Molecular Markers Help with Breeding for Agronomic Traits of Spring Wheat in Kazakhstan and Siberia.

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.

Morphological and Molecular Characterization of Bacterial Pathogens Associated with Leaf Mottle of Sunflower in Northern Kazakhstan.

Leaf mottle is a serious disease in the common sunflower (Helianthus annuus L.), which affects plant growth and development and seed quality and yield. Over the past few years, the North Kazakhstan region, a sunflower-producing area in Kazakhstan, has been seriously affected by leaf mottle. Since 2021, symptomatic leaves have been collected from production areas of this base to determine the pathogens causing sunflower foliar diseases. One hundred bacterial strains were isolated, and two genera and five species were identified based on morphological characteristics, molecular genetics, and phylogenetic analysis (16S gene region). The genus Bacillus was represented by four species: Bacillus subtilis, B. megaterium, B. amyloliquefaciens, and B. flexus. The genus Paenibacillus was represented by one species, P. peoriae. Pathogenicity experiments showed that B. subtilis, B. megaterium, B. flexus, and P. peoriae could cause leaf mottle disease symptoms. However, disease symptoms caused by B. flexus were highly similar to those observed on infected leaves under natural conditions in the field. Therefore, these bacterial isolates were found to be the primary pathogens causing sunflower leaf mottle, and B. flexus was the most common and virulent pathogen in this study. In addition, this is the first report of B. megaterium, B. flexus, and P. peoriae as pathogens associated with sunflower leaf mottle in Kazakhstan.

Genetic Characterization of Spring Wheat Germplasm for Macro-, Microelements and Trace Metals.

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.

Variation of Macro- and Microelements, and Trace Metals in Spring Wheat Genetic Resources in Siberia.

Western Siberia is one of the major spring wheat regions of Russia, cultivating over 7 Mha. The objective of the study was to evaluate the variation of macro- and microelements, and of trace metals in four distinct groups of genetic resources: primary synthetics from CIMMYT (37 entries), primary synthetics from Japan (8), US hard red spring wheat cultivars (14), and material from the Kazakhstan-Siberian Network on Spring Wheat Improvement (KASIB) (74). The experiment was conducted at Omsk State Agrarian University, using a random complete block design with four replicates in 2017 and 2018. Concentrations of 15 elements were included in the analysis: macroelements, Ca, K, Mg, P, and S; microelements, Fe, Cu, Mn, and Zn; toxic trace elements, Cd, Co, Ni; and trace elements, Mo, Rb, and Sr. Protein content was found to be positively correlated with the concentrations of 11 of the elements in one or both years. Multiple regression was used to adjust the concentration of each element, based on significant correlations with agronomic traits and macroelements. All 15 elements were evaluated for their suitability for genetic enhancement, considering phenotypic variation, their share of the genetic component in this variation, as well as the dependence of the element concentration on other traits. Three trace elements (Sr, Mo, and Co) were identified as traits that were relatively easy to enhance through breeding. These were followed by Ca, Cd, Rb, and K. The important biofortification elements Mn and Zn were among the traits that were difficult to enhance genetically. The CIMMYT and Japanese synthetics had significantly higher concentrations of K and Sr, compared to the local check. The Japanese synthetics also had the highest concentrations of Ca, S, Cd, and Mo. The US cultivars had concentrations of Ca as high as the Japanese synthetics, and the highest concentrations of Mg and Fe. KASIB's germplasm had near-average values for most elements. Superior germplasm, with high macro- and microelement concentrations and low trace-element concentrations, was found in all groups of material included.

Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study.

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.