Stem rust in recent years has acquired an epiphytotic character, causing significant economic damage for wheat production in some parts of Western Siberia. On the basis of a race composition study of the stem rust populations collected in 2016–2017 in Omsk region and Altai Krai, 13 pathotypes in Omsk population and 10 in Altai population were identified. The race differentiation of stem rust using a tester set of 20 North American Sr genes differentiator lines was carried out. The genes of stem rust pathotypes of the Omsk population are avirulent only to the resistance gene Sr31, Altai isolates are avirulent not only to Sr31, but also to Sr24, and Sr30. A low frequency of virulence (10–25 %) of the Omsk population pathotypes was found for Sr11, Sr24,Sr30, and for Altai population – Sr7b,Sr9b,Sr11,SrTmp, which are ineffective in Omsk region. Field evaluations of resistance to stem rust were made in 2016–2018 in Omsk region in the varieties and spring wheat lines from three different sources. The first set included 58 lines and spring bread wheat varieties with identified Sr genes – the so-called trap nursery (ISRTN – International Stem Rust Trap Nursery). The second set included spring wheat lines from the Arsenal collection, that were previously selected according to a complex of economically valuable traits, with genes for resistance to stem rust, including genes introgressed into the common wheat genome from wild cereal species. The third set included spring bread wheat varieties created in the Omsk State Agrarian University within the framework of a shuttle breeding program, with a synthetic wheat with the Ae. tauschiigenome in their pedigrees. It was established that the resistance genes Sr31, Sr40,Sr2 complexare effective against stem rust in the conditions of Western Siberia. The following sources with effective Srgenes were selected: (Benno)/6*LMPG-6 DK42, Seri 82, Cham 10, Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo (Sr24,1RS-Am), Siouxland (Sr24,Sr31), Roughrider (Sr6, Sr36), Sisson (Sr6,Sr31,Sr36), and Fleming (Sr6,Sr24,Sr36,1RS-Am), Pavon 76 (Sr2 complex) from the ISRTN nursery; No. 1 BC 1F2 (96 × 113) × 145 × 113 (Sr2,Sr36,Sr44), No. 14а F 3(96 × 113) × 145 (Sr36,Sr44), No. 19 BC 2F3(96 × 113) × 113 (Sr2, Sr36, Sr44), and No. 20 F 3 (96 × 113) × 145 (Sr2,Sr36,Sr40, Sr44) from the Arsenal collection; and the Omsk State Agrarian University varieties Element 22 (Sr31,Sr35), Lutescens 27-12, Lutescens 87-12 (Sr23,Sr36), Lutescens 70-13, and Lutescens 87-13 (Sr23,Sr31,Sr36). These sources are recommended for inclusion in the breeding process for developing stem rust resistant varieties in the region.

Exploiting genetically diverse lines to identify genes for improving crop performance is needed to ensure global food security. A genome-wide association study (GWAS) was conducted using 46,268 SNP markers on a diverse panel of 143 hexaploid bread and synthetic wheat to identify potential genes/genomic regions controlling agronomic performance (yield and 26 yield-related traits), disease resistance, and grain quality traits. From phenotypic evaluation, we found large genetic variation among the 35 traits and recommended five lines having a high yield, better quality, and multiple disease resistance for direct use in a breeding program. From a GWAS, we identified a total of 243 significant marker-trait associations (MTAs) for 35 traits that explained up to 25% of the phenotypic variance. Of these, 120 MTAs have not been reported in the literature and are potentially novel MTAs. In silico gene annotation analysis identified 116 MTAs within genes and of which, 21 MTAs were annotated as a missense variant. Furthermore, we were able to identify 23 co-located multi-trait MTAs that were also phenotypically correlated to each other, showing the possibility of simultaneous improvement of these traits. Additionally, most of the co-located MTAs were within genes. We have provided genomic fingerprinting for significant markers with favorable and unfavorable alleles in the diverse set of lines for developing elite breeding lines from useful trait-integration. The results from this study provided a further understanding of genetically complex traits and would facilitate the use of diverse wheat accessions for improving multiple traits in an elite wheat breeding program.

Intermediate wheatgrass (IWG; Thinopyrum intermedium), a nutritionally dense and sustainable crop, is a promising novel ingredient in bakery applications. The main aim of this study was to investigate the potential of IWG as a novel ingredient in breadmaking. The second aim was to investigate the characteristics of breads substituted with 15, 30, 45, and 60% IWG flour compared to control bread produced using wheat flour. The gluten content and quality, bread quality, bread staling, yellow pigment, and phenolic and antioxidant properties were determined. Enrichment with IWG flours significantly affected the gluten content and quality and bread characteristics. Increased levels of IWG flour substitution significantly decreased the Zeleny sedimentation and gluten index values and increased the dry and wet gluten contents. The bread yellow pigment content and crumb b* colour value increased with the increasing level of IWG supplementation. IWG addition also had a positive effect on the phenolic and antioxidant properties. Bread with 15% IWG substitution had the highest bread volume (485 mL) and lowest firmness values (654 g-force; g-f) compared to the other breads, including the control (i.e., wheat flour bread). The results indicated that IWG has great potential to be used in bread production as a novel, healthy, and sustainable ingredient.

