Phenotyping and Identification of Molecular Markers Associated with Leaf Rust Resistance in the Wheat Germplasm from Kazakhstan, CIMMYT and ICARDA.

Leaf rust (LR) is the most widespread disease of common wheat worldwide. In order to evaluate leaf rust resistance, 70 uncharacterized wheat cultivars and promising lines with unknown leaf rust resistance genes (Lr genes) were exposed to Kazakhstani Puccinia triticina (Pt) races at the seedling stage. Field tests were performed to characterize leaf rust responses at the adult plant growth stage in the 2020-2021 and 2021-2022 cropping seasons. The wheat collection showed phenotypic diversity when tested with two virulent races of Pt. Thirteen wheat genotypes (18.6%) showed high resistance at both seedling and adult plant stages. In most cases, breeding material originating from international nurseries showed higher resistance to LR. Nine Lr genes, viz. Lr9, Lr10, Lr19, Lr26, Lr28, Lr34, Lr37, Lr46, and Lr68, either singly or in combination, were identified in 47 genotypes. Known Lr genes were not detected in the remaining 23 genotypes. The most commonly identified resistance genes were Lr37 (17 cultivars), Lr34 (16 cultivars), and Lr46 (10 cultivars), while Lr19, Lr68, Lr26, and Lr28 were the least frequent. Four Lr genes were identified in Keremet and Hisorok, followed by three Lr genes in Aliya, Rasad, Reke, Mataj, Egana and Almaly/Obri. The molecular screening revealed twenty-nine carriers of a single Lr gene, ten carriers of two genes, six carriers of three genes, and two carriers of four genes. Most of these accessions showed a high and moderate level of APR (Adult plant resistance) and may be utilized for the incorporation of Lr genes in well-adapted wheat cultivars. The most effective combination was Lr37, Lr34, and Lr68, the carriers of which were characterized by a low disease susceptibility index. The obtained results will facilitate breeding programs for wheat resistance in Kazakhstan.

QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations.

The two recombinant inbred line (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). The quantitative trait loci (QTLs) were detected through multi-year phenotypic evaluations (2018-2020) and using high-throughput DArTseq genotyping technology. RILs exhibited significant genetic variation with p < 0.001, and the coefficient of variation ranged from 9.79% to 47.99% for both LR and YR in all Environments and stages of evaluations. The heritability is quite high and ranged between 0.47 and 0.98. We identified nine stable QTLs for YR APR on chromosomes 1B, 2A, 2B, 3D, and 4D and four stable QTLs for LR APR on chromosomes 2B, 3B, 4A, and 5A. Furthermore, in silico analysis revealed that the key putative candidate genes such as cytochrome P450, protein kinase-like domain superfamily, zinc-binding ribosomal protein, SANT/Myb domain, WRKY transcription factor, nucleotide sugar transporter, and NAC domain superfamily were in the QTL regions and probably involved in the regulation of host response toward pathogen infection. The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS).

Identification of Stripe Rust Resistance Genes in Common Wheat Cultivars and Breeding Lines from Kazakhstan.

Stripe (yellow) rust, caused by Puccinia striiformis f.sp. tritici (Pst), is a fungal disease that presents one of the most serious threats to the wheat crops, causing severe yield losses worldwide, including Kazakhstan. The objectives of this study were to: (1) evaluate a winter wheat collection for stripe rust resistance during an adult plant growth stage, (2) identify the presence of selected Yr genes using linked molecular markers in wheat germplasm, (3) identify potentially useful resistant wheat genotypes among leading cultivars and advanced breeding lines. This study evaluated 70 winter wheat genotypes for stripe rust resistance. According to the field reactions, 42 entries (60%) had R or MR reactions including 27 breeding lines (38.6%) and 15 (21.4%) cultivars. Twenty-eight breeding lines/cultivars (40.0%) were susceptible in both years. According to the average coefficient of infection value (ACI) six genotypes were regarded as possessing high level of adult plant resistance. Cultivars/lines carrying Yr10 alone or in combination with other Yr resistance genes provided resistance to stripe rust. Eleven breeding lines showed <5% disease severity in both years. Linked marker analysis revealed the presence of several gene and gene complexes (Yr5, Yr10, Yr15, Yr17/Lr37/Sr38 and Yr18/Lr34). Among a collection of 70 winter wheat breeding lines and cultivars produced in Kazakhstan three stripe rust resistance genes (Yr10, Yr5 and Yr15) demonstrated high frequency occurrence (31.4%, 14.0% and 7.0%, respectively). The most abundant was gene Yr10 identified in 22 genotypes. It was followed by the Yr5 gene, which conferred resistance in 14 lines (20%) and Yr18 gene-11 lines (15.7%). Yr15 was identified in 7 genotypes. Yr17/Lr37/Sr38 gene complex was found in 2 entries. Among 70 evaluated germplasm sources, 42 disease resistant entries are potentially useful resistant wheat genotypes. These carriers of different Yr genes can be used directly in breeding programs to improve stripe rust resistance of winter wheat. Marker-assisted selection can be efficiently applied to develop wheat cultivars with effective gene combinations that would directly assist in developing durable resistance in Kazakhstan.

