Molecular screening of wild and cultivated tomato germplasm reveals potential materials for multi-locus disease resistance breeding

Tomato (Solanum lycopersicum L.) production faces major yield loss due to biotic stresses. Developing genetically resistant cultivars presents a sustainable alternative to chemical controls, which are often costly and ineffective. This study utilized 10 molecular markers, including SSR, SCAR, and CAPS markers, to assess resistance to six major diseases, including Fusarium wilt, late blight, bacterial wilt, root-knot nematode, Tomato Mosaic Virus (ToMV), and Tomato Yellow Leaf Curl Virus (TYLCV), across 964 tomato accessions comprising both wild germplasm (371) and cultivars (593). Wild germplasm, especially S. peruvianum, showed the highest frequencies of resistance loci. Markers linked to TYLCV and Fusarium wilt were particularly prevalent, with frequencies of 31.8% (TY-1/3_K), 34.0% (P1-16), and 55.8% (I2(OH)). Several wild accessions carried up to six resistance loci, highlighting the potential for gene pyramiding and the utility of wild species as reservoirs of multi-locus resistance. In contrast, resistance loci were limited in S. lycopersicum. Two S. lycopersicum germplasm collections were screened: a geographically representative collection from four Southeast Asian national genebanks and a genetically representative core collection from global public genebanks. The highest resistance frequencies in S. lycopersicum were observed for bacterial wilt-associated markers SLM12-2 and SLM12-10. However, the overall scarcity of resistance alleles in S. lycopersicum emphasizes the need for further introgression of resistance genes from wild relatives. This study provides valuable genetic insights into tomato germplasm for combating biotic stress, forming a foundation for sustainable breeding strategies to enhance disease resistance and safeguard global tomato production.