Potato is one of the most consumed crops worldwide. One strategy aimed at pathogen and pest management is the cultivation of resistant varieties. In this study, 352 genotypes from the Kazakhstan potato germplasm collection were screened for the presence of loci for resistance to the most harmful pathogens and pests using 30 DNA markers. ‘Rucheek’ and ‘Spiridon’, among the top global varieties, and ‘Janaisan’ and ‘Fedor’, among the top local varieties, were identified as bearing the most resistance loci in the collection, with at least 14 markers each. The specimens carrying the genes Ryadg (ADG1, ADG2), Nb (SPUD237), Ns (SC811, CP16), Rpi-phu1 (GP94), and GroV1 (X02), which demonstrate confirmed resistance to PVY, PVA, PVX, PVS, Phytophthora infestans, and Globodera rostochiensis, were most frequently found in the collection. Loci for resistance to Synchytrium endobioticum and Globodera pallida were less introgressed into the Kazakhstani cultivars and were almost absent in the germplasm collection. The less abundant loci found in the current potato collection were Ryadg (RysC3), Gro1-4 (Gro1-4), and Rladg (RGASC₈₅₀). Screening of the potato collection showed that the markers SPUD237, CP60, 45/X1, and CT214 generated additional polymorphic amplicons, while markers Nl25, C237, GP179, and GP122₇₁₈ were less applicable in robust large-scale screening. The results from this study may greatly contribute to marker-assisted selection and gene pyramiding strategies aimed at developing new potato varieties with multiple resistance to biotic stress

Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.

Sugar beet hybrids are essential in modern agriculture due to their superior yields, disease resistance, and adaptability. This study investigates the role of the Rz2 gene in conferring resistance to beet necrotic yellow vein virus (BNYVV) in 14 sugar beet hybrids cultivated in Kazakhstan, including local and European varieties. The Rz2 gene, encoding a CC-NB-LRR protein, is a known resistance factor against BNYVV. Using RT-qPCR, we assessed Rz2 expression and detected BNYVV in bait plants inoculated with virus-infested soil. Our findings identified two highly resistant varieties: the Kazakh cultivar ‘Abulhair’ and the French line 22b5006. Additionally, the Kazakh cultivar ‘Pamyati Abugalieva’ and the French hybrid ‘Bunker’ exhibited increased resistance, suggesting involvement of other resistance loci. Notably, the Danish hybrid ‘Alando’, despite resistance to rhizomania, did not effectively resist BNYVV, highlighting possible evasion of its genetic factors by local virus strains. Our results emphasize the importance of Rz2 in resistance breeding programs and advocate for further research on additional resistance genes and the genetic variability of BNYVV in Kazakhstan. This work pioneers the molecular evaluation of BNYVV resistance in sugar beet in Kazakhstan, contributing to sustainable disease management and improved sugar beet production.

NDVI is one of the most common vegetation indices for solving various problems of assessing the state of vegetation cover and its dynamics. The purpose of the study was to evaluate the state of wild Sievers apple trees in the territory of Phenological area, Genetic Reserve of Sievers, Tauturgen and Sievers apple reserve (Zhongar-Alatau and Ile-Alatau SNNP) using the NDVI index. The period of study was season’s autumn 2022 and spring 2023. Created interactive maps of the study area with multispectral reconstructions in NDVI formats let us was established the condition of the Sievers apple tree. Which was based on an analysis of the deviation of the NDVI of each tree in the study area from the average index value for the vegetation of the entire type of area. This allowed us to identify the territorial features of the state of the Sievers apple trees and identify degraded trees. The results obtained can be used for the rational management of environmental management by the Zhongar-Alatau SNNP and the Ile-Alatau SNNP.

The present study provides a comprehensive account of the advancement and utilization of guide RNAs (gRNAs) through the utilization of CRISPR/Cas systems in the identification of two prominent apple viruses, namely Apple Chlorotic Leaf Spot Virus (ACLSV) and Apple Stem Pitting Virus (ASPV). The presence of these viruses presents significant risks to the worldwide apple production industry, due to their adverse effects on fruit quality and yield. The primary objective of this study is to investigate the utilization of CRISPR technology, namely the CRISPR/Cas12a and Cas13a systems, when employed for accurate and highly sensitive diagnostic applications. The present methodology focuses on exploiting conserved areas within the viral genome to improve the efficacy of detection.The methodology involves the development of guide RNAs (gRNAs) that selectively bind to con-served areas within the viral genomes of ACLSV and ASPV. This is achieved by the application of bioinformatics techniques, which aim to reduce unintended effects and enhance the specificity of the targeting. The first stage of in vitro testing entails the production of synthetic viral RNA, followed by live plant testing to verify the efficacy of the gRNAs in real-world settings. Furthermore, the research project includes the generation of complete cDNA clones of the viruses in order to enhance comprehension of their genomic architectures, a critical aspect in the improvement of gRNA designs.This study highlights the incorporation of sophisticated genomic methodologies alongside conven-tional virology approaches in order to enhance the identification and control of plant viral illnesses. The objective is to enhance agricultural well-being and productivity by develop novel diagnostic strategies.

