IRN BR28712539
« Molecular-genetic patterns in the development of economically valuable traits and biological characteristics of major agricultural crops »
Program Supervisor:
Kabyl Zhambakin
Academician of the National Academy of Sciences of Kazakhstan, Professor, Doctor of Biological Sciences, General Director
The program aims to address the strategic task of developing the scientific foundations of breeding and seed production in Kazakhstan in line with modern global requirements. Population growth and climate change require the development of productive and sustainable crop varieties. Social demand for products with improved quality characteristics (nutritional value, disease resistance, etc.) underscores the relevance of the program. The low resistance of domestic varieties of grain, vegetable, potato, fruit, and berry crops to abiotic and biotic stress factors leads to their low productivity. In this regard, for the first time in Kazakhstan, comprehensive genetic research will be conducted on the resistance and productivity of major agricultural crops that determine the country's food security. In addition, varieties will be systematized through certification and the creation of databases for seed producers. This will ensure the uniqueness and competitiveness of the results obtained. A systematic approach to studying the genomic potential of varieties, including DNA methylation and transcriptomics analysis, will contribute to increasing productivity, crop resistance to adverse factors, and the optimization of agricultural technologies
Goal:
To study the molecular genetic patterns of the formation of economically valuable traits and biological characteristics of major agricultural crops.

Tasks/projects:
Жарияланымдар (2025–2026 жж.)
Тезистер:
  1. Kushnarenko S.V., Rymkhanova N.K., Manapkanova U.A., Romadanova N.V., Rakhimbaev I.R.
  2. Cryobiotechnologies for preservation of plant germplasm in Kazakhstan // Еуропалық биотехнологиялық конгресс, 8–13 қыркүйек 2025 ж., Тирана, Албания (баспаға дайындалуда).
  3. Rymkhanova N.K., Manapkanova U.A., Kushnarenko S.V.
  4. Development of in vitro technique for elimination of Raspberry bushy dwarf virus // Еуропалық биотехнологиялық конгресс, 8–13 қыркүйек 2025 ж., Тирана, Албания (баспаға дайындалуда).
  5. Genotyping of wheat germplasm using functional molecular markers for key genes that determine resistance to biotic and abiotic stresses
  6. Study of molecular-genetic bases for increasing yield and grain quality improvement of domestic rice breeding.
  7. Molecular genetic studies of tetraploid and diploid species to improve the efficiency of potato breeding and seed production.
  8. Genetic diversity and population structure of varieties and lines collection of the main vegetable and melon crops of Kazakhstan.
  9. Identify new transcripts, DNA methylation variations, and functional genetic links that form stress tolerance in fruit crops.
  10. Study of the genetic diversity of berry plants and development of ways to improve the health of commercially valuable varieties based on the use of molecular methods and cryobiotechnology.

