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HomeАР 08855387 (superviser Turuspekov Y.)

АР 08855387 (superviser Turuspekov Y.)

Brief description of the project

(Project’s duration is 27 months, 2020-2022)

 

  Project title: ИРН АР08855387 «Nested association mapping for gene discovery and deployment for improvement of yield, quality, and disease resistance in bread wheat».

Wheat breeding projects in Kazakhstan, which is one of the top wheat exporters in the World, is relying on classical breeding methods. However, recent advances in the development of genetic resources and SNP (single nucleotide polymorphism) genotyping arrays have provided molecular toolkits for the enhancement of wheat breeding studies. These technologies may lead to the development of informative DNA markers for complex quantitative traits, and promote breeding projects based on marker-assistant breeding.

Despite an average annual cultivating area of 12 million hectares, Kazakhstan still has rarely overpassed 1.3 t/ha of yield. This fact is associated with abiotic stresses and biotic stresses influenced by leaf, stem, and yellow rust diseases. On the other hand, according to available reports (FAO), the average wheat yield in Kazakhstan may potentially increase to 3.0 t/ha. To achieve this goal, breeding organizations in the country should take into account new advances in agricultural sciences, including development of diverse genetic resources of wheat and modern molecular toolkits.

Here, NAM population (300 recombinant inbred lines) and 180 local accessions will be tested in Northern and South-eastern Kazakhstan to identify genes for agronomic traits related to improvement of productivity, grain quality, and rust diseases resistance. NAM panel was already genotyped using 30,800 SNPs (Affymetrix platform). Phenotypic results will be processed for revealing QTL using TASSEL and GAPIT packages. SNP validation will be performed using genes expression via RT-PCR. Next, sets of informative DNA markers will be developed for the enhancement of yield, improving grain quality, and rust diseases resistance in spring common wheat.

  The goal of the project: Identification of DNA markers of quantitative trait loci (QTL) and specific genes associated with complex the agronomic traits, including yield components, grain quality, and rust disease resistance by using nested association mapping (NAM) methodology in spring bread wheat T. aestivum L.

  Expected results:

  1. Phenological and phenotypic characterization 300 RILs of NAM-population and 180 local accessions of spring bread wheat in conditions of North and South-east Kazakhstan
  2. Characterization of NAM population and local samples of bread wheat harvested in North and South-east Kazakhstan by grain quality and genetic variation using specific genes of grain quality.
  3. The NAM population and local collection of bread wheat will be evaluated for resistance to leaf, stem, and yellow rust diseases.
  4. The NAM and genomic prediction of identified QTN will be accomplished for QTL associated with yield components, grain quality, and rust disease resistances based on using phenotypic and genotypic data of the NAM population.
  5. The set of PCR-based DNA markers for identified QTL associated with yield components, grain quality, and resistance to rust diseases will be developed.

  Scientific Supervisor of the project:

Yerlan Turuspekov, Head of the Laboratory, candidate of science (PhD) in fields of genetics, breeding and seed production; professor. Dr. Y.Turuspekov has many-years experience in molecular genetics of cereal crops, including studies in the USA, UK, and Japan. In 2015-2017 – PI of scientific and technical Program (2015-2017), and three projects (2015-2017; 2018-2020). He has more than 100 publication, including 50 in refereed international journals listed in Web of Science (H-index 12, Researcher ID: C-3458-2011) and Scopus (H-index 14, Scopus Author ID: 57197860996), including 29 articles in 2016-2021. ORCID https://orcid.org/0000-0001-8590-1745

  Research group:

  Dr. Saule Abugaieva, leading research scientist, doctor of biological sciences, professor. She has 34 years of research experience, co-author of more than 100 publications, including 37 articles in Web of Science (ResearcherID: M-6690-2015) and/or Scopus (H-index 8, Scopus Author ID: 6507029042); 50 papers in journals of CCES list, co-author of 6 books,  5 scientific-methodological recommendations, two patents, three cultivars of bread wheat, 6 of barley.  ORCID https://orcid.org/0000-0002-9748-507X 

  Dr. Shyryn Almerekova, PhD, senior researcher, 5-years of research experience, co-authored more than 20 publications, including 11 indexed in Web of Science (ResearcherID: AAO-1157-2020) and Scopus (H-index – 3, Scopus Author ID: 57196952712), and two of them related to this proposal (Plos ONE 2018, 2019); 7 articles in CCES. ORCID https://orcid.org/0000-0002-6079-264X

