Next-generation sequencing based identification of novel resistance genes in wild tomato species

Abstract:

Wild relatives of tomato harbour a wealth of disease resistance genes that have been largely untapped by modern breeding, mainly because the traditional map-based cloning approach is too slow and expensive for systematic gene discovery across multiple species. This research applied whole-genome sequencing on the Illumina NovaSeq platform to 36 accessions from four wild Solanum species (S. pimpinellifolium, S. habrochaites, S. pennellii, and S. chilense) and four cultivated tomato references at British Columbia Agricultural University and Prairie Agricultural University, Canada, during 2022-2023. A total of 1,490 NBS-LRR (nucleotide-binding site leucine-rich repeat) resistance gene candidates were identified, of which 137 were novel sequences absent from the cultivated tomato reference genome SL4.0. S. pimpinellifolium contributed the largest number of novel candidates (42), concentrated in five gene clusters on chromosomes 2, 4, 6, 9, and 11. Expression analysis by RT-qPCR confirmed that 28 of the 137 novel genes were upregulated in response to Phytophthora infestans challenge. Functional markers were developed for the five largest gene clusters to enable marker-assisted introgression into cultivated backgrounds. These results expand the catalogue of available resistance genes for tomato improvement and demonstrate the efficiency of NGS-based approaches for mining wild germplasm.