Program applicability: The program results are applicable in the field of breeding and seed production of grain, vegetable, potato, fruit, melon, and berry crops. The developments can be used by breeders, seed producers, geneticists, biotechnologists, as well as research and educational organizations. The implementation of the program will contribute to import substitution in the field of seed production, increase crop yields, and reduce production costs. The scientific results obtained have the potential for implementation and commercialization in the fields of biology, biotechnology, and agricultural production..
Publications:
  • Publications of the research supervisor:
    1. Sapakhova Z.; Abilda, Z.; Toishimanov, M.; Daurov, D.; Daurova, A.; Raissova, N.; Sidorik, A.; Kanat, R.; Zhambakin, K.; Shamekova, M. Early Generation Selection of Potato Breeding Lines. Horticulturae – 2024, Vol. 10, P. 1121.  Квартиль - Q1, Процентиль – 74 https://doi.org/10.3390/horticulturae10101121
    2. Kanat, R.; Shamekova, M.; Sapakhova, Z.; Toishimanov, M.; Daurov, D.; Raissova, N.; Abilda, Z.; Daurova, A.; Zhambakin, K. Gene Expression Analysis for Drought Tolerance in Early Stage of Potato Plant Development. Biology – 2024, Vol. 13, P. 857. https://doi.org/10.3390/biology13110857 , Квартиль - Q1, Процентиль – 85. Автор для корреспонденции.
    3. Sapakhova Z., Islam K.R, Toishimanov M., Zhapar K., Daurov D., Daurova A., Raissova N., Kanat R., Shamekova M., Zhambakin K. Mulching to improve sweet potato production. Journal of Agriculture and Food Research. 2024. 15. 101011. Квартиль – Q1, Процентиль – 78. https://doi.org/10.1016/j.jafr.2024.101011. Автор для корреспонденции.
    4. Sapakhova Z., Raissova N., Daurov D., Zhapar K., Daurova A., Zhigailov A., Zhambakin K., Shamekova M. Sweet potato as a key crop for food security under the conditions of global climate change: A Review. Plants. 2023. 12. 2516. https://doi.org/10.3390/plants12132516. Индекс цитирования (FWCI)– 2.55, Квартиль – Q1, Процентиль – 83.
    5. Daurov D., Daurova A., Sapakhova Z., Kanat R., Akhmetzhanova D., Abilda Z., Toishimanov M., Raissova N., Otynshiyev M., Zhambakin K., Shamekova M. The Impact of the Growth Regulators and Cultivation Conditions of Temporary Immersion Systems (TISs) on the Morphological Characteristics of Potato Explants and Microtubers. Agronomy. 2024. 14(8), 1782. https://doi.org/10.3390/agronomy14081782. Квартиль – Q1, Процентиль – 84.
    6. Daurov D., Lim Y.H., Park S.U., Kim Y.H., Daurova A., Sapakhova Z., Zhapar K., Abilda Z., Toishimanov M., Shamekova M., Zhambakin K., Kim H.S., Kwak S.S. Selection and characterization of lead-tolerant sweetpotato cultivars for phytoremediation. Plant Biotechnology Reports. 2024. https://doi.org/10.1007/s11816-024-00900-w. Квартиль – Q2, Процентиль – 69.
    7. Toishimanov M., Abilda Z., Daurov D., Daurova A., Zhapar K., Sapakhova Z., Kanat R., Stamgaliyeva Z., Zhambakin K.*, Shamekova M. Phytoremediation properties of sweet potato for soils contaminated by heavy metals in South Kazakhstan. Applied Sciences. 2023. 13. 9589. https://doi.org/10.3390/app13179589. Индекс цитирования (FWCI)– 2.44, Квартиль – Q2, Процентиль – 83.
    8. Daurov D., Zhambakin K., Shamekova M. Phytoremediation as a way to clean technogenically polluted areas of Kazakhstan. Brazilian journal of biology = Revista brasleira de biologia. 2023. 83. e271684. https://doi.org/10.1590/1519-6984.271684. Индекс цитирования (FWCI)– 3.05, Квартиль – Q3, Процентиль – 61.
    9. Gritsenko D., Daurova A., Pozharskiy A., Nizamdinova G., Khusnitdinova M., Sapakhova Z., Daurov D., Zhapar K., Shamekova M., Kalendar R., Zhambakin K. Investigation of mutation load and rate in androgenic mutant lines of rapeseed in early generations evaluated by high-density SNP genotyping. Heliyon. 2023. 9(3). e14065. https://doi.org/10.1016/j.heliyon.2023.e14065. Индекс цитирования (FWCI) – 0.41, Квартиль – Q2, Процентиль – 86. Автор для корреспонденции.
    10. Daurov D., Argynbayeva A., Daurova A., Zhapar K., Sapakhova Z., Zhambakin K., Shamekova M. Monitoring the spread of potato virus diseases in Kazakhstan. American Journal of Potato Research. 2023. 100(1). 63-70. https://doi.org/10.1007/s12230-022-09895-y. Индекс цитирования (FWCI) – 0.55, Квартиль – Q3, Процентиль – 76.
  • Information on available patents and other title documents:
    1. Raisova N.U., Zhambakin K.Zh., Sapakhova Z.B., Kurdyumov A.A., Dauron D.L., Dauronova A.K., Toishimanov M.R., Shamechova M.Kh. Computer program Digital platform for seed quality control “E-Tukym”. Certificate of entry in the state register of rights to copyrighted objects No. 45900 dated May 16, 2024.
    2. Authors: Zhambakin K.Zh., Daurova A.K., Shamekova M.Kh., Sapakhova Z.B., Daurov D.L., Oshergina I.P., Ten E.A., Kradetskaya O.O. Patent of the Republic of Kazakhstan for selection achievement No. 1178 dated 22.11.2024 “Tengri”.
  • Information about publications by key members of the research team:
    Task 1
    1. Malysheva, A., Kokhmetova, A., Urazaliev, R., Kumarbayeva, M., Keishilov, Z., Nurzhuma, M., Bolatbekova, A., & Kokhmetova, A. (2023). Phenotyping and identification of molecular markers associated with leaf rust resistance in the wheat germplasm from Kazakhstan, CIMMYT, and ICARDA. Plants, 12(2786). https://doi.org/10.3390/plants12152786..
    2. Kumarbayeva, M., A. Kokhmetova, N. Kovalenko, M. Atishova, Zh. Keishilov, and K. Aitymbetova. "Characterization of Pyrenophora tritici-repentis (Tan Spot of Wheat) Races in Kazakhstan." Phytopathologia Mediterranea 6 (2022): 243–257. https://doi.org/10.36253/phyto-13178.
    3. Kokhmetova A., Rsaliyev S., Atishova M., Kumarbayeva M., Malysheva A., Keishilov Z., Zhanuzak D., Bolatbekova A. Evaluation of wheat germplasm for resistance to leaf rust (puccinia triticina) and identification of the sources of Lr resistance genes using molecular markers. Plants. 2021. Vol. 10(7). 1484. https://doi.org/10.3390/plants10071484
    4. Kokhmetova A., Rsaliyev A., Malysheva A. et al. Identification of stripe rust resistance genes in common wheat cultivars and breeding lines from Kazakhstan. Plants. 2021. Vol. 10(11). 2283. https://doi.org/10.3390/plants10112283..
    5. Kokhmetova A., Kumarbayeva M., Atishova M. Identification of high-yielding wheat genotypes resistant to Pyrenophora tritici-repentis (tan spot). Euphytica. 2021. Vol. 217. 97. https://doi.org/10.1007/s10681-021-02822-y.

    Task 2
    1. Baiseitova G., Kh.Berkimbay, D.Mynbayeva, A.Nussupova, A.K.Amirova, B.Usenbekov, Zh.Kulakhmetova, G.Yernazarova, D.Yussayeva, D.Kazkeyev, S.Mukhambetzhanov. Heritability and amylose content in hybrid lines of late-generation rice with colored pericarp. Brazilian Journal of Biology. 2023.vol. 83. e280919; рр. 1-7, (ISSN 1678-4375). https://doi.org/10.1590/1519-6984.280919
    2. Amirova А., B.Usenbekov*, Kh. Berkimbay, D. Mynbayeva, S. Atabayeva, G. Baiseitova, A. Meldebekova, Zh. Zhunusbayeva, S. Kenzhebayeva and S. Mukhambetzhanov. Selection of rice breeding lines for resistance to biotic and abiotic stresses. Brazilian Journal of Biology. 2024. Vol. 84, e282495 https://doi.org/10.1590/1519-6984.282495 (IF-1.71, Scopus Процентиль – 59).
    3. Usenbekov B., А. Amirova, Z.Zeinalov, A.Meldebekova, D.Mynbayeva, Kh. Berkimbay and T. Kurbangaliyeva. Creation of rice doubled haploids with low amylose content using in vitro anther culture. Brazilian Journal of Biology. 2024. Vol. 84. e284946 https:// https://doi.org/10.1590/1519-6984.284946

