on the marker genotypes, 86.3% accessions carried at least one of disease resistance genes. Most (84.2%) Contemporary Processing F1 (CPF) carried 4–8 genes and 74.1% Contemporary Fresh-market F1 (CFF) carried 4–6 genes, while 87.4% Contemporary Processing Inbreds (CPI) carried 1–5 genes and 85.3% Contemporary Fresh-market Inbreds (CFI) carried 1–4 genes. Furthermore, the numbers of disease resistance genes were lower in Latin American Landrace (1–3), Vintage (1–3), and CFI (1–4) than in CFF (1–8), CPI (1–7), and CPF (2–10). Among multiple markers used for detection of the single gene, markers CAUTy4 and 18IY13 had the highest consistency (100%) of genotypes for the Ty-4 gene, followed by SM-InDel and InDel-FT-29 (94.0%) for the Sm gene, while markers AW910upF2R3, 20IY10, and TG0302 for detecting the Ty-2 gene had the lowest consistency (44.4%). Disease evaluation confirmed the accuracy of marker-assisted identification of corresponding genes except that the accessions carrying the Ty-1 gene uniquely detected by the CAPS1 marker were susceptible to tomato yellow leaf curl virus. The data obtained here provide valuable information for marker-assisted selection of these disease resistance genes and the use of these germplasm in tomato breeding and production.