Screening of wheat genotypes for the presence of common bunt resistance genes.

Common bunt is known to cause grain yield and quality losses in wheat due to bunt ball formation and infestation of the grain. The aim of this study is to identify for sources of resistance to common bunt in wheat genotypes using phytopathological and molecular methods. In general, studied 60 Kazakh and foreign wheat genotypes were found 15 samples with the Bt9, Bt8 and Bt11 genes. Carriers of the Bt10 gene include the five varieties. The four resistance genes, Bt8, Bt10, Bt11, Bt9, and Bt10 were identified in the Karasai variety. Phytopathological and molecular screening of Kazakh and foreign wheat genotypes selected 18 with genes for resistance to the disease. According to evaluation on an artificial infection 19 varieties showed an immune type of reaction. These varieties will be used in breeding programs as donors to create resistant varieties against the common bunt. Thus, approaches can reduce the level of fungicides use and the most effective method to control the common bunt.

Evaluation of Wheat Germplasm for Resistance to Leaf Rust (Puccinia triticina) and Identification of the Sources of Lr Resistance Genes Using Molecular Markers.

Leaf rust, caused by Puccinia triticina (Ptr), is a significant disease of spring wheat spread in Kazakhstan. The development of resistant cultivars importantly requires the effective use of leaf rust resistance genes. This study aims to: (i) determine variation in Ptr population using races from the East Kazakhstan, Akmola, and Almaty regions of Kazakhstan; (ii) examine resistance during seedling and adult plant stages; and (iii) identify the sources of Lr resistance genes among the spring wheat collection using molecular markers. Analysis of a mixed population of Ptr identified 25 distinct pathotypes. Analysis of these pathotypes using 16 Thatcher lines that are near-isogenic for leaf rust resistance genes (Lr) showed different virulence patterns, ranging from least virulent "CJF/B" and "JCL/G" to highly virulent "TKT/Q". Most of the pathotypes were avirulent to Lr9, Lr19, Lr24, and Lr25 and virulent to Lr1, Lr2a, Lr3ka, Lr11, and Lr30. The Ptr population in Kazakhstan is diverse, as indicated by the range of virulence observed in five different races analyzed in this study. The number of genotypes showed high levels of seedling resistance to each of the five Ptr races, thus confirming genotypic diversity. Two genotypes, Stepnaya 62 and Omskaya 37, were highly resistant to almost all five tested Ptr pathotypes. Stepnaya 62, Omskaya 37, Avangard, Kazakhstanskaya rannespelaya, and Kazakhstanskaya 25 were identified as the most stable genotypes for seedling resistance. However, most of the varieties from Kazakhstan were susceptible in the seedling stage. Molecular screening of these genotypes showed contrasting differences in the genes frequencies. Among the 30 entries, 22 carried leaf rust resistance gene Lr1, and two had Lr9 and Lr68. Lr10 and Lr28 were found in three and four cultivars, respectively. Lr19 was detected in Omskaya 37. Two single cultivars separately carried Lr26 and Lr34, while Lr37 was not detected in any genotypes within this study. Field evaluation demonstrated that the most frequent Lr1 gene is ineffective. Kazakhstanskaya 19 and Omskaya 37 had the highest number of resistance genes: three and four Lr genes, respectively. Two gene combinations (Lr1, Lr68) were detected in Erythrospermum 35 and Astana. The result obtained may assist breeders in incorporating effective Lr genes into new cultivars and developing cultivars resistant to leaf rust.