    Task 3
    1. Sapakhova, Z.; Abilda, Z.; Toishimanov, M.; Daurov, D.; Daurova, A.; Raissova, N.; Sidorik, A.; Kanat, R.; Zhambakin, K.; Shamekova, M. Early Generation Selection of Potato Breeding Lines. Horticulturae.2024, Vol. 10, P. 1121. https://doi.org/10.3390/horticulturae10101121
    2. Kanat, R.; Shamekova, M.; Sapakhova, Z.; Toishimanov, M.; Daurov, D.; Raissova, N.; Abilda, Z.; Daurova, A.; Zhambakin, K. Gene Expression Analysis for Drought Tolerance in Early Stage of Potato Plant Development. Biology. 2024, Vol. 13, P. 857. https://doi.org/10.3390/biology13110857
    3. Sapakhova Z., Islam K.R, Toishimanov M., Zhapar K., Daurov D., Daurova A., Raissova N., Kanat R., Shamekova M., Zhambakin K. Mulching to improve sweet potato production. Journal of Agriculture and Food Research. 2024. 15. 101011.. https://doi.org/10.1016/j.jafr.2024.101011
    4. Mukhametov A., Shamekova M., Dautkanova D., Kazhymurat A., Ilyassova G. Seed potato production regulatory framework established in top potato producing countries: Comparison of the GOST (Russia) and UNECE S-1 certification systems. Journal of Agriculture and Food Research. 2023. 11. 100520. https://doi.org/10.1016/j.jafr.2023.100520.

    Task 4
    1. Genievskaya Y., Chudinov V., Abugalieva S., Turuspekov Y. Novel QTL Hotspots for Barley Flowering Time, Plant Architecture, and Grain Yield. Agronomy. 2024. V. 14. 1478. https://doi.org/10.3390/agronomy14071478.
    2. Almerekova, S., Genievskaya, Y., Abugalieva, S., Sato, K., & Turuspekov, Y. Population structure and genetic diversity of two-rowed barley accessions from Kazakhstan based on snp genotyping data. Plants. 2021.Vol.10 (10). 2025.,. https://doi.org/ 10.3390/plants10102025
    3. Zatybekov A., Yermagambetova M., Genievskaya Y., Didorenko S., Abugalieva S. Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers. Plants. 2023; 12(19):3445. https://doi.org/10.3390/plants12193445.
    4. Amalova A., Yermekbayev K., Griffiths S., Winfield M.O., Morgounov A., Abugalieva S., Turuspekov Y. Population structure of modern winter wheat accessions from Central Asia. Plants. 2023. Vol.; 12(12). 2233. https://doi.org/10.3390/plants12122233.
    5. Chao Fang, Zhihui Sun, Shichen Li, Tong Su, Lingshuang Wang, Lidong Dong, Haiyang Li, Lanxin Li, Lingping Kong, Zhiquan Yang, Xiaoya Lin, Alibek Zatybekov, Baohui Liu, Fanjiang Kong & Sijia Lu. Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation. Nat Commun. 2024. 15, 6184. https://doi.org/10.1038/s41467-024-50623-3

    Task 5
    1. Pozharskiy, A., Kostyukova, V., Nizamdinova, G., Kalendar, R., & Gritsenko, D. (2022). MLO proteins from tomato (Solanum lycopersicum L.) and related species in the broad phylogenetic context. Plants, 11(12), 1588. https://doi.org/10.3390/plants11121588
    2. 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... https://doi.org/10.1016/j.plantsci.2022.111190
    3. Kolchenko, M., Nurtaza, A., Pozharskiy, A., Dyussembekova, D., Kapytina, A., Nizamdinova, G., ... & Gritsenko, D. (2023). Wild Malus Niedzwetzkyana Dieck Ex Koehne as a Genetic Resource for Fire Blight Resistance. Horticulturae, 9(10), 1066.. https://doi.org/10.3390/horticulturae9101066.
    4. Taskuzhina, A., Pozharskiy, A., Jumanova, Z., Soltanbekov, S., Issina, Z., Kerimbek, N., Gritsenko, D. (2024). Identifying Fire Blight-Resistant Malus sieversii Rootstocks Grafted with Cultivar ‘Aport’Using Monitoring Data. Horticulturae, 10(10), 1052.4. https://doi.org/10.3390/horticulturae10101052
    5. Tegtmeier, R., Švara, A., Gritsenko, D., & Khan, A. (2024). Malus sieversii: a historical, genetic, and conservational perspective of the primary progenitor species of domesticated apples. Horticulture Research, uhae244.. https://doi.org/10.3390/horticulturae10101052

