ipbbkz@gmail.com
+ 7 (727) 394 75 62
HomeAP 09259168 (superviser Turuspekov Y.)

AP 09259168 (superviser Turuspekov Y.)

Brief description of the project

(Project’s duration is 36 months, 2021-2023)

  Project title: IRN AP09259168 «Genome-wide association study of yield and grain quality traits for enhancing efficiency in winter wheat breeding in Kazakhstan».

Kazakhstan is one of the leading wheat exporting countries in the world, growing wheat on an area of 12 million hectares. Due to the limiting environmental factors, the average productivity of spring wheat rarely exceeds 1.3 t/ha, while the average yield of winter wheat cultivated annually on the territory of 500 thousand hectares is 1.8-2.0 t/ha. In this regard, it is necessary to pay special attention to enhancing breeding and genetic research on the winter form of common wheat through 1) active use of promising genetic resources of winter wheat from other countries and regions of the world in local breeding programs, and 2) the introduction of modern methods of molecular genetics, including new genomic technologies.

The aim of this project is to search for genes of valuable traits associated with yield and quality of winter wheat based on genome-wide association study (GWAS) for the development of molecular selection of Triticum aestivum L. in Kazakhstan.

The project is a next step in the work of the Central Asian Wheat Breeding Initiative (CAWBIN), created within the framework of an international seminar in Almaty, Kazakhstan, in 2018. In this project, a homozygous CAWBIN collection was formed. It consists of 289 cultivars and lines of winter wheat (200 samples from Central and West Asia and 89 samples from Europe), created via the SSD (single seed descent) method. The collection was tested in the field at scientific research institutes in Turkestan and Almaty regions. The formed CAWBIN collection is studied using complex quantitative traits that determine the yield and quality of grain. As a result of research, the CAWBIN collection was genotyped using 35K SNP markers, the Axiom platform (Affymetrix company). The data will be used to identify genes and quantitative trait loci that determine yield and grain quality via genome-wide association study (GWAS). At the last stage of the project, new informative DNA markers will be created for the studied economically valuable traits and recommended for use in winter wheat breeding.

  The goal of the project: поиск генов ценных признаков урожайности и качества озимой пшеницы на основе полногеномного анализа ассоциаций (ПГАА) для развития молекулярной селекции Triticum aestivum L. в Казахстане.

  Expected results:

  1. The CAWBIN collection of winter wheat will be formed. It will be consisting of 289 samples from Central and Western Asia and Europe. The collection will be genotyped using 35K SNP markers based on the Affymetrix platform.
  2. Phenotypic assessment of the yield traits in CAWBIN winter wheat collection will be carried out under conditions of South and South-East Kazakhstan.
  3. The variability of the collection will be studied in terms of grain quality traits of winter bread wheat samples grown under conditions of South (Krasnovodopad agricultural experimental station) and South-East Kazakhstan.
  4. Clustering of winter wheat samples from Central and West Asia will be carried out based on the use of 35K SNP markers genotyping and comparison with samples from the world wheat collection. The level of diversity of the known key wheat genes in the CAWBIN collection will be determined.
  5. Genes that determine grain yield and quality will be identified based on the GWAS methodology and various statistical methods to search for associations between SNP markers and quantitative traits.
  6. The significance of the identified SNP markers will be confirmed based on the study of a variety of genetic material and PCR with reverse transcription for wheat samples at various stages of plant development.

  Scientific Supervisor of the project:

  Yerlan Turuspekov Head of the Laboratory, candidate of biological sciences (PhD), professor. He has co-authored over 100 publications, including 50 in peer-reviewed international journals indexed in Web of Science databases (H-index 12, Researcher ID: C-3458-2011) and/or having a CiteScore percentile in the Scopus database (H-index 14, Scopus Author ID: 57197860996), including 29 articles for the period of 2016-2021. ORCID https://orcid.org/0000-0001-8590-1745

  Research group:

  Saule Abugaieva, leading research scientist, doctor of biological sciences, professor. She is a co-author of more than 100 publications (37 articles in peer-reviewed international journals indexed in Web of Science databases (ResearcherID: M-6690-2015) and/or Scopus (H-index 8, Scopus Author ID: 6507029042); 50 articles in CCES. She is also a co-author of 6 monographs, 5 scientific and methodological recommendations, cultivars of spring bread wheat, spring and winter barley.

