Spring durum wheat occupies over 0.5 M ha in Kazakhstan and represents an important domestic and export commodity. This study aimed to characterize 151 durum wheat cultivars and advanced lines originating from eight breeding programs of the Kazakhstan–Siberia Spring Wheat Improvement Network (KASIB) between 2003 and 2018. The phenotypic characterization was performed in two contracting evaluation sites more than 1000 km apart (Almaty in the Southeast and Shortandy in the North) for two years and a total of 11 agronomic traits were recorded. Field trials at both locations followed regional agronomy practices, including sowing, harvesting, and genotype evaluation using a randomized complete block design (RCBD). The growing season was longer in Almaty, resulting in a higher number of grains per spike. Though grains are smaller in size with an overall higher yield, 243 g/m² versus 170 g/m², there was no correlation between germplasm performance at the two sites. Molecular characterization was performed with 10 iPBS-retrotransposons primers that resulted in a total of 345 bands and showed a mean polymorphism of 91.9%. Mean values of gene diversity (0.251), Shannon’s information index (0.388), and expected heterozygosity (0.233) revealed a relatively high level of genetic diversity in the KASIB set. AMOVA revealed higher genetic variations due to differences within the populations. Marker-based cluster analysis, including STRUCTURE and neighbor-joining algorithms, divided the material into two populations with clear differences in geographic origin. Superiors and diverse germplasm identified in the study are recommended for marker assisted selection and breeding.

Wheat production, globally and in Kazakhstan, is significantly limited by heat stress and drought. The evaluation of agronomic traits related to yield under stress conditions is crucial for identifying yield-limiting factors and selecting drought-tolerant germplasm. The aim of this study was to evaluate the variability of the main agronomic and physiological characteristics of 45 winter wheat collection accessions obtained during CIMMYT international variety trials (23IWWYT-IRR and 22IWWYT-SA) in the arid conditions of Southeastern Kazakhstan (foothills of the Zailiyskiy Alatau, 48° N, 77° E, 740 m above sea level) and to identify drought-resistant germplasm. As a result of three years of research (2019–2022) under drought conditions during the 2020–2021 growing season with a high negative environment index (Ij = −3.07), three adapted genotypes were identified: BONITO-37/MV10-2000, LYMARIVNA, and OK12D22004-016. They had yields of 5.3, 5.6, and 5.2 t/ha, respectively, significantly exceeding the yield of the local commercial variety STEKLOVIDNAYA 24 by 15.4–22.8%. The correlation coefficient between productivity variables was significant and varied from 0.55 ** to 0.82 ***. The percentage decrease in yield under drought conditions was 72.3%, while the drought resistance index was 0.27.

Common bunt (CB), caused by Tilletia caries and Tilletia laevis, poses a significant threat to wheat grain quality and yield. In organic farming, the development of resistant genotypes is the most effective way to combat the pathogen. This study aimed to identify new resistance sources against CB in international nurseries: Winter Wheat Nursery from Central Asia (WWN-CA) and International Common Bunt Resistance Nursery (CBUNT-RN), for strengthening winter breeding programs in Kazakhstan. Germplasm panels were evaluated against CB under artificial infection conditions in southeastern Kazakhstan and genotyped with KASP markers associated with QTLs (QBt.ifa-1AL, QBt.ifa-1BS, QBt.ifa-7AL and QBt.ifa-7DS) conferring bunt resistance. Results of immunological experiments and genotyping revealed 7 and 11 genotypes in WWN-CA and CBUNT-RN, respectively, and resistance to CB. CB incidence negatively correlated with SL (r = −0.23), NSS (r = −0.31), NKS (r = −0.41), and GWS (r = −0.44) (all p ≤ 0.01), in WWN-CA. ANOVA confirmed these findings, in which a pronounced reduction in these yield components was observed between inoculated and control HS groups (p ≤ 0.05). The QTL QBt.ifa-1AL on chromosome 1A shows promise for MAS against CB. The novel genetic knowledge and resistant resources identified here represent a valuable tool to enrich Central Asian germplasm with new alleles of resistance genes to advance organic farming in Kazakhstan.