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HomeAP 23489531 (superviser Zatybekov A.)

AP 23489531 (superviser Zatybekov A.)

Brief description of the project

(2024-2026)

 

Project title: IRN AP13068118 « Mining for genes associated with agronomic traits of soybean (Glycine max (L.) Merr.)  using whole-genome resequencing of world collection».

 Relevance. The creation of highly productive soybean varieties is of key importance for ensuring food security and sustainable development of agriculture in Kazakhstan. Given the current challenges in the agro-industrial sector, accelerating the breeding process using advanced genomic technologies is becoming an urgent task.

The use of whole genome resequencing (WGRS) in the framework of research opens up new perspectives for studying and improving soybeans. The analysis of 252 varieties and lines of the global collection, including Kazakhstani varieties, implemented through the cooperation of scientists from Kazakhstan and China, will reveal genes related to yield and seed quality. The WGRS technique has high accuracy and makes it possible to identify more than 3 million polymorphic SNP markers, which increases the genome coverage density hundreds of times compared to traditional SNP genotyping methods. This makes it possible to effectively conduct a genome-wide analysis of associations to identify DNA markers associated with economically valuable traits.

Of particular value to the project is the possibility of identifying loci of quantitative traits and genes that control economically valuable traits based on WGRS data, as well as the results of field and laboratory tests of a collection of soybeans grown in various environmental conditions in the south-east and north of Kazakhstan.

The results of the study will make it possible to develop sets of informative KASP markers that will greatly simplify soybean breeding and identify highly productive lines adapted to the conditions of Kazakhstan. These achievements will help to increase the efficiency of soybean production and strengthen the country’s agricultural potential.

 The goal of the project: Identification of quantitative trait loci and genes that control productivity and quality, based on the whole-genome re-sequencing of 252 samples of the world soybean collection and the development of two sets of KASP markers for agronomic traits in the southeast and north regions of the country.

 Expected results:

  1. WGRS of 31 local accessions using Illumina HiSeq X Ten System platform, in addition to the 221 accessions that already re-sequenced as a groundwork for the project. The genetic variability in the collection will be determined; polymorphic SNPs will be identified; matrix data for GWAS will be prepared.
  2. Soybean collection consisting of 252 accessions harvested in southeast and north of Kazakhstan will be studied for agronomic traits. The variability of morphological, yield and quality traits tested in two regions will be assessed.
  3. Based on WGRS of 252 accessions GWAS will be carried out to identify QTLs and genes that are significantly associated with morphological, yield and quality traits.
  4. Population analysis will be done to determine the genetic clustering of Kazakh and foreign genotypes, including samples of wild-growing soybeans.
  5. SNP markers will be validated for the traits that determine soybean yield and quality.
  6. Informative sets of KASPs will be developed for the breeding of soybeans with high values of agronomic traits.

 Scientific Supervisor of the project:

Leading Researcher, PhD, Zatybekov Alibek Kamzabekovich

 Research group: 

