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HomeAP 13067825 (superviser Sapakhova Z.B.)

AP 13067825 (superviser Sapakhova Z.B.)

Brief description of the project

(2022-2024)

 Project title: IRN АР13067825 « Study of genetic resistance of sugar beet to rhizomania and selection of promising varieties for targeted breeding».

 Relevance. Currently, the fight against dangerous pathogens is focused on the genomic selection of resistant genotypes rather than on the use of pesticides. Varieties resistant to various fungal, bacterial, and viral pathogens have been bred in the world with the help of directed selection. Breeding of resistant sugar beet genotypes is hampered by the limited genetic diversity of the available varieties. The main way of breeding resistant varieties to biotic stress is the introgression of genes of wild species such as B. vulgaris L. ssp. maritima L. (Arcang.) and Patellifolia species. It is known that there are resistant lines and varieties of European selection to a widespread and dangerous disease — beet rhizomania caused by BNYVV (beet vein yellow virus). Rhizomania can lead to a decrease in beet yield by 45-50% and a decrease in sugar content in root crops by 60-79%. A rare and poorly studied P strain of BNYVV identified in 2000 is widespread in Kazakhstan. It is known that there are Rz genes associated with resistance to BNYVV, which were obtained by introgression. Local varieties of sugar beet have not previously been studied for resistance to rhizomania, and the distribution of strains A and B on the country’s beet fields is not known.

The goal of the project: The goal of the project is a molecular genetic study of the resistance of local sugar beet varieties to rhizomania in order to select promising certified varieties for targeted breeding.

 Expected results:

1) publication of articles in peer-reviewed foreign scientific journals

— at least 2 (two) articles and (or) reviews in peer-reviewed scientific journals in the scientific direction of the project, indexed in the Science Citation Index Expanded of the Web of Science database and (or) having a CiteScore percentile in the Scopus database of at least 35 (thirty five) ;

— either at least 1 (one) article or review in a peer-reviewed scientific publication in the scientific direction of the project, indexed in the Science Citation Index Expanded of the Web of Science database and (or) having a CiteScore percentile in the Scopus database of at least 35 (thirty five), and at least 1 (one) patent included in the Derwent Innovations Index database (Web of Science, Clarivate Analytics);

— at least 1 (one) article or review in a peer-reviewed foreign or domestic publication recommended by CCSES;

— either at least 1 (one) article or review in a peer-reviewed scientific journal included in the 1 (first) quartile of the impact factor in the Web of Science database;

Expected journals: Phytopathology, CiteScore 2020-5.5, Percentile-88%, Q-1 https://www.scopus.com/sourceid/16559$; Virology, CiteScore 2020-6.2, Percentile-68%, Q-3 https://www.scopus.com/sources.uri; Journal of Phytopathology, CiteScore 2020-2.6, Percentile — 64%, Q-3, https://www.scopus.com/sourceid/19226;  Plant Disease, CiteScore 2020 — 3.0, Percentile-71%, Q-1, https://www.scopus.com/sourceid/60195.

2) publication of monographs, books and (or) chapters in books of foreign and (or) Kazakhstan publishing houses; no

3) obtaining patents in foreign patent offices (European, American, Japanese), in Kazakhstan or Eurasian patent offices; a patent will be obtained for the development of an accelerated virus detection system based on isothermal amplification.

4) development of scientific, technical, design documentation; no

5) dissemination of the results of work among potential users, the community of scientists and the general public; scientific articles and guidelines based on the results of the study of the spread of BNYVV strains, the level of resistance of local varieties of sugar beet to rhizomania, genetic passports of local varieties will be published and disseminated.

6) other measurable results in accordance with the requirements of the tender documentation and the features of the project.

1) the scope and target consumers of each of the expected results; agro-industrial complex, directed plant breeding, phytosanitary. Research laboratories for plant breeding, Educational Research and Production Center Baiserke-Agro, Kazakh Research Institutes of Agrarian Direction.

2) the impact of the expected results on the development of the main scientific field and related fields of science and technology; the study of the spread of the BNYVV virus in Kazakhstan, as well as the identification of the composition of the strains, will make it possible to understand the global map of the virus circulation, the dynamics of strains in the region and the relationship between the virus and resistant varieties of sugar beet. The study of local varieties of sugar beets will replenish the international gene pool for identifying genes for resistance to dangerous phytopathogens. The results of the study will make it possible to improve breeding approaches in breeding new varieties, as well as to use passports of resistant varieties in marker-assisted selection.

