Genetic Dissection of Triple Rust Resistance (Leaf, Yellow, and Stem Rust) in Kenyan Wheat Cultivar, “Kasuku”

Climate change is driving the spread of transboundary wheat diseases, necessitating the development of resilient wheat varieties for sustainable agriculture. Wheat rusts, including leaf rust (LR), yellow rust (YR), and stem rust (SR), remain among the most economically significant diseases, causing substantial yield losses worldwide. Enhancing genetic diversity by identifying and deploying rust resistance genes is crucial for durable resistance in wheat breeding programs. This study aimed to identify quantitative trait loci (QTL) associated with rust resistance in the CIMMYT wheat line Kasuku, released in Kenya in 2018. A recombinant inbred line (RIL) population (181 lines) derived from Kasuku (triple rust-resistant) and Apav#1 (triple rust-susceptible) was evaluated under artificial LR and YR epidemics in Mexico and YR and SR in Kenya. QTL mapping using genotyping-by-sequencing (DArTSeq) and phenotypic data identified four major loci: <i>QLrYrSr.cim-1BL</i> (<i>Lr46</i>/<i>Yr29</i>/<i>Sr58</i>) on 1BL, conferring resistance to LR, YR, and SR; <i>QLrYr.cim-2AS</i> (<i>Yr17</i>/<i>Lr37</i>) on 2AS, providing LR and YR resistance; <i>QLrYr.cim-3AL</i> on 3AL; and <i>QLrYrSr.cim-6AL</i> on 6AL, representing novel loci associated with multiple rust resistances. Additionally, minor QTL were also identified: for LR (<i>QLr.cim-2DS</i> on 2DS, <i>QLr.cim-6DS</i> on 6DS), for YR (<i>QYrKen.cim-3DS</i> on 3DS, <i>QYrKen.cim-6BS</i> on 6BS), and for SR (<i>QSr.cim-2BS</i> on 2BS, <i>QSr.cim-5AL</i> on 5AL, <i>QSr.cim-6AS</i> on 6AS). RILs carrying these QTL combinations exhibited significant reductions in rust severity. Flanking markers for these loci are being used to develop Kompetitive Allele-Specific PCR (KASP) markers for fine mapping and marker-assisted selection (MAS). These findings contribute to the strategic deployment of rust resistance genes in wheat breeding programs, facilitating durable resistance to multiple rust pathogens.