Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’

Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity

SSR-based evaluation of genetic diversity in populations of Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. collected in South-East Kazakhstan

The development of informative polymorphic DNA markers for poorly studied genera is an important step in population analyses of living organisms, including those that play very important ecological roles in harsh environments, such as desert and semi-desert area. Examples of those poorly studied desert species are Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. However, a recent RNA-sequencing project in A. squarrosum has proposed a large set of hypothetical SSR (simple sequence repeat) markers. In this work, 11 novel polymorphic SSRs were found due to the screening of 24 randomly selected SSRs for three populations of A. squarrosum and one population of A. minus. The analysis of 11 SSRs revealed 16 polymorphic loci in two Agriophyllum species, 8 polymorphic loci within three populations of A. squarrosum, and 6 polymorphic loci in the population of A. minus. Statistical analyses showed high interspecific, but relatively low intraspecific genetic diversity. The phylogenetic clusterization and population structure analysis have demonstrated a clear segregation of A. minus from A. squarrosum, as well as the separation of population 1 from populations 2 and 3 of A. squarrosum. Thus, we identified the set of novel and informative SSR markers suitable for the study of genetic diversity in Agriophyllum

Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan

Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50–60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars