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:
1. Genotyping of wheat germplasm using functional molecular markers for key genes that determine resistance to biotic and abiotic stresses
2. Study of molecular-genetic bases for increasing yield and grain quality improvement of domestic rice breeding.
3. Molecular genetic studies of tetraploid and diploid species to improve the efficiency of potato breeding and seed production.
4. Genetic diversity and population structure of varieties and lines collection of the main vegetable and melon crops of Kazakhstan.
5. Identify new transcripts, DNA methylation variations, and functional genetic links that form stress tolerance in fruit crops.
6 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..
To study the molecular genetic patterns of the formation of economically valuable traits and biological characteristics of major agricultural crops.
Tasks/projects:
1. Genotyping of wheat germplasm using functional molecular markers for key genes that determine resistance to biotic and abiotic stresses
2. Study of molecular-genetic bases for increasing yield and grain quality improvement of domestic rice breeding.
3. Molecular genetic studies of tetraploid and diploid species to improve the efficiency of potato breeding and seed production.
4. Genetic diversity and population structure of varieties and lines collection of the main vegetable and melon crops of Kazakhstan.
5. Identify new transcripts, DNA methylation variations, and functional genetic links that form stress tolerance in fruit crops.
6 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 documents1. 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.
15Kushnarenko 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 description of 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 nationally and internationally recognized expert in the field of plant protection and quarantine, as evidenced by more than 25 years of scientific experience, long-term research on economically important and quarantine diseases of wheat, leadership of over 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, the Eurasian Economic Community, and others. Her research covers a wide range of modern phytopathological, molecular genetic and breeding approaches. The scientific results of A.M. Kokhmetova include more than 400 publications, among which are over 35 articles in international peer-reviewed journals ranked in the 1st–2nd quartiles 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 group:
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 Selection of the Institute of Plant Biology and Biotechnology; Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel.: + 7 (727) 394-75-52, fax 394-75-62,E-mail:gen_kalma@mail.ru
Kumarbayeva Madina Talgarovna – PhD (specialty), Leading Research Scientist, Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 3947552, E-mail: madina_kumar90@mail.ru
AidanaKharipzhanova – PhD (specialty), Researcher, Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 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 Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 394-75-52, fax 394-75-62, E-mail:maki_87@mail.ru
Keishilov Zhenis Sovetkanovich – Master of Agricultural Sciences, PhD doctoral student (specialty), researcher, Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 394-75-52, fax 394-75-62, E-mail:Jeka-Sayko@mail.ru
Bolatbekova Ardak Aydinovna – Master of Environmental Science, PhD doctoral student(specialty), Researcher, Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 3947552, Email:ardashka1984@mail.ru
Bakhytuly Kanat – Master of Natural Sciences, (specialty), Researcher, Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 394-75-52, fax 394-75-62, E-mail: kanat1499@gmail.com
Mukhametzhanov Kanat Serikhanovich – Agronomist organizer, (specialty), laboratory assistant, Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 394-75-52, fax 394-75-62, E-mail:kanat.mukhametzhanov@mail.ru
Kokhmetova Asiya Myrzabekovna Bachelor, (specialty), laboratory assistant Laboratory of Genetics and Selection, Institute of Plant Biology and Biotechnology, Republic of Kazakhstan, 050040, Almaty, st. Timiryazev 45, tel: +7 (727) 394-75-52, fax 394-75-62, E-mail: asia.k68@mail.ru
The goal and tasks of the project:
Project objective: «Genotyping of wheat germplasm using functional molecular markers for key genes that determine resistance to biotic and abiotic stresses».
Tasks:
1. Phenotyping and genetic-breeding evaluation of the collection of wheat varieties and lines from the international KASIB nursery (at least 80 accessions) in contrasting ecological zones of Kazakhstan (Almaty and Kostanay), differing in temperature and moisture regimes; including the assessment of field drought tolerance and determination of the drought tolerance index.
