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HomeAP 08052804 (superviser Almerekova Sh.)

AP 08052804 (superviser Almerekova Sh.)

Brief description of the project

(Project’s duration – 2020-2022)

 

  Project title: IRN AP08052804 «Development and validation of KASP arrays efficiency for key productivity and grain quality traits in two-rowed spring barley».

Two-row barley is the main raw material for the world’s brewing industry. In Kazakhstan, there is a high commercial demand for foreign barley cultivars of the brewing direction, due to the low competitiveness of local cultivars. To turn the situation around and create new competitive, highly productive brewing cultivars, it is necessary to develop new breeding and genetic tools. The project is aimed at the development of highly informative DNA markers set using the KASP (Kompetetive allele-specific polymorphism) technology associated with the productivity and grain quality of two-row barley. As a result of the project, a genetic base for the development of new competitive brewing barley cultivars in Kazakhstan will be created.

  The goal of the project: Develop a set of DNA markers using the KASP technology to increase the efficiency of breeding programs aimed at improving the productivity and quality of two-row spring barley grain for the brewing industry in Kazakhstan.

  Expected results:

  1. Characteristics of the collection of two-row spring barley in the north and southeast of Kazakhstan in terms of productivity traits (at least 10) and grain quality traits (at least 5). Sowing, phenological assessment, analysis of the yield and grain quality of the barley collection in two regions of Kazakhstan will be carried out. Promising samples of spring barley will be selected for brewing industry.
  2. Quantitative trait loci (QTL) and SNP markers that are associated with the quality traits of barley grain will be identified.
  3. The design of KASP markers will be carried out in order to identify genotypes of barley with high potential for productivity and grain quality. PCR conditions will be optimized using standard cultivars for northern and southeastern Kazakhstan. KASP markers will be designed for the traits of productivity and grain quality.
  4. The effectiveness of KASP markers set will be confirmed based on the screening of two-row spring barley collection using statistical methods. A set of KASP markers will be developed to identify genotypes of spring barley with high potential for productivity and grain quality in two regions of the country.
  5. Scientific and methodological recommendations for the use of KASP-markers set in marker-assisted selection of brewing spring barley will be prepared for North and South-East Kazakhstan.

 

  Scientific Supervisor of the project:

  Shyryn Almerekova, senior researcher, PhD. She has experience in the relevant field of research. Co-author of over 30 scientific papers, including 10 articles in peer-reviewed journals indexed in the Web of Science (H-index 3, Rsearcher ID AAO-1157-2020) and/or having a CiteScore percentile in the Scopus database (H-index 3, Scopus Author ID: 57196952712). ORCID https://orcid.org/0000-0002-6079-264X

  Research group:

Alibek Zatybekov, senior researcher, PhD, trained in Germany and China. He has 32 scientific articles in the field of biotechnology, plant protection, and molecular genetics, including 3 articles in foreign peer-reviewed journals indexed in Web of Science (H-index 2, ResearcherID: AAC-2978-2019) and Scopus (H-index–3, Scopus Author ID: 57196942983), 16  articles in journals of CCES list. He is a co-author of scientific and methodological recommendation and 2 utility model patents. ORCID https://orcid.org/0000-0003-4310-5753

  Shynar Anuarbek, researcher, Master of science, was trained in scientific centers in Italy; she has more than 20 scientific papers, including 6 articles (5 in peer-reviewed journals, WoS (H-index 3, ResearcherID: AAO-1161-2020) and Scopus (H-index 3, Scopus Author ID: 57192177334); 3 articles in journals of CCES list), 1 scientific and methodological recommendation. ORCID https://orcid.org/0000-0002-8673-9820

  Yuliya Genievskaya, 2nd year PhD-student on the topic of the project, junior researcher; co-author of 10 articles peer-reviewed in Web of Science (H-index 4, Researcher ID: AAF-2410-2019) and/or Scopus (H-index 5, Scopus Author ID: 57196939730); she had an internship at the University of Oxford. ORCID https://orcid.org/0000-0001-5987-2952

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

 

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

  1. 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. Association mapping for agronomic traits in six-rowed spring barley from the USA harvested in Kazakhstan // PLOS ONE. – 2019: 14(8). P.e0221064. https://doi.org/10.1371/journal.pone.0221064
  2. 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. Marker-trait associations in two-rowed spring barley accessions from Kazakhstan and the USA // PLOS ONE. 2018: 13(10). P. e0205421 https://doi.org/10.1371/journal.pone.0205421
  3. Almerekova S., Mukhitdinov N., Abugalieva S. Phylogenetic study of the endemic species Oxytropis almaatensis (Fabaceae) based on nuclear ribosomal DNA ITS sequences // BMC Plant Biology. 2017.  17(S1):19-27. https://doi.org/10.1186/s12870-017-1128-x
  4. Almerekova Sh., Lisztes-Szabo Z., Mukhitdinov N., Kurmanbayeva M., Abidkulova K., Sramko G. Genetic diversity and population genetic structure of the endangered Kazakh endemic Oxytropis almaatensis (Fabaceae) // Acta Botanica Hungarica. 2018. 60(3-4): 263-278. https://doi.org/10.1556/034.2018.1
  5. Almerekova S., Abugalieva S., Mukhitdinov N. Taxonomic assessment of the Oxytropis species from South-East of Kazakhstan // Vavilov Journal of Genetics and Breeding. 22(2):285-290. DOI: http://dx.doi.org/10.18699/VJ18.362
  6. Zatybekov A., Abugalieva S., Didorenko S., Gerasimova Y., Sidorik I., Anuarbek Sh., Turuspekov Y. GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan // BMC Plant Biology. 2017. Vol.17 (Sl.1). Р. 64-70. https://doi.org/10.1186/s12870-017-1125-0
  7. Abugalieva S, Didorenko S, Anuarbek S, Volkova L, Gerasimova Y, Sidorik I, Turuspekov Y (2016) Assessment of Soybean Flowering and Seed Maturation Time in Different Latitude Regions of Kazakhstan. PLoS ONE 11(12): e0166894. https://doi.org/10.1371/journal.pone.0166894
  8. , 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. 2018. Vol.22(5):536-543. https://doi.org/10.18699/VJ18.392
  9. Anuarbek Sh.N., Abugalieva S.I., Chudinov V.A., Tuberosa R., Pecchioni N., Turuspekov Ye.K. Comparative assessment of the yield components of the tetraploid wheat world collection // Вестник КазНУ. Серия экологическая (Eurasian Journal of Ecology). 2:39-49.

