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HomeАР22785823 (superviser Amalova A.Y.)

АР22785823 (superviser Amalova A.Y.)

Brief description of the project

(2024-2026)

Project title: IRN АР22785823  «Identification of DNA markers and genes associated with the “pre-harvest sprouting” in the collection of bread wheat Triticum aestivum L.».

Relevance. Despite the relatively low level of productivity, bread wheat grown in Kazakhstan is  valued on the world market due to its high grain quality. However, farmers in country often face problems with grain pre-harvest sprouting due to heavy rainfall at time of harvest. Sprouted grain has low grain quality and is unsuitable for flour processing. High humidity can contribute to mold development and accumulation of toxins in grain. The problem of pre-harvest sprouting (PHS) is one of reasons for yield reduction, in addition to biotic and abiotic factors. PHS predetermines seeds as unsuitable for use in the next sowing season, which has negative impact on the country’s food security. PHS is widespread in all leading grain-growing regions, such as Canada, European countries, Australia, China, USA, and Japan. PHS is complex quantitative trait controlled by number of different genes. Different methodologies are used to identify quantitative trait loci (QTLs): mapping using bi-parental mapping populations and genome-wide association study (GWAS) methodology for collections with different origins. Research on bread wheat has identified many QTLs associated with PHS resistance in various regions of the world.

The goal of the project: to identify genes and DNA markers associated with the “pre-harvest sprouting” in bread wheat (Triticum aestivum L.) using genome-wide association study methodology.

Expected results:

1. The level of phenotypic variability of bread wheat collection based on the PHS, yield components, and adaptability traits will be assessed. Samples of bread wheat collection with a long dormancy time in seeds will be identified.

2. The level of phenotypic variability of a bread wheat collection based on PHS will be assessed under laboratory conditions.

3. The genetic diversity of a bread wheat collection will be assessed using known specific genes associated with PHS.

4. New genes and DNA-markers of bread wheat responsible for resistance to PHS will be identified using the results of phenotyping and genotyping of bread wheat collection with different geographical origins and GWAS. 

5. A set of KASP-markers associated with PHS resistance in bread wheat will be developed. The effectiveness of genes associated with resistance to PHS based on KASP genotyping of collection of local bread wheat cultivars and lines will be confirmed.

Scientific Supervisor of the project:          

 Amalova Akerke,  PhD (biology), researcher at the Laboratory of Molecular Genetics. She has 7 years of experience in molecular genetics and cereal breeding. Amalova A. is a co-author of more than 22 scientific papers, including 7 articles published in leading scientific publications in the Web of Science (H-index = 4, ResearcherID: AAO-1156-2020) and Scopus ( H-index = 3, Scopus ID: 57213623570) databases. She is a co-author of the Patent (utility model), and bread wheat cultivar.

Research group: 

Sh. Almerekova,  PhD, leading researcher, has 11 years of work experience, co-author of more than 35 scientific articles, including 18 articles in peer-reviewed publications indexed in the Web of Science (ResearcherID: AAO-1157-2020) and Scopus (H-index – 7, Scopus ID: 57196952712). Co-author of a monograph, methodological instructions patent (utility model). Co-author of barley cultivar. Completed internships in research centers in Germany, Spain, and Hungary.

Y. Genievskaya,  PhD, researcher, has 7 years of experience, co-author of 22 articles (17 in peer-reviewed journals, WoS (ResearcherID: AAF-2410-2019) and Scopus (H-index 7, Scopus ID: 57196939730), of which 12 are on the topic of the project. Co-author of monograph, methodological instructions a utility model. Co-author of barley cultivar.  She had an internship at the University of Oxford (2019) and the John Innes Center (2022) (UK).

A. Krempa, MSs, junior researcher, has 4 years of experience; co-author of 7 articles, 4 of them – in peer-reviewed journals, WoS (ResearcherID: CBM-3140-2022), (H-index 1, Scopus ID: 57969501500). Trained at the Siberian Research and Design and Technology Institute (Russia).

              A. Burakhodzha, born in 2000, MSs, laboratory assistant, has 3 years of experience. Co-author of 2 articles, 1 of them – in peer-reviewed journals in the WoS/Scopus databases.