2. Genotyping of wheat accessions using no fewer than 20 functional molecular markers targeting key genes that determine resistance to biotic stresses: Vrn (vernalization response), which defines the plant’s requirement for vernalization; Ppd (photoperiod response), which determines the plant’s reaction to day-length extension; and Lr genes (leaf rust resistance), associated with resistance to leaf rust caused by Puccinia recondita.
3. Genotyping of wheat accessions using functional molecular markers for a key gene determining resistance to abiotic stresses: Dreb-B1 (dehydration responsive element binding), responsible for cellular hydration and associated with drought tolerance. Conducting an integrated analysis of phenotyping and genotyping data to identify climate-resilient wheat genotypes, and selecting genotypes that exhibit high yield potential and resistance to adverse environmental factors.
Interim project results for 2025: Phenotyping and genetic–breeding evaluation of the collection of wheat varieties and lines from the international KASIB nursery were carried out in contrasting ecological zones of Kazakhstan (Almaty and Kostanay), which differ in temperature and moisture regimes. Field drought tolerance and the drought tolerance index were assessed. Under the conditions of the Almaty region, phenological observations and evaluation of 124 spring wheat accessions were conducted. Based on the structural analysis of productivity components, 22 wheat accessions demonstrating the highest values for the complex of productivity traits and 51 accessions with average productivity levels were selected. Phytopathological evaluation and productivity assessment made it possible to identify 64 wheat accessions exhibiting an immune reaction (IT-0) to leaf rust and showing high productivity. High NDVI values (0.50–0.83) were recorded in 72 accessions. In the Almaty region, 27 samples wheat accessions were selected that combined a high biomass index with field drought tolerance. The assessment of morphological traits in the Almaty region revealed high diversity in the collection regarding the length of the last internode and spike exertion, allowing clear adaptive patterns to be identified. The most valuable samples for the arid conditions of the Almaty region were eight accessions (Lutescens 48-204-03, Lutescens 393/05, Lutescens 932, Stepnaya 259, Liniya 4-10-16, Lutescens KS 140/08-3, Lutescens 1300, Hordeiforme 829), which are characterized by a moderate length of the last internode and high spike exertion. These traits ensure efficient heat exchange and preservation of reproductive organs during periods of severe stress.
Similar comprehensive studies, including phenotyping and genetic selection, were conducted in the Kostanay region. Fifty-nine accessions were selected, featuring a combination of leaf rust resistance, drought tolerance, and high productivity. Based on biomass index, 37 accessions were identified with high NDVI values (0.55–0.67) and were also characterized by leaf rust resistance. Correlations between biomass accumulation and grain yield were evaluated. Twenty-seven wheat accessions were selected for their high values across a complex of productivity traits. A wide variability in the length of the last internode and spike exertion was observed in the Kostanay region. It was determined that the greatest adaptation to the moderately arid climate was exhibited by 14 accessions with medium internode length and high spike exertion (Lutescens 932, Lutescens 48-204-03, Lutescens 2102, Pamyati Azieva, Saratovskaya 29, Lutescens 8-108-1, Lutescens 1300, Novosibirskaya 41, Lutescens 90-12, Kargala 223, Liniya 9-25-016, 107/00i, F6[(119x96) x113]). Correlation analysis between the studied traits was performed. As a result of evaluating spring wheat varieties and lines from the KASIB nursery, 22 accessions were selected in the Almaty region and 23 accessions were selected in the Kostanay region, all of which exhibited a high biomass index, strong field drought tolerance (DSI ≤ 0.50), and high productivity. Significant differences were identified in key yield indicators and the drought tolerance index (DSI). High-yielding and promising lines and varieties—Hordeiforme 2264, Annushka, Kargala 223, Liniya 19003, Bezenchukskaya 139, and Leukurum 1469-21—were identified, distinguished by strong field drought tolerance and low drought tolerance index values.
The study is distinguished by a high level of scientific rigor: comprehensive research was carried out, including phytopathological and genetic–breeding evaluations on a large volume of experimental material tested in contrasting ecological zones of Kazakhstan (Almaty and Kostanay).