3) the applicability and (or) the possibility of commercializing the obtained scientific results; the results of the study can be used in the rapid and highly sensitive detection of the BNYVV virus, as well as in the differentiation of virus strains. The results of the study have high potential for commercialization and can be used to provide services for the detection of the virus in plant material and the selection of resistant varieties of sugar beet.

4) social, economic, environmental, scientific and technical, multiplicative and (or) other effect of the project results with justification; cultivation and breeding of high-quality varieties of cultivated plants will increase productivity and meet the need for agricultural products. The cultivation of varieties with resistance to phytopathogens will reduce the intensity of pesticide treatments, environmental pollution and, in a short time, make it possible to switch to organic products. Cultivation of GM plants is prohibited in Kazakhstan, therefore, improving the productivity of cultivated plants through marker-assisted selection is an urgent task for the development of the country’s agro-industrial complex.

5) other direct and indirect results of the project indicating their qualitative and quantitative characteristics; For the first time, data on the prevalence of BNYVV virus strains in the beet fields of Kazakhstan will be obtained, varieties of sugar beet with resistance to the dangerous BNYVV virus will be selected and genetic passports for them will be generated and offered to breeders of the country.

 Scientific Supervisor of the project: Sapakhova Zagipa

 Research group: 

  1. Gritsenko D.
  2. Nizamdinova G.
  3. Khusnitdinova M.
  4. Taskuzhina A.
  5. Kapytina A.
  6. Kerimbek N.
  7. Kostyukova V.

 List of publications of the project’s participants (2017-2022)

  1. Bassova, T., Khusnitdinova, M., Geldyeva, G., & Skorintseva, I. (2016). Anthropogenic disturbance of landscapes in the border area of Kazakhstan and Kyrgyzstan. International Multidisciplinary Scientific GeoConference: SGEM, 2, 45-52. Индекс цитирования – 0, DOI — 10.5593/SGEM2016/B52/S20.007
  2. Barrett, T., Feola, G., Khusnitdinova, M., & Krylova, V. (2017). Adapting agricultural water use to climate change in a post-Soviet context: Challenges and opportunities in Southeast Kazakhstan. Human ecology, 45(6), 747-762. Индекс цитирования – 16, Процентиль – 91, Квартиль- Q2
  3. Barrett, T., Feola, G., Krylova, V., & Khusnitdinova, M. (2017). The application of Rapid Appraisal of Agricultural Innovation Systems (RAAIS) to agricultural adaptation to climate change in Kazakhstan: A critical evaluation. Agricultural Systems, 151, 106-113. Индекс цитирования – 6, Процентиль – 99, Квартиль- Q1.
  4. Omasheva, M., Pozharskiy, A., Galiakparov, N. (2017). To what extent do wild apples in Kazakhstan retain their genetic integrity? Tree Genetics and Genomes. Индекс цитирования – 18, DOI -10.1007/s11295-017-1134-z
  5. Gritsenko, D., Pozharsky, A, Deryabina, N., Kassenova, A, Galiakparov N. Genetic analysis of hemagglutinin proteins of H3 and H1 subtypes in Kazakhstan // Genetika, 2019. Индекс цитирования – 0, Процентиль – 32, Квартиль- Q3 DOI: 10.2298/GENSR1902511G.
  6. Gritsenko D., Aubakirova K., Galiakrapov N. Simultaneous detection of five apple viruses by RT-PCR. International Journal of Biology and Chemistry (2020) v. 13, n. 1, p. 129-134. 2020. Индекс цитирования –0, doi: 10.26577/ijbch.2020.v13.i1.13.
  7. A.S. Pozharskiy, K. Aubakirova, D. Gritsenko, N. Galiakparov. Genotyping and morphometric analysis of Kazakhstani grapevine cultivars versus Asian and European cultivars // Genet. Mol. Res., 2020. Индекс цитирования – 0, DOI: 10.4238/gmr18482.
  8. Gritsenko, P., Gritsenko, I., Seidakhmet, A., & Kwolek, B. (2018, September). Plane object-based high-level map representation for slam. In International Conference on Computer Vision and Graphics (pp. 91-102). Springer, Cham. Индекс цитирования – 3, DOI: 10.1007/978-3-030-00692-1_9.
  9. Gritsenko, I., Seidakhmet, A., Abduraimov, A., Gritsenko, P., & Bekbaganbetov, A. (2017, August). Delta robot forward kinematics method with one root. In 2017 International Conference on Robotics and Automation Sciences (ICRAS) (pp. 39-42). IEEE. Индекс цитирования – 3, DOI: 10.1109/ICRAS.2017.8071913.
  10. Gritsenko, P. S., Gritsenko, I. S., Seidakhmet, A. Z., & Abduraimov, A. E. (2017, September). Generation of RGB-D data for SLAM using robotic framework V-REP. In AIP Conference Proceedings (Vol. 1880, No. 1, p. 060005). AIP Publishing LLC. Индекс цитирования – 0, DOI: 10.1109/ICRAS.2017.8071913.
  11. Zhigailov, A. V., Stanbekova, G. E., Nizkorodova, A. S., Galiakparov, N. N., Gritsenko, D. A., Polimbetova, N. S., … & Iskakov, B. K. (2022). Phosphorylation of the alpha-subunit of plant eukaryotic initiation factor 2 prevents its association with polysomes but does not considerably suppress protein synthesis. Plant Science, 111190. Индекс цитирования – 1, Процентиль – 92, Квартиль- Q1 PubMed: 26964019.
  12. Gritsenko, D., Zulfiya Kachiyeva, Gulzhan Zhamanbayev, Bakhytzhan DuisembekoV, Abai Sagitov. Detection of five potato viruses in Kazakhstan // IX International scientific agriculture symposium “AGROSYM 2018”., p. 611