Senior Researcher, PhD, Anuarbek Shynar Nurlankyzy

Junior Researcher, Doszhanova Botakoz Nurmaganbetovna

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

  1. Zatybekov A., Abugalieva S., Didorenko S., Rsaliyev A., Turuspekov Y. GWAS of soybean breeding collection for resistance to fungal diseases in condition of South-East and South Kazakhstan // Vavilov Journal of Genetics and Breeding (Vavilovskii Zhurnal Genetiki i Selektsii=Вавиловский журнал генетики и селекции) (SJR=0.147, Q3 – Agricultural and Biological Sciences; percentile: 38 –General Agricultural and Biological Sciences) — 2018. — Vol. 22(5). — P.536-543. DOI 10.18699/VJ18.392.
  2. Затыбеков А.К., Ануарбек Ш.Н., Абугалиева С.И., Туруспеков Е.К. Изучение коллекции сои с использованием ДНК маркеров устойчивости к грибным болезням // Ізденістер, нəтижелер – Исследования, результаты. – 2018. – №.3(79). – C.212-218.
  3. Zatybekov A.K., Agibaev A.Z., Didorenko S.V., Abugalieva S.I., Turuspekov Y.K. Analysis of resistance to Septoria glycines in soybean world collection harvested in south-eastern Kazakhstan // News of the NAS of RK, series of agricultural sciences. – 2018. – №.5. – P.44-52.
  4. Doszhanova B.N., Didorenko S.V., Zatybekov A.K., Turuspekov Y.K., Abugalieva S.I. Analysis of soybean world collection in the conditions of Southeast Kazakhstan // International Journal of Biology and Chemistry — 2019. — Vol. 12(1). — P.33-40. doi.org/10.26577/ijbch-2019-1-i5.
  5. Zatybekov A., Abugalieva S., Didorenko S., Turuspekov Y. Effect of Population Size on Genome-Wide Association Study of Agronomic Traits in Soybean // Proceedings of the Latvian Academy of Sciences. Section B. (SJR=0.168, Q3 – Multidisciplinary, percentile: 39 – Multidisciplinary)- 2020. — Vol. 74, No. 4 (727). — P.244-251. DOI: 10.2478/prolas-2020-0039.
  6. Zatybekov A.K., Turuspekov Y.T., Doszhanova B.N., Abugalieva S.I. A study of the genetic diversity in the world soybean collection using microsatellite markers associated with fungal disease resistance // Proceedings on Applied Botany, Genetics and Breeding (Труды по прикладной ботанике, генетике и селекции). (IF=0.365 (РИНЦ)) – 2020. — Vol. 181, No. (3). — P.81-90. DOI: 10.30901/2227-8834-2020-3-81-90.
  7. Zatybekov A., Anuarbek S., Abugalieva S., Turuspekov Y. Phenotypic and genetic variability of a tetraploid wheat collection grown in Kazakhstan // Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. (SJR=0.147, Q3 – Agricultural and Biological Sciences; percentile: 38 –General Agricultural and Biological Sciences). 2020;24(6):605-612. DOI 10.18699/VJ20.654
  8. Zatybekov A, Genievskaya Y, Rsaliyev A, Maulenbay A, Yskakova G, Savin T, Turuspekov Y, Abugalieva S. Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study. Plants. 2022; 11(1):74. https://doi.org/10.3390/plants11010074
  9. Genievskaya Y., Pecchioni N., Laidò G., Anuarbek S., Rsaliyev A., Chudinov V., Zatybekov A., Turuspekov Y., Abugalieva S. Genome-wide association study of leaf rust and stem rust seedling and adult resistances in tetraploid wheat accessions harvested in Kazakhstan // Plants. 2022; 11(15):1904. https://doi.org/10.3390/plants11151904.
  10. Podzorova T., Zatybekov A., Didorenko S., Abugalieva S. Genetic variation of soybean collection based on microsatellite DNA markers related to plant height // Eurasian Journal of Applied Biotechnology. – 2022. – Vol. №3. – P.3-12. https://doi.org/10.11134/btp.2.2022.1.
  11. Genievskaya Y., Zatybekov A., Abugalieva S., Turuspekov Y. Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan // Plants. 2023; 12(12):2375. https://doi.org/10.3390/plants12122375.
  12. Zatybekov A., Abugalieva S., Didorenko S., Rsaliyev A., Maulenbay A., Fang C., Turuspekov Y. Genome-wide association study for charcoal rot resistance in soybean harvested in Kazakhstan. Vavilovskii Zhurnal Genetiki i Selektsii=Vavilov Journal of Genetics and Breeding. 2023;27(6):565-571. DOI 10.18699/VJGB-23-68
  13. Zatybekov A., Yermagambetova M., Genievskaya Y., Didorenko S., Abugalieva S. Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers // 2023; 12(19):3445. https://doi.org/10.3390/plants12193445.
  14. Fang, C., Sun, Z., Li, S., Su T., Wang L., Dong L., Li H., Li L., Kong L., Yang Z., Lin, Zatybekov A., Liu B., Kong F., Lu S.Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation. Nat Commun 15, 6184 (2024). https://doi.org/10.1038/s41467-024-50623-3.
  15. Doszhanova B.N., Zatybekov A.K., Didorenko S.V., Suzuki T., Yamashita Y., Turuspekov Y. Identification of quantitative trait loci of pod dehiscence in a collection of soybean grown in the southeast of Kazakhstan. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2024;28(5):515-522. DOI18699/vjgb-24-58.

Results for 2024:

Studies conducted in 2024 revealed a significant effect of growing conditions on agronomic characteristics, including yield, plant height and flowering time. Domestic varieties and genotypes from Eastern Europe and North America have demonstrated the best results in the conditions of southeastern Kazakhstan.

The GWAS results revealed 83 significant associations between SNP markers and economically valuable traits, of which 38 were stable for two years. This opens up opportunities to improve protein content, oil, and yield. Phylogenetic analysis confirmed the differences between wild and cultivated soybean forms, emphasizing the importance of wild samples for breeding. Analysis of the population structure revealed several clusters, which is important for understanding the mechanisms of domestication.

KASP markers have been created, adapted to the conditions of the south-east and north of Kazakhstan, which optimizes breeding programs. These markers confirmed the associations between genotypes and phenotypes and demonstrated reliability. The identified promising varieties and lines will improve yields and product quality, ensuring the region’s food security and adaptation to changing climatic conditions.

 Publications (2024):

  1. Doszhanova B.N., Zatybekov A.K., Didorenko S.V., Suzuki T., Yamashita Y., Turuspekov Y. Identification of quantitative trait loci of pod dehiscence in a collection of soybean grown in the southeast of Kazakhstan. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2024;28(5):515-522. DOI18699/vjgb-24-58.
  2. Doszhanova B., Zatybekov A., Didorenko S., Fang C., Abugalieva S., Turuspekov Y. Genome-wide association study of seed quality and yield traits in a soybean collection from Southeast Kazakhstan // Agronomy (Q1 Agronomy, процентиль 84 Agronomy and Crop Science. – 2024. – 14(11):2746. https://doi.org/10.3390/agronomy14112746.
  3. KZ No. 9289 State Register bulletin. Satybekov A.K., Doszhanova B.N., Abugalieva S.I., Turuspekov E.K. Method of identification of breeding valuable soybean lines (Glycine max (L.) Merr.) using a set of KASP markers.