    Task 6
    1. Kushnarenko S., Aralbayeva M., Rymkhanova N., Reed B.M. Initiation pretreatment with Plant Preservative MixtureTM increases the percentage of aseptic walnut shoots // In Vitro Cellular & Developmental Biology. Plant. 2022. https://doi.org/10.1007/s11627-022-10279-4
    2. Romadanova N.V., Tolegen A.B., Kushnarenko S.V., Zholdybayeva E.V., Bettoni J.C. Effect of Plant Preservative MixtureTM on endophytic bacteria eradication from in vitro-grown apple shoots. Plants. 2022. 11. 2624-2635. https://doi.org/10.3390/plants11192624
    3. Kushnarenko S.V., Rymkhanova N.K., Aralbayeva M.M., Romadanova N.V. In vitro cold acclimation is required for successful cryopreservation of Juglans regia L. shoot tips. CryoLetters. 2023. 44 (4). 240-248. https://doi.org/10.54680/fr23410110612
    4. Romadanova N.V., Aralbaeva M.M., Zemtsova A.S., Aleksandrova A.M., Kazybaeva S.Zh., Mikhailenko N.V., Kushnarenko S.V., Bettoni J.C. In vitro collection for the safe storage of grapevine hybrids and identification of the presence Plasmopara viticola resistance genes. Plants. 2024. 13. 1089-10106. https://doi.org/10.3390/plants13081089
    5. Nurzhanova A.A., Mamirova A., Mursaliyeva V., Nurmagambetova A.S., Zhumasheva Z., Turdiyev T., Kushnarenko S., Ismailova E. In vitro approbation of microbial preparations to shield fruit crops from fire blight: physio-biochemical parameters. Plants. 2024. 13. 1431.. https://doi.org/10.3390/plants1311143
  • Information on available patents and other title documents
    1. Madenova A.K., Kokhmetova A.M., Atishova M.N., Galymbek K., Keishilov Zh.S., Kumarbayeva M.T. Method for creating wheat lines resistant to smut. Patent for utility model No. 5188 dated July 24, 2020.
    2. Kokhmetova A. M., Kumarbayeva M. T., Nurzhum M. N., Keishilov Zh. S. Bolatbekova A. A. Method for creating winter wheat lines resistant to brown rust. Utility model patent No. 9828 dated November 22, 2024..
    3. Usenbekov B.N., Amirova A.K., Zhanbyrbaev E.A., Berkimbay Kh.A., Sartbaeva I.A., Kazkeev D.T. “Method of haploid biotechnology for obtaining green regenerant plants in rice anther culture with colored pericarp.” Patent No. 5962 for a utility model, April 2, 2021.
    4. Raisova N.U., Zhambakin K.Zh., Sapakhova Z.B., Kurdyumov A.A., Daurov D.L., Daurova A.K., Toishimanov M.R., Shamekova M.Kh. Computer program Digital platform for seed quality control “E-Tukym”. Certificate of entry of information into the state register of rights to copyrighted objects No. 45900 dated May 16, 2024.
    5. Zhambakin K.Zh., Daurova A.K., Shamekova M.Kh., Sapakhova Z.B., Daurov D.L., Oshergina I.P., Ten E.A., Kradetskaya O.O. Patent of the Republic of Kazakhstan for selection achievement No. 1178 dated 22.11.2024 “Tengri”
    6. Gritsenko D.A., Shamekova M.H. Igen computer program (for bioinformatic processing of genomic research). Certificate of entry of information into the State Register of copyrighted objects No. 16693 dated 04/15/2021.
    7. Genievskaya Y.A., Almerekova S.S., Abugalieva S.I., Turuspekov E.K. Method of identification of high-quality lines of barley (Hordeum vulgare L.) using molecular markers using KASP technology. Utility Model Patent of the Republic of Kazakhstan No. 6643 dated 05.11.2021
    8. Genievskaya Y.A., Turuspekov E.K., Abugalieva S.I. Method of identification of highly productive lines of barley (Hordeum vulgare L.) using KASP genotyping technology. Utility Model Patent of the Republic of Kazakhstan No. 9288 dated 04/16/24
    9. Gritsenko D.A., Gritsenko I.S., Adilbaeva K.S. "Portable device for accelerated detection of phytopathogens by isothermal amplification". Utility Model Patent No. 9641 (2024).
    10. Omasheva M., Galiakparov N., Pozharsky A.S. "A set of synthetic oligonucleotides for the diagnosis of bacterial burns on fruit crops by the LAMP method". Patent for invention No. 33633 (2019).
    11. Gritsenko D.A., Khusnitdinova M.A., Taskuzhina A.K., Nizamdinova G.K. "A method for determining the dynamics of the vegetation index of wild apple trees using an interactive map." Utility Model Patent No. 9543 (2024)
    12. Turdiev T.T., Kovalchuk I.Yu., Mukhitdinova Z.R., Frolov S.N., Rymkhanova N.K., Belgozhaev E.M., Beschetnov A.P. Method of obtaining raspberry planting material in vitro. Certificate of entry of information into the State Register of copyrighted objects No. 6332 dated 08/20/2021.
    13. Kushnarenko S.V., Rymkhanova N.K., Manapkanova U.A., Turdiev T.T. Method of elimination of raspberry bushy dwarf virus in raspberry plants cultivated in vitro. The application was filed and the Patent of the Republic of Kazakhstan for utility model No. 9594 was obtained. Registration number 2024/0874.2. Date of receipt 07/09/2024.
Project 1

Brief Information About the Project

(2025–2027)


Project Title:

TFP BR 28712539 «Genotyping of wheat germplasm using functional molecular markers for key genes that determine resistance to biotic and abiotic stresses».


Brief Information About the Scientific Supervisor of the Project:
Professor A.M. Kokhmetova is a recognized specialist at both national and international levels in the field of plant protection and quarantine. This is confirmed by more than 25 years of scientific experience, long-term research on economically significant and quarantine diseases of wheat, leadership of more than 20 scientific and technical projects funded by the Ministry of Science and Higher Education and the Ministry of Agriculture of the Republic of Kazakhstan, as well as participation in international programs such as CIMMYT, ICARDA, EurAsEC, and others.

Her research covers a wide range of modern phytopathological, molecular-genetic, and breeding approaches. The scientific output of A.M. Kokhmetova includes more than 400 publications, among them over 35 articles in international peer-reviewed journals ranked in Q1–Q2 of JCR (Web of Science) with a CiteScore Percentile above 50. Her Hirsch index is 14, reflecting a significant contribution to the development of phytopathology and plant breeding. Under her supervision, one Candidate of Sciences and five PhD doctors have been successfully trained.

Brief Information About the Members of the Research Team:
Kokhmetova Alma Myrzabekovna– Doctor of Biological Sciences, Professor, Academician of the National Academy of Sciences of the Republic of Kazakhstan, Head of the Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology; Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel.: +7(727)394-75-52, fax: 394-75-62,
E-mail: gen_kalma@mail.ru
Kumarbayeva Madina Talgarovna– PhD (specialty), Leading Researcher, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)3947552, E-mail: madina_kumar90@mail.ru
Kharipzhanova Aidana Isenbaykyzy– PhD (specialty), Researcher, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)394-75-52, fax: 394-75-62,
E-mail: aidana.kharipzhanova@kaznaru.edu.kz
Nurzhuma Makpal Nurzhumakyzy – Master of Pedagogical Sciences, PhD doctoral student (specialty), Senior Researcher, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)394-75-52, fax: 394-75-62, E-mail: maki_87@mail.ru
Keishilov Zhenis Sovetkanovich – Master of Agricultural Sciences, Researcher, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)394-75-52, fax: 394-75-62,
E-mail: Jeka-Sayko@mail.ru
Bolatbekova Ardak Aidynovna – Master of Environmental Sciences, PhD doctoral student (specialty), Junior Researcher, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)3947552, E-mail: ardashka1984@mail.ru
Bakhytuly Kanat – Master of Natural Sciences (specialty), Junior Researcher, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)394-75-52, fax: 394-75-62,
E-mail: kanat1499@gmail.com
Kokhmetova Asiya Myrzabekovna – Bachelor’s degree, Laboratory Assistant, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Timiryazev St. 45, Almaty, Kazakhstan, 050040, tel: +7(727)394-75-52, fax: 394-75-62, E-mail: asia.k68@mail.ru