N. Muratbek was born in 1999, bachelor, and laboratory assistant.

List of publications of the project’s participants (2018-2023)

  1. Amalova A., Yessimbekova M., Ortaev A., Rsaliyev S., Griffiths S., Burakhoja A., Turuspekov Y., Abugalieva, S.  (2023) Association mapping of quantitative trait loci for agronomic traits in a winter wheat collection grown in Kazakhstan // Agronomy (IF= 3.7, Q1 y; SJR= 0.663, percentile: 79). Vol. 13. P. 2054. DOI:10.3390/agronomy13082054
  2. Amalova A., Yermekbayev K., Griffiths S., Winfield M.O., Morgounov A., Abugalieva S., Turuspekov Y. (2023) Population structure of modern winter wheat accessions from Central Asia // Plants (IF= 3.7, Q1; SJR= 0.663, percentile: 83). Vol.; 12(12). P. 2233. DOI:10.3390/plants12122233 
  3. Amalova, A., Abugalieva S, Babkenov A., Babkenova S., Turuspekov Y. (2021). Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan. PeerJ (IF= 2.7, Q2; SJR= 0.695, percentile: 83-) 9:e11857. DOI:10.7717/peerj.11857.
  4. Amalova A., Yermekbayev K., Griffiths  S., Abugalieva S., Babkenov A., Fedorenko E.,  Abugalieva A., Turuspekov Y. Identification of quantitative trait loci of agronomic traits in bread wheat using a Pamyati Azieva × Paragon mapping population harvested in three regions of Kazakhstan // PeerJ (IF= 2.7, Q2; SJR= 0,695, percentile: 83). – 2022. – Vol. 10. – P. e14324 DOI:10.7717/peerj.14324   
  5. Amalova A., Abugalieva S., Chudinov V.,  Sereda G.,  Tokhetova L., Abdikhalyk A., Turuspekov Y. QTL mapping of agronomic traits in common wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan // PeerJ (IF= 2.7, Q2; SJR= 0.695, percentile: 83). – 2021 – Vol 9. –  P. e10733. DOI: 10.7717/peerj.10733
  6. Amalova A.Y., Yessimbekova M.A., Ortaev A.K., Baimagambetova M.M., Burakhoja A.M., Abugalieva S.I., Turuspekov Y.K. Phenotypic variation of winter wheat collection from Central Asia harvested in Kazakhstan // Вестник КазНУ.Серия биологическая. – 2023. – № 3 (96). – P.82-90 https://doi.org/10.26577/eb.2023.v96.i3.06
  7. Amalova A.Y., Genievskaya, Y., Abugalieva, S., Chudinov, V., & Turuspekov, Y. Validation of marker-trait associations in six-rowed barley lines bred in Kazakhstan // Eurasian Journal of Applied Biotechnology. – 2022. –  № 4. – P. 40-48.
  8. Amalova A.Y., Turuspekov Y.K. Agronomic performance of common wheat nested association mapping (NAM) population in Kazakhstan // Eurasian Journal of Ecology (Вестник КазНУ, Серия экологическая). – 2021. – Vol. 67 (2). – P. 58-67. https://doi.org/10.26577/EJE.2021.v67.i2.06
  9. Yermekbayev K., Griffiths S., Chhetry M., Leverington-Waite, M., Orford, S., Amalova, A., Abugalieva S.,Turuspekov Y.(2020). Construction of a Genetic Map of RILs Derived from Wheat (T. aestivum L.) Varieties Pamyati Azieva × Paragon Using High-Throughput SNP Genotyping Platform KASP-Kompetitive Allele Specific PCR // Russian Journal of Genetics (IF=0.6, квартиль-Q4, SJR=0.180, процентиль-7) 56(9):1090-1098. DOI: 10.1134/S102279542009015X.
  1. Genievskaya Y., Fedorenko Y., Sarbayev A., Amalova A., Abugalieva S., Griffiths S., Turuspekov Y. Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of «Pamyati Azieva×Paragon» // Вавиловский журнал генетики и селекции (Percentile -46, SJR=0.223). – 2019. – Vol. 23(7). – P. 887-895 DOI 10.18699/VJ19.563 