The Kazakhstan-Siberia Network for Spring Wheat Improvement (KASIB) was established in 2000, forming a collaboration between breeding and research programs through biannual yield trials. A core set of 142 genotypes from 15 breeding programs was selected, genotyped for 81 DNA functional markers and phenotyped for 10 agronomic traits at three sites in Kazakhstan (Karabalyk, Shortandy and Shagalaly) and one site in Russia (Omsk) in 2020–2022. The study aim was to identify markers demonstrating significant effects on agronomic traits. The average grain yield of individual trials varied from 118 to 569 g/m². Grain yield was positively associated with the number of days to heading, plant height, number of grains per spike and 1000-kernel weight. Eight DNA markers demonstrated significant effects. The spring-type allele of the Vrn-A1 gene accelerated heading by two days (5.6%) and was present in 80% of the germplasm. The winter allele of the Vrn-A1 gene significantly increased grain yield by 2.7%. The late allele of the earliness marker per se, TaMOT1-D1, delayed development by 1.9% and increased yield by 4.5%. Translocation of 1B.1R was present in 21.8% of the material, which resulted in a 6.2% yield advantage compared to 1B.1B germplasm and a reduction in stem rust severity from 27.6 to 6.6%. The favorable allele of TaGS-D1 increased both kernel weight and yield by 2–3%. Four markers identified in ICARDA germplasm, ISBW2-GY (Kukri_c3243_1065, 3B), ISBW3-BM (TA004946-0577, 1B), ISBW10-SM2 (BS00076246_51, 5A), ISBW11-GY (wsnp_Ex_c12812_20324622, 4A), showed an improved yield in this study of 3–4%. The study recommends simultaneous validation and use of selected markers in KASIB’s network.

Wheat as a staple food crop is the main source of micro- and macronutrients for most people of the world and is recognized as an attractive crop for biofortification. This study presents a comprehensive investigation of genomic regions governing grain micro- and macroelements concentrations in a panel of 135 diverse wheat accessions through a genome-wide association study. The genetic diversity panel was genotyped using the genotyping-by-sequencing (GBS) method and phenotyped in two environments during 2017–2018. Wide ranges of variation in nutrient element concentrations in grain were detected among the accessions. Based on 33,808 high-quality single nucleotide polymorphisms (SNPs), 2997 marker-element associations (MEAs) with −log10(p-value) > 3.5 were identified, representing all three subgenomes of wheat for 15-grain concentration elements. The highest numbers of MEAs were identified for Mg (499), followed by S (399), P (394), Ni (381), Cd (243), Ca (229), Mn (224), Zn (212), Sr (212), Cu (111), Rb (78), Fe (63), Mo (43), K (32) and Co (19). Further, MEAs associated with multiple elements and referred to as pleiotropic SNPs were identified for Mg, P, Cd, Mn, and Zn on chromosomes 1B, 2B, and 6B. Fifty MEAs were subjected to validation using KASIB multilocational trial at six sites in two years using 39 genotypes. Gene annotation of MEAs identified putative candidate genes that potentially encode different types of proteins related to disease, metal transportation, and metabolism. The MEAs identified in the present study could be potential targets for further validation and may be used in marker-assisted breeding to improve nutrient element concentrations in wheat grain.

Spring bread wheat is the staple crop in Western Siberia and Kazakhstan, a significant portion of which goes for export. Wheat breeding with a high level of zinc in wheat grain is the most cost-effective and environmentally friendly way to address zinc deficiency in the diet. The purpose of this work was to evaluate the contribution of the factors ‘location’ and ‘genotype’ in the variability of zinc content in wheat grain, and to identify the best varieties as sources of this trait for breeding. The research on screening zinc content in the wheat grain of 49 spring bread wheat varieties from the KazakhstanSiberia Spring Wheat Trial (KASIB) nursery was carried out at 4 sites in Russia (Chelyabinsk, Omsk, Tyumen, Novosibirsk) and 2 sites in Kazakhstan (Karabalyk and Shortandy) in 2017–2018. The content of zinc in wheat grain was evaluated at the Ionomic Facility of University of Nottingham in the framework of the EU project European Plant Phenotyping Network-2020. The analysis of variance showed that the main contribution into the general phenotypic variation of the studied trait, 38.7 %, was made by the factor ‘location’ due to different contents of zinc and moisture in the soil of trial sites; the effect of the factor ‘year’ was 13.5 %, and the effect of the factor ‘genotype’ was 8.0 %. The most favorable environmental conditions for accumulation of zinc in wheat grain were observed in the Omsk region. In Omsk, the average zinc content in all studied varieties was 50.4 mg/kg, with 63.7 mg/kg in the best variety ‘OmGAU 100’. These values are higher than the target values of the international program Harvest Plus. ‘Novosibirskaya 16’ (49.4 mg/kg), ‘Silach’ (48.4 mg/kg), ‘Line 4-10-16’ (47.2 mg/kg), ‘Element 22’ (46.3 mg/kg) and ‘Lutescens 248/01’ (46.0 mg/kg) were identified as being the best varieties. Significant possibilities for the production of wheat grain with high zinc content, which is in demand for the production of bread and pastry products with functional properties, were identified in the Western Siberian region.