The practical significance of the results and their potential for future commercialization are confirmed by the selection of more than 20 wheat accessions with a high biomass index, strong field drought tolerance, and high productivity. These accessions will be incorporated into the breeding process as candidates for new wheat varieties and represent valuable material for breeding aimed at improving wheat drought tolerance.
Publications (2025):
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, 8-13 September, 2025.Tirana, Albania. Р. 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, 1-5 Desember, 2025. Turkey, Antalya.
Project 2
Brief description of the project
(2025–2027)
Project title: "Study of molecular genetic basis for increasing yield and improving the quality of rice grain of domestic breeding"
Brief information about the Scientific Supervisor of the project:
Bakdaulet Naubaevich Usenbekov, PhD, Associate Professor
Brief information about the Members of the Research group:
Leading scientist, PhD, Aigul Kuzembaevna Amirova
Senior researcher, PhD, Innabat Abibullakyzy Sartbaeva
Research Assistant, Master's Degree, Dana Omarovna Mynbaeva
Laboratory Assistant, Nurlybay Balnur Azilhanqyzy
Laboratory Assistant, Nurlan Nurdauletuly Usenbekov
The goal and tasks of the project:
Project Goal: To study the molecular genetic basis for increasing yield and improving the grain quality of domestically bred rice.
Project Objectives:
Conduct a molecular genetic screening of rice genotypes using molecular markers associated with yield.
Conduct a molecular genetic screening of rice genotypes that carry the traits "high amylose content" and "low amylose content."
Conduct hybridization to introgresse genes with low and high amylose content into high-yielding rice varieties to create promising forms and lines with varying amylose content and high yield.
Interim project results for 2025:
Molecular genetic screening of rice genotypes using molecular markers associated with yield was conducted.
Molecular genetic screening of rice genotypes that carry the traits "high amylose content" and "low amylose content" was conducted.
Hybridization was conducted to introgresse genes with low and high amylose content into high-yielding rice varieties to create promising forms and lines with varying amylose content and high yields.
Publications (2025):
Project 3
Brief description of the project
(2025-2027)
Project title: Molecular genetic studies of tetraploid and diploid species to improve the efficiency of potato breeding and seed production
Brief information about the Scientific Supervisor of the project:
Zhambakin Kabyl Zhaparov, Academician of the National Academy of Sciences of the Republic of Kazakhstan, Professor, Doctor of Biological Sciences. H-index – 8 in Scopus and WoS databases.
Brief information about the Members of the Research group:
Malika Khabidulaevna Shamekova, 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 WoS (https://www.webofscience.com/wos/author/record/98695).
Ainash Kenenbaevna Daurova, 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 WoS (https://www.webofscience.com/wos/author/record/2024273)
Dmitry Vladimirovich Volkov, master’s degree, PhD Student, Senior Research Fellow. H-index: 4 according to Scopus (https://www.scopus.com/authid/detail.uri?authorId=57218835515&origin=resultslist) and WoS (https://www.webofscience.com/wos/author/record/636236)
Aset Maulenovich Akbaev, Master's Degree, Junior Research .
The goal and tasks of the project: Molecular genetic studies of tetraploid and diploid species to improve the efficiency of potato breeding and seed production.
Interim project results for 2025:
During this work, a working collection of tetraploid and diploid potatoes was formed, including both domestic and international genotypes, including those from Kazakhstan, Russia, Germany, the Netherlands, the international CIP organization, Pakistan, and China, as well as hybrid lines we had previously developed.
Molecular screening of the working potato collections was conducted using 29 molecular SCAR and CAPS markers. The analysis revealed significant genetic diversity among the studied lines, including markers associated with earliness, starch, 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 desired tuber quality characteristics and biochemical properties.
Hybridization studies were conducted with 12 CIP genotypes, resulting in the production of 14 berries in 7 hybrid combinations. The most productive combinations were CIP 10 × CIP 3, CIP 17 × CIP 18 and CIP 18 × CIP 17, which indicates the high compatibility and fertility of these lines.