Grapevine viroids are the smallest pathogens affecting viticulture. Infected grapevines may show symptoms such as leaf yellowing, mottling, stunted growth, reduced fruit quality, and overall vine decline. Asymptomatic viroid infections in grapevines can still decrease grapevine productivity, thereby posing a hidden economic threat to viticulture (Wolpert et al., 1996; Wu et al., 2023). This study aimed to detect three widely distributed viroid species of the Pospiviroidae family: Grapevine yellow speckle viroid 1 (GYSVd-1), Grapevine yellow speckle viroid 2 (GYSVd-2), and Hop stunt viroid (HSVd). The study focused on grapevine (Vitis vinifera) cultivars 'Saperavi' and 'Rkatsiteli' cultivated in Kazakhstan. Three fields in Shirin village and one field in Tyulkubas village (each about 600 ha) in Almaty region were tested for the presence of viroids due to a decline in yield observed despite the negative tests for common viruses (past 3 years). Symptoms typical for viral infections were observed sporadically without a consistent pattern of infection. Total 17 samples from Shirin (July 2023) and 14 from Tyulkubas (June 2024) with visible symptoms were collected randomly. Validated primers were used to identify GYSVd-1 (mF/mR1, 250 bp) (Hajizadeh et al. 2012) GYSVd-2 (P1/P2, 375 bp) (Jiang et al. 2009) and HSVd (78P/83M, 312 bp) (Sano et al. 2001) using conventional RT-PCR. Among the analyzed samples, in Shirin village, 6 samples tested positive for GYSVd-1, 15 for GYSVd-2, and 15 for HSVd, including 2 positive for both HSVd and GYSVd-1. In Tyulkubas village, 2 samples were positive for GYSVd-1 and 12 for HSVd; GYSVd-1 positive samples als were positive for HSVd, including 8 positive for both HSVd and GYSVd-2 and 6 positive for three viroids. Amplicons for each viroid were further sequenced using the Sanger's method on ABI 3500 Genetic Analyser with BigDye v.3.1 kit and using MinION sequencer with the Rapid Barcoding Kit 96 V14 (Oxford Nanopore Technologies) according to the manufacturer's protocol. The obtained reads were mapped to reference sequences from GenBank-GYSVd-1 NC_001920.1, HSVd NC_001351.1, and GYSVd-2 MG780425.1-using Minimap v.2.2.0 with default parameters in Geneious software. Sequencing produced total 2253 reads for GYSVd-1 (average length 159 bp, range 42-296), 2095 for GYSVd-2 (203.6 bp, 49-578), and 1235 for HSVd (218.5 bp, 53-440). Of these, 947 (42.0%) were been mapped to GYSVd-1, 1778 (84.9%) to GYSVd-2, and 678 (54.9%) to HSVd. Genome coverage was 62.3% (GYSVd-1), 98.1% (GYSVd-2), and 73.8% (HSVd), with mean depths of 889X, 1282X, and 659X, respectively. Each viroid resulted a single contig corresponding to the target amplicon. No reads corresponding to other viral or bacterial agents have been identified. NCBI BLASTn search resulted total 141 hits with coverage 59-68% and identity 98.69-99.35% for GYSVd-1; 128 hits with coverage 82-100% and identity 97.59-100% for GYSVd-2; 157 hits with coverage 99-100% and identity 95.49-97.29%; no not-specific matches were identified for three viroids. The assembled viroid sequences obtained using nanopore sequencing have been uploaded into NCBI database (accessions PV341024-PV341026). Viroids GYSVd-1,2 and HSVd have been detected for the first time in Kazakhstan. The results indicate the need for further studies to estimate impact of these viroids on viticulture and lay a basis for their monitoring in the country.