Shynar Anuarbek, researcher, Master of science. She has more than 20 scientific papers, including 6 articles (5 in peer-reviewed journals, WoS and Scopus (H-index 3, Scopus Author ID: 57192177334); 3 articles in CCES journals), 2 patents (utility model), 1 scientific and methodological recommendation, etc. ORCID https://orcid.org/0000-0002-8673-9820

  Akerke Amalova, researcher, Master of science, co-author of 5 articles (2 WoS, H-index 2, ResearcherID: AAO-1156-2020), Scopus Author ID: 57213623570; 3 articles in journals of CCES list). ORCID https://orcid.org/0000-0002-7903-3467

  Foreign scientist-consultant: Professor Simon Griffiths, John Innes Center, Norwich, UK. He has more than 100 publications indexed in Web of Science and Scopus (H-index 34 Scopus Author ID: 7102341547).

   List of publications of the project’s participants (2015-2020)

  1. Turuspekov Y., Plieske J., Ganal M., Akhunov E., Abugalieva S. (2017) Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90K single nucleotide polymorphism array. Plant Genetic Resources: Characterisation and Utilisation (IF=0.792, Q4, SJR=0.312, percentile: 43). 15(1):29-35. DOI: https://doi.org/10.1017/S1479262115000325 .
  2. Turuspekov Y., Baibulatova A., Yermekbayev K., TokhetovaL., Chudinov V., SeredaG., Ganal M.W, Griffiths S., Abugalieva S. (2017). GWAS for plant growth stages and yield components in spring wheat (Triticum aestivum) harvested in three regions of Kazakhstan. BMC Plant Biology (IF=4.311, Q1; SJR=1.687, percentile 92). 17(S1):51-61. DOI: https://doi.org/10.1186/s12870-017-1131-2 .
  3. Turuspekov Y., Ormanbekova D., Rsaliev A., Abugalieva S. (2016) Genome-wide association study on stem rust resistance in Kazakh spring barley lines. BMC Plant Biology (IF=4.311, Q1, SJR=1.687, percentile 92). 16(1):13-21. DOI: https://doi.org/1186/s12870-015-0686-z .
  4. Anuarbek S, Abugalieva S, Pecchioni N, Laidò G, Maccaferri M, Tuberosa R, Turuspekov Y. (2020) Quantitative trait loci for agronomic traits in tetraploid wheat for enhancing grain yield in Kazakhstan environments. PloSONE (IF=3.337, Q2; SJR=1.100, percentile 89). 15(6): e0234863. https://doi.org/10.1371/journal.pone.0234863
  5. Genievskaya Y., Fedorenko Y., Sarbayev A., Amalova А., Abugalieva S., Griffiths S., Turuspekov Y. (2019). QTL mapping of adult-plant resistance to leaf and stem rusts in Pamyati Azieva × Paragon mapping population of common spring wheat. Vavilovskii Zhurnal Genetiki i Selektsii (SJR=0.147, percentile 31). 23(7):887-895. DOI: https://doi.org/10.18699/VJ19.563.
  6. 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, PlosONE (IF=3.337, Q2; SJR=1.100, percentile 89). 14(8):e0221064. DOI: https://doi.org/10.1371/journal.pone.0221064
  7. Anuarbek S., Abugalieva S., Turuspekov Y.* (2019). Validation of bread wheat KASP markers in durum lines in Kazakhstan, Proceeding of the Latvian Academy of Sciences. Section B (SJR=0.137, percentile 31). 73(5):462-465. DOI: https://doi.org/10.2478/prolas-2019-0071
  8. 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, PlosONE (IF=3.337, Q2; SJR=1.100, percentile 89). 13(10):e0205421. DOI: http://doi.org/10.1371/journal.pone.0205421
  9. Farré, A., Sayers, L., Leverington-Waite, M., Goram, R., Orford, S., Wingen, L., C. Mumford & Griffiths, S*. (2016). Application of a library of near isogenic lines to understand context dependent expression of QTL for grain yield and adaptive traits in bread wheat. BMC plant biology, (IF= 3.67, Q1) 16(1):161.
  10. Griffiths, S.*, Wingen, L., Pietragalla, J., Garcia, G., Hasan, A., Miralles, D., … & Snape, J. (2015). Genetic dissection of grain size and grain number trade-offs in CIMMYT wheat germplasm. PloSONE (IF=2.776 Q2; SJR=1.100, percentile 90) 10(3).