Ms. Shynar Anuarbek, researcher, MSci, with 7-years experience, co-author of more than 20 publications, including 6 papers (5 indexed in WoS и Scopus (H-index 3, Scopus Author ID: 57192177334); 3 in CCES), 2 patents (utility models), 1 scientific-methodological recommendations. ORCID https://orcid.org/0000-0002-8673-9820

  Ms. Akerke Amalova, junior researcher, PhD student, co-author of 5 papers (2 WoS, H-index 2, ResearcherID: AAO-1156-2020; Scopus Author ID: 57213623570), 3 CCES). ORCID https://orcid.org/0000-0002-7903-3467

Ms. Yulia Genievskaya, junior researcher, MSci, with 5-years of research experience, she is co-author of 10 papers indexed in Web of Science (Researcher ID: AAF-2410-2019) and Scopus (H-index 5, Scopus Author ID: 57196939730). ORCID https://orcid.org/0000-0001-5987-2952

  Foreign scientist–consultant: Dr. Simon Griffiths, John Innes Centre, Norwich, UK. Dr.Griffiths has more than 100 papers indexed in Web of Science https://app.webofknowledge.com/author/record/338665?lang=ru_RU&SID=F1OJWUnogUoVu1f8PYM and Scopus (H-index 34 Scopus Author ID: 7102341547).

 

  List of publications of the project’s participants (2016-2020)

  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-Plant sciences, 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. 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 .
  6. 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.
  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, 89–General Agricultural & Biological Sciences) 10(3).

 

  Results for 2020-2021:

  1. Phenological and phenotypic assessment and characterization of the NAM-population (300 RILs) and 180 local samples of spring bread wheat, were performed under conditions of Northern and Southeastern Kazakhstan.
  2. Grain quality of bread wheat from NAM-population and local samples was assessed under conditions of North and South-East Kazakhstan.
  3. An assessment of resistance to leaf, stem and yellow rusts in the NAM-population and in the local collection of spring wheat under field conditions was carried out.
  4. Genotyping and phenotyping data of NAM and local populations were used for the nested association mapping (NAM) of quantitative trait loci (QTL) for yield components, grain quality, and resistance to rust diseases. As a result of a genome-wide association study (GWAS) of bread wheat yield components and adaptability, 143 QTLs were identified for Almaty region and 289 QTLs for Akmola region; 92 QTLs for grain quality traits, 89 QTLs for resistance to rust diseases. Among the detected QTLs associated with yield components and adaptability of bread wheat, 13 QTLs were observed under conditions of Almaty region and 37 QTLs were in Akmola region showing a pleiotropic effect. Also, 17 QTLs with pleiotropic effect were found on chromosomes 1A, 4A, 5A, associated with yield components and adaptability, grain quality traits and resistance to rust diseases.
  5. A set of DNA markers is being developed for the identified QTLs for yield components, grain quality traits, as well as resistance to rust diseases.

 

  Publications (2020-2021):

  List of publications in peer-reviewed scientific journals indexed in the Web of Science and (or) Scopus databases:

  1. Amalova A., Abugalieva S., Babkenov A., Babkenova S., & Turuspekov Y. Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan // PeerJ. – 2021. – Vol. 9. – P. e11857. https://doi.org/10.7717/peerj.11857 (IF= 2.984, Q2; SJR= 0.927, percentile: 83).

  Articles in a peer-reviewed foreign and (or) domestic edition with a non-zero impact factor (recommended by CCES):

  1. Amalova A.Y., Turuspekov Y.K.  Agronomic performance of common wheat nested association mapping (NAM) population in Kazakhstan / / Eurasian Journal of Ecology. – 2021. – Vol. 67 (2).  – P. 58-67. https://doi.org/10.26577/EJE.2021.v67.i2.06

  International conference abstracts:

  1. Amalova A., Abugalieva S., Babkenov A., Babkenova S., Turuspekov Y. Association mapping of quantitative trait loci for agronomic traits in spring wheat collection tested under two water regimes in Northern Kazakhstan // The 6th international conference PlantGen2021, Novosibirsk, June 14-18, 2021. – P. 23. https://www.elibrary.ru/item.asp?id=46169804

  Oral presentations on 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. (oral presentation)
  2. Turuspekov Y. Application of SNP genotyping Illumina arrays in spring wheat projects for stress resistance in conditions of Kazakhstan // The 6th international conference PlantGen2021, Novosibirsk, June 14-18, 2021. https://conf.icgbio.ru/plantgen2021/program/ (oral presentation)

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  (in Russian).