Mukhametzhanov Kanat Serikkhanovich – Agronomist-organizer, Laboratory Assistant, Laboratory of Genetics and Breeding, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, Timiryazev St. 45, tel: +7(727)394-75-52, fax: 394-75-62,

E-mail: kanat.mukhametzhanov@mail.ru

Project Goal and Objectives:
Project Goal:
“Genotyping of wheat germplasm using functional molecular markers for key genes determining resistance to biotic and abiotic stresses.”
Objectives:
  1. Phenotyping and genetic-breeding study of a collection of wheat varieties and lines from the international nursery KASIB (at least 80 samples) in contrasting ecological zones of Kazakhstan (Almaty, Kostanay), differing in temperature and humidity regimes; assessment of field drought resistance and determination of the drought tolerance index.
  2. Genotyping of wheat samples using (at least 20) functional molecular markers for key genes determining resistance to biotic stresses: Vrn (vernalization response) – determining the requirement for vernalization; Ppd (photoperiod response) – determining plant response to extended daylight; Lr genes (Leaf rust)– associated with resistance to brown rust (Puccinia triticina).
  3. Genotyping of wheat samples using functional molecular markers for a key gene determining resistance to abiotic stresses: Dreb-B1 (dehydration responsive element binding) – responsible for cell hydration and associated with drought resistance.
Conducting integrated analysis of phenotyping and genotyping data to identify climate-resilient wheat genotypes; selection of genotypes with high yield potential and resistance to adverse environmental factors.

Interim Results of the Project for 2025–2026:
Phenotyping and genetic-breeding studies of wheat varieties and lines from the KASIB international nursery were carried out in contrasting ecological zones of Kazakhstan (Almaty and Kostanay), differing in temperature and humidity regimes. Field drought resistance and drought tolerance index were evaluated.
In the conditions of Almaty region, phenological observations and evaluation of 124 spring wheat samples were conducted. Based on structural analysis of productivity elements, 22 wheat samples with the highest productivity traits and 51 samples with medium productivity were selected.
Phytopathological assessment and productivity analysis identified 64 wheat samples with an immune reaction (IT-0) to brown rust and high productivity. High NDVI values in the range of 0.50–0.83 were observed in 72 samples. A total of 27 wheat samples combining high biomass index and field drought resistance were selected.
Morphological trait evaluation in the Almaty region revealed high diversity in the length of the last internode and spike exertion, allowing identification of clear adaptive trends. The most valuable for arid conditions of Almaty region were 8 samples (Lutescens 48-204-03, Lutescens 393/05, Lutescens 932, Stepnaya 259, Line 4-10-16, Lutescens KS 140/08-3, Lutescens 1300, Gordeiforme 829), characterized by moderate internode length and high spike exertion, ensuring effective heat exchange and preservation of reproductive organs under stress.
Similar studies were conducted in Kostanay region. A total of 59 samples were selected, combining resistance to brown rust, drought tolerance, and high productivity. Thirty-seven samples showed high NDVI values (0.55–0.67) and resistance to brown rust. Correlations between biomass accumulation and grain yield were evaluated.
Twenty-seven wheat samples with high productivity traits were selected. Wide variability in internode length and spike exertion was observed. Fourteen samples showed maximum adaptation to arid climate conditions.
Differences in yield and drought tolerance index (DSI) were identified. High-yielding varieties and promising lines were identified (Gordeiforme 2264, Annushka, Kargala 223, Line 19003, Bezenchukskaya 139, Leukurum 1469-21).
The study is characterized by a high level of scientific rigor, including large-scale phytopathological and genetic-breeding research in contrasting ecological zones.

The practical significance and commercialization potential are confirmed by the selection of more than 20 wheat samples with high biomass index, drought resistance, and productivity, recommended for breeding programs.

Phenotyping and Genetic-Breeding Study
Phenotyping of at least 80 wheat varieties and lines from KASIB was conducted in Almaty and Kostanay regions.
Field drought resistance was assessed and the drought tolerance index (DSI) was calculated.

Genotyping Using Functional Markers
At least 20 wheat samples were genotyped using markers for key genes: Vrn, Ppd, Lr.
Markers were used to select genotypes combining resistance to biotic and abiotic stresses with high productivity.

Results
In Almaty region:
  • 22 high-yield and 51 medium-yield samples identified
  • 64 samples resistant to brown rust
  • 72 samples with high NDVI (0.50–0.83)
  • 27 genotypes combining high NDVI and drought resistance
In Kostanay region:
  • 59 samples combining resistance and productivity
  • 37 samples with high NDVI (0.55–0.67)
  • 27 samples selected for productivity traits
Comparative NDVI analysis showed strong drought adaptation. Identified drought-resistant genotypes include Tyumenskaya Yubileynaya, Kargala 223, Line 19003, Nauryz 6, Seymour, and others.
The project enables the formation of a set of promising genotypes for marker-assisted breeding of drought- and disease-resistant wheat.
Publications (2025–2026):
  1. Kokhmetova A., Nurzhuma M., Bolatbekova A., Kumarbayeva M., Keishilov Zh., Mukhametzhanov K., Kokhmetova As., Bakhytuly K. Genotyping and Molecular Analysis of Wheat Germplasm for Resistance to Drought and Leaf Rust // The European Biotechnology Congress 2025, September 8–13, 2025, Tirana, Albania. p. 54.
  2. Keishilov Zh., Kokhmetova A., Kumarbayeva M., Nurzhuma M., Kharipzhanova A., Bolatbekova A., Bakhytuly K. Evaluation of resistance of spring bread wheat samples to leaf rust and drought with structural characteristics of productivity // International V Plant Breeding Congress 2025, December 1–5, 2025, Antalya, Turkey.
  3. Kokhmetova A. et al. (2025) Genetic dissection of Septoria tritici blotch and Septoria nodorum blotch resistance in wheat using GWAS. Frontiers in Plant Science, 16:1524912. (WOS Q1, IF 4.8, Scopus percentile 92)
  4. Sultanova N. et al. (2026) Integrated Management and Fungicide Efficacy of Foliar Diseases in Spring Wheat in Kazakhstan. Online Journal of Biological Sciences. (Accepted for publication, Scopus percentile 54)
  5. Keishilov Zh.S. et al. (2026) Evaluation of resistance of spring wheat samples to abiotic (drought) and biotic (brown rust – Puccinia recondita) stresses and structural analysis under Almaty conditions. “Research, Results” Journal, Vol. 28, Issue 1 (109), pp. 83–92. DOI: 10.37884/1-2026/09
Project 2