  Results for 2021:

  1. The CAWBIN collection of winter wheat, consisting of 289 samples from Central and West Asia and Europe was formed using the SSD method.
  2. The formed collection was genotyped using 35K SNP markers of the Affymetrix platform, the data were provided by a foreign participant (consultant) of the project, P S. Griffiths (John Innes Center, UK).
  3. Phenological and phenotypic data of the winter bread wheat collection were obtained in two randomized replicates in two regions of the country — in the south (Turkestan region) and southeast (KRIAPI, Almaty region) in 2020-2021. Evaluation of grain quality traits in winter bread wheat samples grown in Krasnovopad AES and KRIAPI has been started.
  4. The phylogenetic relationships between accessions of the collection were studied. The clustering of winter wheat accessions from Central and Western Asia (200 cultivars and lines) was carried out based on the use of SNP genotyping data (35K SNP markers) and comparison with accessions of the world wheat collection (> 600).
  5. A genome-wide association study (GWAS) using 10481 polymorphic SNP markers of the winter bread wheat collection consisted from 289 accessions grown under field conditions of Almaty and Turkestan regions in 2020-2021 was carried out. 127 QTLs (47 for adaptability traits and 80 for productivity, respectively) were identified according to the experiment in the Almaty region, and 52 QTLs for the studied traits in the Turkestan region. Among them 14 of the identified QTLs showed the pleiotropic effect.

  Oral presentations in the international conferences, seminars:

  1. Turuspekov Y. Deployment of SNP genotyping in wheat genetics and breeding projects of Kazakhstan // Training Webinar on Acquisition, Conservation, Exchange and Safety Duplication of Plant Genetic Resources in OIC Member Countries – ASIA”. — 13-14 July 2021- Islamabad, Pakistan.

  Media appearances:

Prof. Turuspekov Y.K. – national TV channel Khabar 24 – #Science #Agriculture #Seeds – « How science is getting through tough times in agriculture | Science». https://youtu.be/sO8f-auMBeU

Results for 2022:

  1. Phenological and phenotypic observations of the winter bread wheat collection were carried out in two randomized replications in two regions of the country — in the south (Turkestan region) and southeast (KRIAPG, Almaty region) in 2021-2022.
  2. An assessment of the grain quality traits of winter bread wheat accessions was made under conditions of the Almaty region by the following traits: grain vitreousness, protein content in flour, ash content in flour, gluten content, gluten deformation index, sedimentation in a 2% acetic acid.
  3. A genome-wide association study in the collection of winter bread wheat, consisting of 289 accessions grown in the field of Almaty and Turkestan regions in 2021-2022, was carried out using 10481 polymorphic SNP markers. Seventy eight quantitative trait loci (QTLs, 62 for adaptability traits and 16 for productivity) were identified according to the experiment in the Almaty region, and 80 QTLs (57 for adaptability traits and 23 for productivity) for the studied traits in the Turkestan region. Nine of the identified QTLs showed a pleiotropic effect.
  4. The work on the isolation and purification of DNA and RNA for further confirmation of the significance of identified SNP markers using RT-PCR at various stages of plant development was done.