Publications (2025):
Project 4
Brief description of the project
(2025-2027)
Project title: Genetic diversity and population structure of collections of cultivars and lines of the main vegetable and melon crops of Kazakhstan
Brief information about the Scientific Supervisor of the project:
A.A. Alikhanova, MSc, Junior Researcher in the Laboratory of Molecular Genetics. She has three years of experience studying the wild flora of Kazakhstan. She completed internships at research centers in South Korea and Hungary and completed training in modern methods of species distribution analysis and forecasting (SDM, certificate).
Brief information about the Members of the Research group:
Yu.A. Geniyevskaya, PhD, Researcher in the Laboratory of Molecular Genetics, has 8 years of experience, co-author of 23 articles, of them 18 in peer-reviewed journals, Scopus (H-index=9) and WoS (H-index=8). Co-author of 2 monographs, guidelines, and a utility model. Co-author of a barley variety. Internships in the UK and Japan.
M.M. Yermagambetova, PhD, Researcher in the Laboratory of Molecular Genetics, has 6 years of experience. Internships at research centers in China, Hungary, England, and Korea. Co-author of over 20 articles, including 14 articles in peer-reviewed journals Scopus (H-index=5) and WoS (H-index=4).
A.K. Zatybekov, PhD, Leading Researcher in the Laboratory of Molecular Genetics, has 13 years of experience in the field. Molecular genetics and breeding, co-author of 25 scientific articles: 14 in peer-reviewed journals of Web of Science and Scopus (H-index=5), 17 in publications of SHEQAC MSHE RK; co-author of a soybean variety; 1 scientific and methodological recommendation, 2 patents for a utility model. Supervisor of 2 grant-funded projects (2022-2025). Internships at research centers in Germany and China.
A.Y. Amalova, PhD, Senior Researcher in the Laboratory of Molecular Genetics. Amalova has 8 years of experience in molecular genetics and breeding. She completed scientific internships in England, Lithuania, and Japan. Amalova is the co-author of 25 scientific papers, including 9 articles published in leading scientific journals of foreign countries included in the Web of Science databases. (H-index = 4) and Scopus (H-index = 3).
The goal and tasks of the project:
Study of the genetic diversity and population structure of collections of cultivars and lines of the main vegetable and melon crops of Kazakhstan.
Collections of vegetable (tomato, cucumber, onion, carrot) and melon (watermelon, melon) crops will be formed. DNA extraction from the tomato, cucumber, onion, carrot, watermelon, and melon collections will be started. Optimization of PCR conditions for the analysis of genetic diversity in the context of 6 crops using informative SSR markers will be started. Genotyping of domestic and foreign samples of tomato and cucumber using informative SSR markers will be started. Preparation of genetic passports of domestic forms of vegetable crops (tomato, cucumber) will be started. Determination of the genetic structure of populations of tomato and cucumber collections will be started. Phenotyping of samples of vegetable (tomato, cucumber) and melon (watermelon, melon) crop collections will be carried out to search for associations between DNA markers and economically valuable traits that determine productivity and quality.
Interim project results for 2025:
Working collections of six crops were formed: tomato, cucumber, onion, carrot, melon, and watermelon. Genomic DNA was isolated in triplicate for the tomato and cucumber collections. SSR genotyping was conducted for 49 tomato cultivars and lines using 12 markers, six of which exhibited polymorphism. Genotyping was conducted for 60 cucumber cultivars and lines using 15 SSR markers, ten of which exhibited high levels of polymorphism. Clustering analysis, based on genetic distance matrices, revealed a clear division of the studied tomato and cucumber accessions into several genetic groups. Three main clusters were identified for the tomato collection based on the dendrogram and STRUCTURE analysis. Three genetic clusters were also identified in the cucumber collection. The genetic passports for domestic tomato and cucumber cultivars are being developed. Both cultivars demonstrated genetic homogeneity and a lack of intravarietal polymorphism.