Brief Information About the Project

(2025–2027)


Project Title:
“Study of the molecular-genetic foundations for increasing yield and improving grain quality of domestically bred rice.”

Brief Information About the Scientific Supervisor of the Project:
Usenbekov Bakdaulet Naubaevich, higher education, Candidate of Biological Sciences (PhD equivalent), Associate Professor.

Brief Information About the Members of the Research Group:
Leading Researcher, Candidate of Biological Sciences – Amirova Aigul Kuzembaeva
Leading Researcher, PhD – Sartbayeva Innabat Abibullakyzy
Researcher, Master’s degree – Mynbayeva Dana Omarovna
Laboratory Assistant – Nurlybay Balnur Azilkhanqyzy
Laboratory Assistant – Usenbekov Nurlan Nurdauletuly

Project Goal and Objectives:
Project Goal:
Study of the molecular-genetic foundations for increasing yield and improving grain quality of domestically bred rice.
Project Objectives:
  • To conduct molecular-genetic screening of rice genotypes using molecular markers associated with yield.
  • To conduct molecular-genetic screening of rice genotypes—donors of the traits “high amylose content” and “low amylose content.”
  • To carry out hybridization aimed at introgression of genes for low and high amylose content into high-yielding rice varieties in order to create promising forms and lines with varying amylose content and high productivity.
Interim Results of the Project for 2025–2026:
Molecular-genetic screening of rice genotypes using molecular markers associated with yield has been carried out.
Molecular-genetic screening of rice genotypes—donors of the traits “high amylose content” and “low amylose content”—has been conducted.
Hybridization has been performed to introgress genes for low and high amylose content into high-yielding rice varieties to create promising forms and lines with varying amylose content and high productivity.
A molecular screening of 32 rice genotypes was carried out, which made it possible to identify samples differing in 1000-grain weight and belonging to high-yielding and medium-yielding groups.
Additionally, genotypes promising for hybridization based on traits of increased and decreased amylose content were identified.

Publications for 2025:
Usenbekov, B., Mukhambetzhanov, S., Kurbangaliyeva, T., Amirova, A., Sartbayeva, I., Kirshibaev, E., … Yerezhepov, A. (2026).
Anther culture in rice: from an experimental model to breeding practice.
Fundamental and Experimental Biology, 12131(1), 72–83.
https://doi.org/10.31489/2026feb1/72-83

Patent:
Utility model patent No. 11924, dated 07.11.2025
Enriched mixture of glutinous rice with the addition of Aisparagus officinalis for the production of bakery products and instant porridge
Project 3

Brief Information About the Project

(2025–2027)


Project Title:

Molecular-genetic studies of tetraploid and diploid species to increase the efficiency of potato breeding and seed production.


Brief Information About the Scientific Supervisor of the Project:
Zhambakin Kabyl Zhaparovich, Academician of the National Academy of Sciences of the Republic of Kazakhstan, Professor, Doctor of Biological Sciences.

Hirsch Index – 8 in the Scopus and Web of Science databases.

Brief Information About the Members of the Research Group:
Shamekova Malika Khabidulaevna – PhD, Professor, Head of the Laboratory of Breeding and Biotechnology. H-index – 8 according to Scopus (https://www.scopus.com/authid/detail.uri?authorId=55617198500) and Web of Science (https://www.webofscience.com/wos/author/record/98695) databases.
Daurova Ainash Kenenbaevna – Master’s degree, PhD student, Senior Researcher. H-index – 6 according to Scopus (https://www.scopus.com/authid/detail.uri?authorId=57201673636&origin=resultslist) and Web of Science (https://www.webofscience.com/wos/author/record/2024273) databases.
Volkov Dmitry Vladimirovich – Master’s degree, PhD student, Senior Researcher. H-index – 4 according to Scopus (https://www.scopus.com/authid/detail.uri?authorId=57218835515&origin=resultslist) and Web of Science (https://www.webofscience.com/wos/author/record/636236) databases.
Akbaev Aset Maulenuly – Master’s degree, Junior Researcher.
Project Goal and Objectives:
Molecular-genetic studies of tetraploid and diploid species to increase the efficiency of potato breeding and seed production.

Interim Results of the Project for 2025–2026:
During the implementation of the work, a working collection of tetraploid and diploid potatoes was formed, including both domestic and foreign genotypes from Kazakhstan, Russia, Germany, the Netherlands, the international organization CIP, as well as from Pakistan and China, along with hybrid lines previously obtained by the research team.
A molecular screening of the working potato collection was carried out using 29 molecular SCAR and CAPS markers. The analysis results showed significant genetic diversity among the studied lines, both for markers associated with traits such as earliness, starch content, and carotenoid content. Thus, the studied lines demonstrate that such diversity in starch and carotenoid markers makes the collection a valuable resource for breeding, enabling the selection of lines with desirable tuber quality traits and biochemical characteristics.
Hybridization work was carried out with 12 CIP genotypes, resulting in 14 berries in 7 hybrid combinations. The most productive combinations were CIP 10 × CIP 3, CIP 17 × CIP 18, and CIP 18 × CIP 17, indicating high compatibility and fertility of these lines. A working collection of 214 lines and hybrids of tetraploid and diploid potatoes was formed.
Molecular analysis using 29 SCAR and CAPS markers revealed significant genetic diversity in markers associated with starch and carotenoid metabolism.
Publications for 2025–2026:
Project 4

Краткая информация о проекте

(2025–2027 гг.)