 

  Results for 2020-2021: 

  1. A collection of barley, consisting of 532 samples (357 cultivars and lines of Kazakh and American breeding and 175 lines of “2775 x M176” mapping population) was studied under the field conditions of southeastern (KRIAPI, Almaty region) and northern Kazakhstan (KAES, Kostanay region). The following 10 traits associated with the productivity of barley were analyzed — phenological traits: heading time and time from heading to maturity; morphological traits: plant height and peduncle length; yield components: spike length, 1000 kernel weight, yield per m2, grain weight per plant, number of grains per plant, grain weight per spike. Biochemical analysis of grain quality was carried out for 7 traits: grain plumpness, grain moisture, protein, starch, lipids, ash and cellulose content.
  2. A genome-wide association study (GWAS) for the grain quality traits of two-row spring barley, and identification of quantitative traits loci, as well as SNP-markers, statistically associated with the traits of barley grain quality. Samples of spring barley with optimal performance for both the brewing industry and fodder crop production have been identified. Based on the data obtained, a genome-wide association study was carried out, as a result of which 20 marker-trait associations were identified and grouped into 7 quantitative trait loci (QTL). The pleiotropic QTLs were in close proximity to the known barley flowering genes. All QTLs found in the course of this work, as well as selected promising barley samples, can be integrated into the process of barley breeding.
  3. The development of KASP markers set for the traits of productivity and grain quality has been continued. During the implementation of the project in 2020 and 2021, the set included 30 KASP markers associated with the traits of productivity and grain quality (1000 grain weight, yield per 1 m2, spike length, peduncle length, heading time and time from heading to maturity, productive tillering, content of protein and starch in the grain, extractivity and grain plumpness).
  4. Confirmation (validation) of the effectiveness of KASP markers set has begun on the basis of screening a collection of two-row spring barley using statistical methods and modern applied programs. To validate the reliability of the association between markers and quality and productivity traits of spring barley, a collection of 34 promising lines grown in 2020 in the fields of the Karabalyk agricultural experimental station was used. Traits selected for the validation are important indicators of barley grain quality.

 

  Publications (2020-2021):

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

  1. 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 (Q1 – Plant Sciences, IF=3.935, Процентиль 56 – Plant Science). – 2021. – V. 10. – № 10. – P. 2025. https://www.mdpi.com/2223-7747/10/10/2025

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

  1. Genievskaya Y., Almerekova S., Abugalieva A., Abugalieva S. Genome-wide association study of grain quality traits in spring barley collection grown in Kyzylorda region // KazNU bulletin. Experimental Biology. – 2021. – V. 87. – №2. – P. 36-47. https://bb.kaznu.kz/index.php/biology/article/view/1606/1472
  2. Genievskaya Y., Almerekova S., Abugalieva A., Chudinov V., Abugalieva S. Genotype × environment interactions in grain quality traits and yield of barley grown in Kostanay and Almaty regions // KazNU bulletin. Eurasian Journal of Ecology. – 2021. – V. 68. – № 3. – P. 44-54. https://bulletin-ecology.kaznu.kz/index.php/1-eco/article/view/1185/933

 

  International conference abstracts:

  1. Genievskaya Y., Almerekova S., Abugalieva A., Abugalieva S., Turuspekov Y. Marker-trait associations for barley grain quality traits identified in Karaganda and Kostanay regions using GWAS. The 6th international scientific conference Plant Genetics, Genomics, Bioinformatics, and Biotechnology (PlantGen2021). June 14–18, 2021, Novosibirsk, Russia. https://conf.icgbio.ru/plantgen2021/wp-content/uploads/sites/4/2021/06/PlantGene2021_v19.06.pdf

 

  Patent of the Republic of Kazakhstan on the utility model:

  1. Genievskaya Y., Almerekova S., Abugalieva S., Turuspekov Y. Identification method of high quality barley lines (Hordeum vulgare) using molecular markers via KASP technology. Utility model patent of the Republic of Kazakhstan №6643, 05.11.2021.

 

  Reports at conferences, seminars (form of presentation):

  1. Genievskaya Y. – poster presentation at an international conference PlantGen2021. https://conf.icgbio.ru/plantgen2021/2021/06/11/rumarker-trait-associations-for-barley-grain-quality-traits-identified-in-karaganda-and-kostanay-regions-kazakhstan-using-gwasenmarker-trait-associations-for-barley-grain-quality-traits-identi/