  2. Amalova A., Yermekbayev K., Griffiths S., Abugalieva S., Turuspekov Y. Phenotypic variation of common wheat mapping population Pamyati Azieva x Paragon in south-east of Kazakhstan // International Journal of Biology and Chemistry. IJBCH-D-19-00008. – 2019. – Vol. 12, N.1. – P. 11-17. https://doi.org/10.26577/ijbch-2019-i1-3
  3. Genievskaya Y.A., Amalova A.Y., Ydyrys A.A., Sarbayev A.T., Griffith S., Abugalieva S.I., Turuspekov Y.K. Resistance of common wheat (Triticum aestivum L.) mapping population Pamyati Azieva × Paragon to leaf and stem rusts in conditions of South-East Kazakhstan // Eurasian Journal of Ecology (Вестник КазНУ, Серия экологическая). 2019. — №4(61). – P. 14-23. https://doi.org/10.26577/EJE.2019.v61.i4.02
  4. Almerekova S., Sariev B., Abugalieva A., Chudinov V., Sereda G., Tokhetova L., Ortaev A., Tsygankov V., Blake T., Chao S., Genievskaya Y., Abugalieva S., Turuspekov Y.(2019). Association mapping for agronomic traits in six-rowed spring barley from the USA harvested in Kazakhstan, PLoS ONE (IF=3.7 Q2; SJR=0.885, 87). 14(8):e0221064. DOI: 10.1371/journal.pone.0221064.
  5. Genievskaya Y, Turuspekov Y, Rsaliyev A, Abugalieva S. (2020). Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan // PeerJ (IF= 2.7, Q2; SJR= 0.695, percentile: 83) 8:e9820. DOI: 10.7717/peerj.9820.
  6. Genievskaya Y., Almerekova S., Sariev B., Chudinov V., Tokhetova L., Sereda G., Ortaev A., Tsygankov V., Blake T., Chao S., Sato K., Abugalieva S., Turuspekov Y. (2018). Marker-trait associations in two-rowed spring barley accessions from Kazakhstan and the USA. PLoS ONE (IF=3.7 Q2; SJR=0.885, 87) 3(10): e0205421. DOI: 10.1371/journal.pone.0205421.
  7. Shuliko, N. N., Khamova, O. F., Timokhin, A. Y. Y., Boiko, V. S., Tukmacheva, E. V., & Krempa, A. (2022). Influence of long-term intensive use of irrigated meadow-chernozem soil on the biological activity and productivity of the arable layer. Scientific Reports (IF= 4.9, Q2; SJR= 0.973, percentile: 92), 12(1), 14672.
  8. Genievskaya, Y., Zatybekov, A., Abugalieva, S., & Turuspekov, Y. (2023). Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan // Plants (IF= 3.7, Q1; SJR= 0.663, percentile: 83). 12(12), 2375. DOI: 10.3390/plants12122375   
  9. Zatybekov, A. Genievskaya Y, Rsaliyev A, Turuspekov Y, Abugalieva S. (2022). Identification of quantitative trait loci for leaf rust and stem rust seedling resistance in bread wheat using a genome-wide association study // Plants (IF= 3.7, Q1; SJR= 0.663, percentile: 83) 11(1):74. DOI: 10.3390/plants11010074. (

Results for 2024:

  1.  Evaluation of the phenological and phenotypic variability of a bread wheat collection was conducted in two regions of Kazakhstan: the north (Kostanay region) and the southeast (Almaty region). Traits related to adaptability, productivity components, and pre-harvest sprouting (PHS) were studied. Seven samples demonstrated resistance to PHS based on laboratory experiments.
  2. To assess the genetic diversity of the soft wheat collection, DNA was isolated from 90 samples, and genotyping was initiated for specific genes associated with grain color, seed dormancy period, and PHS resistance. Additionally, the DNA bank was expanded with 20 samples from the collection of local varieties and lines of soft wheat for further genotyping and testing of KASP markers associated with PHS resistance.
  3. As a result of a genome-wide association study (GWAS), 98 quantitative trait loci (QTLs) were identified for the traits studied under the conditions of the Almaty region and 75 QTLs under the conditions of the Kostanay region.