Наименование проекта: Генетическое разнообразие и структура популяций коллекций сортов и линий основных овощных и бахчевых культур Казахстана.


Краткая информация о научном руководителе проекта:

А.А. Алиханова, магистр, младший научный сотрудник лаборатории молекулярной генетики ИББР, имеет 3-летний опыт работы по изучению дикорастущей флоры Казахстана. Проходила стажировку в научных центрах Южной Кореи и Венгрии. Прошла обучение по современным методам анализа и прогнозирования распространения видов (SDM, сертификат).

Brief Information About the Members of the Research Group:

Yu.A. Genievskaya – PhD, Researcher, Laboratory of Molecular Genetics; 8 years of experience; co-author of 23 articles (18 in peer-reviewed journals), Scopus (H-index = 10) and WoS (H-index = 8); co-author of 2 monographs, methodological guidelines, and a utility model; co-author of a barley variety; internships in the UK and Japan.

M.M. Yermagambetova – PhD, Researcher, Laboratory of Molecular Genetics; 6 years of experience; internships in China, Hungary, England, and Korea; co-author of more than 20 articles, including 14 in peer-reviewed journals (Scopus H-index = 6, WoS H-index = 4).

A.K. Zatybekov – PhD, Leading Researcher, Laboratory of Molecular Genetics; 13 years of experience in molecular genetics and breeding; co-author of 25 scientific articles: 14 in Scopus-indexed journals (H-index = 7), 17 in publications of the Committee for Quality Assurance in Science and Higher Education of the Republic of Kazakhstan; co-author of a soybean variety; author of 1 scientific-methodological recommendation and 2 utility model patents; project leader of 2 grant-funded projects (2022–2025); internships in Germany and China.

A.Y. Amalova – PhD, Senior Researcher, Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology; 8 years of experience in molecular genetics and breeding; internships in England, Lithuania, and Japan; co-author of 25 scientific works, including 9 articles in leading international journals indexed in Web of Science (H-index = 4) and Scopus (H-index = 3).

Project Goal and Objectives:
Study of genetic diversity and population structure of collections of varieties and lines of major vegetable and melon crops of Kazakhstan.
Collections of domestic and foreign vegetable crops will be formed:
  • Tomato (at least 25 varieties and lines)
  • Onion (at least 25)
  • Carrot (at least 30)
  • Cucumber (at least 30)
Melon crops:
  • Watermelon (at least 20 varieties and lines)
  • Melon (at least 20 varieties and lines)
Genotyping of domestic and foreign tomato and cucumber samples will be initiated using informative SSR markers.
Preparation of genetic passports for domestic vegetable forms (tomato, cucumber) will begin.
Determination of the genetic population structure of tomato and cucumber collections will be initiated.
Phenotyping of vegetable (tomato, cucumber) and melon (watermelon, melon) collections will be conducted to identify associations between DNA markers and economically valuable traits determining productivity and quality.

Interim Results for 2025–2026:
Working collections of six crops (tomato, cucumber, onion, carrot, melon, watermelon) were formed.
Phenotyping of tomato, cucumber, melon, and watermelon collections was carried out at KazNIIPO based on phenological and biometric parameters.
Genomic DNA extraction in triplicate was performed for tomato and cucumber collections.
SSR genotyping was conducted for 49 tomato varieties and lines using 6 polymorphic markers.
Genotyping of 60 cucumber varieties and lines was performed using 15 SSR markers, 10 of which showed high polymorphism.
Cluster analysis based on genetic distance matrices showed clear separation of samples into several genetic groups. Three main clusters were identified based on dendrogram and STRUCTURE analysis.
Formation of genetic passports for domestic tomato and cucumber varieties has begun.

Publications for 2025–2026:

Project 5

Results for 2025

BR28712539 «To identify novel transcripts, DNA methylation variations, and functional genetic interactions that contribute to stress tolerance in fruit crops» 

Task 05


Results Obtained:
The analysis revealed clear regional differences in transcriptomic responses of both crops:
  • In Almaty region, apple and pear showed high expression of genes related to photosynthesis, primary metabolism, and general growth processes.
  • In Zhetysu region, a pronounced stress profile dominated, with activation of heat shock genes, ABA signaling, water deficit response, antioxidant defense, and stomatal regulation.
Under biotic stress, both species demonstrated activation of conserved immune cascades. However, interspecies differences remained:
  • Apple exhibited a metabolism-oriented strategy, enhancing phenylpropanoid and flavonoid metabolism.
  • Pear showed a stronger stress-oriented response with increased ROS signaling, programmed cell death, and lignification.
Thus, regional factors determine the intensity and direction of stress responses, while species-specific traits shape molecular adaptation strategies.
Рисунок 1. Вулканический график дифференциально экспрессированных генов яблони между популяциями GD2 и GD1
Information for Potential Users:
The obtained molecular profiles are highly promising for developing breeding markers of resistance and for creating adaptive cultivation programs for fruit crops in various climatic conditions.
The analysis provides a scientifically grounded basis for developing adaptive breeding approaches and increasing crop resilience to region-specific stresses.
Рисунок 2. Вулканический график дифференциально экспрессированных генов груши между популяциями FB2 и FB1
Publications and Patents:
Khusnitdinova et al. (2026) Cross-Ecosystem Transmission of Pathogens from Crops to Natural Vegetation. Forests, 17, 76. (Q2, percentile 80)

Kostyukova et al. (2025) Detection of fungal pathogens of the genus Monilinia in cultivated apple orchards. “Science and Education,” Vol. 3, No. 3 (80).
Рисунок 3. Тепловая карта экспрессии топ-50 наиболее вариабельных генов яблони в образцах из Алматинской (GD1) и Жетысуйской (GD2) областей
Руководитель