Publications (2025):
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 for 2025:
The conducted analysis revealed pronounced regional differences in the transcriptomic responses of both crops. In the Almaty region, apple and pear were characterized by dominant high expression of genes associated with photosynthesis, primary metabolism, and general growth-related processes, whereas in the Zhetysu region a distinct stress-related profile prevailed, marked by the activation of heat shock proteins, ABA signaling pathways, water-deficit–responsive genes, antioxidant defense mechanisms, and stomatal regulation.
Under biotic stress conditions, both species exhibited activation of conserved immune signaling cascades. However, interspecific differences remained evident: apple primarily displayed a metabolically oriented adaptive strategy, characterized by enhanced phenylpropanoid and flavonoid metabolism, while pear showed a more rigid stress-oriented response involving intensified ROS signaling, programmed cell death, and lignification processes. Thus, regional environmental factors determine the magnitude and direction of stress responses in both crops, whereas species-specific traits shape differences in the dominant molecular adaptation strategies.
Information for potential users
The obtained molecular profiles demonstrate high potential for subsequent application in the development of resistance-associated breeding markers and the design of adaptive cultivation strategies for fruit crops under diverse climatic conditions.
The conducted analysis effectively revealed key regional differences in the transcriptomic responses of apple and pear, enabling the identification of dominant stress-related and metabolic strategies across contrasting environments. These findings provide a scientifically sound basis for the development of adaptive breeding approaches and for enhancing the resilience of fruit crops to region-specific environmental stresses.
Publications 2025
1. V.S, Kostyukova, et al. Detection of fungal pathogens of the genus monilinia in cultivated apple orchards. Ġylym ža̋ne bìlìm 3.3 (80) (2025): 107-114.
Figure 1. Volcano plot of differentially expressed genes in apple between the GD2 and GD1 populations
Figure 2. Heatmap of expression profiles of the top 50 most variable genes in apple samples from the Almaty (GD1) and Zhetysu (GD2) regions
Figure 3. Volcano plot of differentially expressed genes in pear between the FB2 and FB1 populations
Figure 4. Heatmap of expression profiles of the top 50 most variable genes in pear samples from the Almaty (FB1) and Zhetysu (FB2) regions
Figure 5. Gene Ontology (GO) enrichment analysis of differentially expressed genes in apple in response to Pseudomonas syringae infection
Figure 6. Gene Ontology (GO) enrichment analysis of differentially expressed genes in pear in response to Erwinia amylovora infection
Project 6
Brief description of the project
(2025-2027)
Project title: BR28712539 «Study of the genetic diversity of berry plants and development of methods for sanitation of commercially valuable cultivars using molecular methods and cryobiotechnologies»
Brief information about the Scientific Supervisor of the project: Head of the Germplasm Cryopreservation Laboratory, Candidate of Biological Sciences, Professor S.V. Kushnarenko. She has published more than 230 scientific works, including 29 publications indexed in the Web of Science database and 31 publications indexed in the Scopus database. Her Hirsch index is 12. Scopus ID: 6507153914; Web of Science ID: M-6616-2015.
Brief information about the Members of the Research group:
Aigul Kalikhozhayevna Madenova, Ph.D., Associate Professor. Hirsch index: Scopus – 6, Web of Science – 4; Scopus ID: 56800868300; Web of Science ID: AAQ-2822-2020. A qualified specialist in the field of molecular biology. She has more than 80 publications related to the project topic, including 14 papers published in journals indexed in Scopus and 9 papers indexed in Web of Science.
Nazgul Kabdulakyzy Rymkhanova, Master’s degree in Biotechnology, Ph.D. doctoral student, early-career specialist. Hirsch index: 2. Scopus ID: 57773405800; Web of Science ID: FVM-9722-2022. She has 8 years of experience in the project field. A specialist in plant biotechnology and cryoconservation. On the project topic, she has 24 publications, including 6 papers indexed in Web of Science and Scopus.
Ulzhan Aitmukhametkyzy Manapkanova, Master’s degree in Genetics, Ph.D. doctoral student, early-career specialist. Hirsch index: 1. Scopus ID: 59937998400; Web of Science ID: NQY-4262-2025. A specialist in plant biotechnology and molecular biology. She has 3 years of experience in the project field. On the project topic, she has 10 publications, including 2 papers indexed in Web of Science and Scopus.
