Identification of Stem Rust Resistance Genes in Released Wheat Varieties by Linked SSR Markers and Phenotypic Screening

Abstract

Wheat suffers significant yield losses due to stem rust disease caused by Puccinia graminis Pers. f. sp. tritici Eriks and Henn. Molecular level assessment of existing Sr genes in improved and advanced wheat materials combined with phenotypic screening lays down the basis for effective varietal development against this production constraint. Therefore, this study was carried out: to detect stem rust resistance genes present in Ethiopian bread wheat and durum wheat varieties using molecular markers; and to determine their effectiveness for the virulent Ethiopian stem rust races including Ug99. Screening of 49 wheat varieties with 11 SSR markers linked to 11 Stem rust resistance genes resulted in the detection of 5 Stem rust resistance genes (<i>Sr22, Sr25, Sr24, Sr77</i> and <i>SrTA10187</i>) in a subset of 12 varieties. The detected number of genes ranged between 1 and 2 per genotype. Despite amplifying the expected fragment, the markers have also resulted in several off-target amplifications suggesting the need to develop other relatively stable markers specific to the target genes. Field resistance screening at Debre Zeit Research Center resulted in 20 varieties showing good resistance to stem rust of which 2 are durum wheat cultivars and the rest 18 are bread wheat varieties. Recent data in 2022, however, showed only 5 out of the 20 had a resistant reaction while the other even became susceptible. For instance, most of the mega bread wheat cultivars like Ogolcho also were defeated due to the newly emerging race TTKTT. Among the genes detected by molecular markers, only <i>SrTA10187</i> seems to be effective against the rust population in the field. Seedling resistances screening gave a range of proportion of Resistant (R) to Susceptible (S) variety varying from 12:36 for TTKTT; 40:8 for TKTTF; 39:9 for TTKSK and 44:4 for TTTTF. Eight varieties (Sulla, Galil, Huluka, Kingbird, Millenium, Obsa, Tate and Ilani) exhibited resistant reaction consistently across the four pathotypes. Nine varieties (Honqollo, Millenium, Kulkulu, Shorima, Hogana, Meraro, Ilani and Galil) identified as resistant at both seedling and Adult plant stage. The genes, <i>Sr22</i> in variety Oda and <i>Sr25</i> in variety Dinknesh appeared to be effective for TTKTT, TKTTF, TTKSK and TKTTF, TTKSK, TTTTF, respectively. The detected Stem rust resistance genes in the present study which are effective against the pathotyeps combined with the resistant varieties at seedling and adult plant stage can support the wheat breeding program towards improving the crop.