Гриценко Диляра Александровна, Индекс Хирша – 8, является заведующей лабораторией молекулярной биологии «Институт биологии и биотехнологии растений» Комитета науки Министерства науки и высшего образования Республики Казахстанв течение 6-ти лет, стаж работы в области фитопатологии, молекулярной биологии и молекулярной генетики растений составляет 16 лет. Является специалистом в области сохранения и рационального использования животного и растительного мира. Руководителем опубликовано более 125 научных работ.
Web of Science ResearcherIDD-3918-2015
https://orcid.org/0000-0001-6377-3711

https://www.scopus.com/authid/detail.uri?authorId=57195066016

Рисунок 4. Тепловая карта экспрессии топ-50 наиболее вариабельных генов груши в образцах из Алматинской (FB1) и Жетысуйской (FB2) областей
Project 6

Brief Information About the Project

(2025–2027)


Project Title:
IRN: BR28712539 “Study of genetic diversity of berry plants and development of methods for sanitation of commercially valuable varieties using molecular methods and cryobiotechnologies.”

Brief Information About the Scientific Supervisor:
Kushnarenko S.V. – Head of the Laboratory of Germplasm Cryopreservation, Candidate of Biological Sciences, Professor.
More than 230 publications; 29 indexed in Web of Science, 31 in Scopus.
H-index: 12.
Рисунок – Точки сбора образцов дикой земляники (Fragaria vesca L.) (желтый цвет) и малины ((Rubus idaeus L.) (красный цвет) в Алматинской области 
Краткая информация о членах исследовательской группы:
Маденова Айгуль Калихожаевна, Ph.D., ассоциированный профессор. Индекс Хирша Scopus – 6, WoS – 4; Scopus ID 56800868300; WOS ID AAQ-2822-2020; Квалифицированный специалист в области молекулярной биологии. Имеет более 80 публикаций по теме проекта, в том числе 14 – в изданиях, входящих в базу данных Scopus, 9 – WоS.
Рымханова Назгүл Қабдулақызы, магистр по специальности «Биотехнология», Ph.D.-докторант, молодой специалист. Индекс Хирша 2. Scopus ID: 57773405800; WOS ID FVM-9722-2022. Опыт работы по направлению проекта 8 лет. Специалист в области биотехнологии растений и криоконсервации. По теме проекта имеет 24 публикации, 6 публикаций в базе данных WoS и Scopus.
Манапқанова Ұлжан Айтмұхаметқызы, магистр по специальности «Генетика», Ph.D.-докторант, молодой специалист. Индекс Хирша 1. ScopusID: 59937998400, WOS ID NQY-4262-2025. Специалист в области биотехнологии растений и молекулярной биологии. Опыт работы по направлению проекта 3 года. По теме проекта имеет 10 публикаций, 2 публикации в базе данных WoS и Scopus.

Цель проекта: Фенотипическое и молекулярно-генетическое изучение биоразнообразия ягодных растений и распространенности наиболее вредоносных вирусов на территории Казахстана, разработка способов оздоровления коммерчески ценных сортов земляники и малины на основе использования молекулярных методов и криобиотехнологий.
Рисунок – Места сбора образцов дикой земляники (Fragaria vesca L.) в Алматинской, Северо-Казахстанской и Восточно-Казахстанской областях
Project Objectives:
  1. Field expeditions, phenotyping, sampling of wild and cultivated strawberry and raspberry plants, virus diagnostics.
  2. Creation of in vitro collections.
  3. Development of improved sanitation protocols using molecular methods and cryobiotechnology.
  4. Creation of sanitized plant collections under controlled conditions.
  5. Production of sanitized planting material of at least 3 strawberry and 3 raspberry varieties.
Рисунок – Места сбора образцов дикой малины (Rubus idaeus L.) в Алматинской, Северо-Казахстанской и Восточно-Казахстанской областях
Interim Results of the Project for 2025–2026:
Plant material of wild and cultivated strawberry and raspberry plants was collected in the Almaty, East Kazakhstan, and North Kazakhstan regions. In total, 116 samples were collected, including 56 samples of wild strawberry and 11 cultivar samples, as well as 33 samples of wild raspberry and 16 cultivar samples. Phenotypic characterization of the plants was carried out using international descriptors developed for the genera Fragaria and Rubus.

An analysis for the most harmful viruses was conducted using multiplex TaqMan real-time PCR. In cultivated strawberry samples, Strawberry mottle virus (SMoV) was detected. In raspberry cultivars, three viruses were identified: Raspberry bushy dwarf virus (RBDV), Raspberry yellow net virus (RYNV), and Raspberry enamovirus 1 (EnamoV). No viral infections were detected in wild strawberry and raspberry samples collected in the Almaty region.

Рисунок – Симптомы вирусной инфекции у образца земляники Fra 35, собранного в частном секторе села Большое Аксу
The study of genetic diversity of plant material of Fragaria vesca L. and Rubus idaeus L., collected from various regions of Kazakhstan, has been initiated. Genomic DNA was extracted from 40 samples of wild and cultivated strawberry and 16 samples of wild and cultivar raspberry.

In vitro collections of berry plants, free from epiphytic contamination, have been established. These will be used for further work on plant sanitation and preservation of the gene pool.
Рисунок – Симптомы вирусной инфекции у образцов малины: Rub 19 – образец, собранный в питомнике «Семиречье»; Rub 11 – образец, собранный в частном секторе села Большое Аксу


Publications (2025–2026):
Abstracts:
  1. Kushnarenko et al. – Cryobiotechnologies for plant germplasm preservation (European Biotechnology Congress 2025, in press).
  2. Rymkhanova et al. – In vitro elimination of Raspberry bushy dwarf virus (European Biotechnology Congress 2025, in press).
Рисунок – Растения малины сорта Каскад Делайт (А) и земляники сорта Альбион (Б), размножаемые на среде Мурасиге-Скуга МС с 0,3 мг/л БАП, 0,05 мг/л ИМК, 30 г/л сахарозы, рН 5,8
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