The goal and tasks of the project: The aim of the work was the phenotypic and molecular-genetic assessment of the biodiversity of berry plants and the prevalence of the most harmful viruses in Kazakhstan, along with the development of methods for sanitizing commercially valuable strawberry and raspberry cultivars using molecular approaches and cryobiotechnology.
1 Expeditionary trip, phenotypic description, collection of plant material from wild and cultivated strawberry and raspberry plants, diagnostics for the most harmful viruses.
2. Establishment of in vitro collections of berry plants.
3. Development of an effective protocol for elimination of the most harmful viruses in raspberry and strawberry plants using molecular methods and cryobiotechnology.
4. Establishment of virus-free plants collection of commercially valuable varieties of raspberry and strawberry under controlled conditions (2 in vitro collections, 2 collections under slow growth conditions (cold storage, +4ºС), 2 collections in a cryogenic bank, 2 collections in a greenhouse).
5. Obtaining virus-free planting material of at least three commercially valuable varieties of strawberry and at least three varieties of raspberry.
Interim project results for 2025:
Main results: Plant material of wild and cultivated strawberries and raspberries 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 descriptions of the plants were carried out using international descriptors developed for the genera Fragaria and Rubus.
Figure 1
Collection sites of wild strawberry (Fragaria vesca L.) accessions in the Almaty, North Kazakhstan, and East Kazakhstan Regions.
An analysis for the most harmful viruses was performed using multiplex TaqMan real-time PCR. In the strawberry cultivars, 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.
Initial studies of the genetic diversity of Fragaria vesca L. and Rubus idaeus L. from various regions of Kazakhstan were conducted. Genomic DNA was isolated from 40 samples of wild and cultivated strawberry and 16 samples of wild and cultivated raspberry.
In vitro collections of berry plants free from epiphytic contamination were established, which will be used in further work on sanitization and preservation of the gene pool.
Initial studies of the genetic diversity of Fragaria vesca L. and Rubus idaeus L. from various regions of Kazakhstan were conducted. Genomic DNA was isolated from 40 samples of wild and cultivated strawberry and 16 samples of wild and cultivated raspberry.
In vitro collections of berry plants free from epiphytic contamination were established, which will be used in further work on sanitization and preservation of the gene pool.
Figure 2
Sampling sites of wild raspberry (Rubus idaeus L.) in Almaty, North Kazakhstan, and East Kazakhstan regions
Publications (2025):
Abstracts
a) in the proceedings of international conferences in far-abroad countries:
1. Kushnarenko S.V., Rymkhanova N.K., Manapkanova U.A., Romadanova N.V., Rakhimbaev I.R. Cryobiotechnologies for preservation of plant germplasm in Kazakhstan // European Biotechnology Congress, 8–13 September 2025, Tirana, Albania (in press).
2. Rymkhanova N.K., Manapkanova U.А., Kushnarenko S.V. Development of in vitro technique for elimination of Raspberry bushy dwarf virus // European Biotechnology Congress, 8–13 September 2025, Tirana, Albania (in press).
Abstracts
a) in the proceedings of international conferences in far-abroad countries:
1. Kushnarenko S.V., Rymkhanova N.K., Manapkanova U.A., Romadanova N.V., Rakhimbaev I.R. Cryobiotechnologies for preservation of plant germplasm in Kazakhstan // European Biotechnology Congress, 8–13 September 2025, Tirana, Albania (in press).
2. Rymkhanova N.K., Manapkanova U.А., Kushnarenko S.V. Development of in vitro technique for elimination of Raspberry bushy dwarf virus // European Biotechnology Congress, 8–13 September 2025, Tirana, Albania (in press).
Figure 3
Raspberry plants of the Cascade Delight cultivar (A) and strawberry plants of the Albion cultivar (B) propagated on Murashige and Skoog (MS) medium with 0.3 mg/L BAP, 0.05 mg/L IBA, 30 g/L sucrose, pH 5.8.