Patents:

  1. Patent for invention No. 27409 (2014) A method for increasing the survival rate of explants of the Aport apple tree when introduced into tissue culture, Innovative patent No. 27409, Application No. 2013/0027.1
  2. Patent for invention No. 27410 (2014) A method for increasing the activity of regeneration and reproduction of the Aport apple tree in vitro.
  3. Patent for invention No. 33633 (2019) «A set of synthetic oligonucleotides for the diagnosis of fire blight on fruit crops by the LAMP method»
  4. Patent for invention No. 33634 (2019) «A set of synthetic oligonucleotides for the detection of apple viruses by RT-PCR»

Results for 2022:

  1. The level of variability were identified for each genomic RNA molecule for different

strains located in the NCBI. The variability of RNA1 was found to be 1-4%, RNA2- 5-6%, RNA3- 3-4%, and RNA4- 1-3%. The genes encoding the capsid protein, RNA-dependent RNA polymerase gene, and r42 exhibited the highest conservatism within the species and variability outside the species. Three sets of primers were developed for each gene separately for the capsid protein gene, RNA-dependent RNA polymerase, and r42 gene. The F3 and B3 primers were selected with 100% complementarity to the last 5 nucleotides at the 3′-terminal end to prevent false-negative detection results.

Genes encoding the 42k movement protein, capsid protein, and 14k movement protein on RNA2 were identified to have the highest number of variable positions for differential detection of A and B strains. A regulatory region was identified on RNA3, specifically the promoter region of the r25 gene, which had variable positions, as well as the TGB region on RNA2 for identifying A and B strains. Primers and probes were developed for each promising region for detection, with the highest number of variable positions found in the complementary binding region with the probe. For the identification of the P strain of the virus, primers were developed for the gene encoding the r26 protein sequence on the genomic RNA5.

Positive controls were developed for each selected primer pair for BNYVV detection by synthesizing and cloning target nucleotide sequences into plasmids. Using the developed test system in field conditions, at least 12 samples infected with BNYVV were detected out of 320 sugar beet samples collected from 7 fields in the Almaty region. Roots were collected from plants with rhizomania symptoms and plants without viral infection symptoms. Detection in field conditions was carried out for 5-10% of each field’s samples using LAMP. BNYVV was detected in 290 sugar beet samples, with 15 samples infected with the virus. Ten of the infected samples were collected from plants with rhizomania symptoms.

Publications (2022): none

  1. Khusnitdinova M., Pozharsky A., Nizamdinova G., Sapakhova Z., Gritsenko D. Environmental problems in sugar beet cultivation in Kazakhstan, p. 293. Collection of materials of the International Scientific and Practical Conference «Actual Problems and Prospects of Science Development in the Field of Fruit and Vegetable Growing», dedicated to the 85th anniversary of the Pomological Garden (September 16, 2022), (Husnitdinova M., Pozharskiy A., Nizamdinova G., Sapakhova Z., Gritsenko D. Ekologicheskie problemy v vyrashchivanii sakharnoy svekly v Kazakhstanе, s.293. Sbornik materialov Mezhdunarodnoy nauchno-prakticheskoy konferentsii «Aktualnye problemy i perspektivy razvitiya nauki v oblasti plodooovoshchevodstva», posvyashchennoy 85-letiyu Pomologicheskogo sada (16 sentyabrya 2022g).