Evaluation of promising interspecific tomato rootstocks (Solanum lycopersicum × Solanum habrochaites) for molecular marker-based resistance screening, yield, and fruit quality

Grafting onto interspecific hybrid rootstocks is increasingly important for tomato production; however, producers remain overly dependent on a few commercial cultivars whose immunity is increasingly compromised by evolving diseases. Therefore, the validation of novel rootstock candidates is of considerable practical importance. This study aimed to evaluate six interspecific hybrid ( Solanum lycopersicum × Solanum habrochaites ) rootstock candidates for resistance-associated alleles, graft compatibility, yield performance, and fruit quality in comparison with commercial rootstocks. Six interspecific hybrid rootstock candidates, selected under the TÜBİTAK project from an initial pool of 15 hybrid combinations, were evaluated against the commercial rootstocks Beaufort F₁, Arazi F₁, and Balance F₁, using Fulya F₁ as the scion and an ungrafted Fulya F₁ control. Tube-grafted plants were grown through a spring greenhouse cycle. Molecular marker analyses were conducted to identify resistance-associated alleles linked to Fusarium wilt, Fusarium crown and root rot, Verticillium wilt, and root-knot nematode resistance. Graft success, yield, and fruit-quality traits were evaluated, and multivariate analyses were used to characterize the overall performance of the rootstock–scion combinations. Molecular marker analysis indicated the presence of resistance-associated alleles linked to Fusarium wilt, Fusarium crown and root rot, Verticillium wilt, and root-knot nematode resistance. RSH-6, RSH-16, RSH-17, and RSH-18 carried the most complete set of resistance-associated alleles, with graft success rates ranging from 93.33% to 100.00%. Total yield differed among the combinations (4.70–6.46 kg plant⁻¹; p < 0.05) and was highest in RSH-6, which was statistically comparable to the commercial rootstocks. Several grafted combinations showed greater fruit width and firmness than ungrafted Fulya F₁, while other quality traits were largely comparable among treatments. Multivariate analyses placed RSH-6 close to the commercial standards and supported its favorable overall yield and fruit-quality profile. The findings indicate that several of the newly developed interspecific hybrid rootstock candidates combine a broad set of resistance-associated alleles with high graft success and satisfactory horticultural performance. Among them, RSH-6 showed the most promising overall performance, with yield and fruit-quality characteristics comparable to established commercial rootstocks. These results support RSH-6 as a promising candidate for further validation in multi-location and multi-season trials.