Identification of QTLs for Resistance to Leaf Rust, Yellow Rust, and Septoria Tritici Blotch Using Association and Linkage Mapping in Durum Wheat

Durum wheat (Triticum turgidum subsp. durum) is a key staple crop increasingly challenged by the need to meet global food demands under evolving biotic pressures. A detailed understanding of the genetic basis and regulatory mechanisms underlying disease resistance is essential for the development of high-yielding, resilient cultivars. To this end, accessions from the Tetraploid Germplasm Collection (TGC; Maccaferri et al., 2019) and the Global Durum Panel (GDP; Mazzucotelli et al., 2020) were systematically evaluated for resistance to major fungal diseases—including leaf rust, yellow rust and septoria tritici blotch—across multiple years under field conditions. Several accessions, mainly landraces such as Trinakria, Kyperounda, (both from the Mediterranean germplasm), Russello SG7, two Ethiopians (EP98 and EP54), and T. carthlicum landraces and the modern cultivar Monastir, demonstrated stable and broad-spectrum resistances across multiple field seasons. These resistant lines were selected for the development of biparental mapping populations, following a nested association mapping (NAM)-like design, using elite cultivars such as Svevo, Meridiano, and Kofa as common reference parents, highly susceptible to the main foliar diseases. The resulting populations, comprising between 100 and 200 recombinant inbred lines (RILs) each, were genotyped using an optimized wheat 25K Infinium iSelect SNP array to generate the corresponding linkage maps and to enable the identification of loci associated with disease resistance. The populations were phenotyped for yellow rust (YR), leaf rust (LR), and septoria tritici blotch (STB) under field conditions in Pò Valley and in Tuscany Italian environments in 2024 and 2025. Additionally, the same populations were evaluated for response to rust and Zymoseptoria tritici at seedling stage in greenhouse, with selected strains Genome-Wide Association Studies (GWAS) with four models (MLM, MLMM, FarmCPU, and BLINK) revealed several QTLs significantly associated with Yr, Lr and STB resistance. Haplotype analysis provided insights into allelic diversity, origin, and phenotypic effects, increasing our understanding of resistant genetic variants within the Triticum turgidum Sps. global gene pool.