Brief description of the project
(2021-2023)
Project title: IRN AP0925899 «Mapping of genetic factors determining resistance to Septoria nodorum based on genome-wide association study in the collection of hexaploid wheat».
Relevance.
In Kazakhstan, Septoria nodorum (SNB) is a serious problem for wheat, yield losses during epiphytoties can reach 40-50%. Breeding for host plant resistance remains the most economical, efficient and environmentally friendly strategy to control the disease. Effective combinations of resistance genes are best achieved through marker selection. The development of SNB-resistance genotypes depends on understanding host resistance mechanisms and identifying disease resistance genes. Genome wide association study (GWAS) is one of the advanced molecular and genomic selection approaches providing high resolution mapping. Identification of novel QTLs and genomic regions associated with SNB resistance, this will deepen understanding of the nature of resistance to the disease. The Project will apply the GWAS approach using DArTseq™ next generation sequencing technology, which is new and modern in the field of molecular plant breeding. Compared to SSR markers, DArT markers have advantages in terms of cost and time of genotyping. However, the highly efficient DArT technology is currently not widely used in Kazakhstan. Although Septoria is a potential hazard and harmfulness, no GWA studies have been conducted to identify genomic regions associated with resistance to Septoria in Kazakh germplasm.
The goal of the project: «Mapping of genetic factors that determine resistance to Septoria nodorum based on a genome-wide association study (GWAS) in the collection of hexaploid wheat from Kazakhstan»
Expected results:
Based on the use of the modern GWAS approach, a search for new genetic factors (QTL and DNA markers) that determine resistance to Septoria will be carried out; the genetic structure of the population has been studied, carriers of valuable alleles for their marker introgression into new wheat varieties will be identified. Promising lines and varieties of wheat resistant to isolates and selective toxins of the fungus, characterized by seedling and field resistance to Septoria in 2-contrast regions of Kazakhstan will be identified.
Scientific Supervisor of the project: A.M. Kokhmetova, Doctor of Biological Sciences (Genetics), professor, corresponding member of the National Academy of Sciences RK, head of Genetics and Breeeding Laboratory, Institute of Plant Biology and Biotechnology (IPBB), National Coordinator European Biotechnology Association (EBTNA) for Kazakhstan. Work experience is related to the study of disease resistance using Marker Assisted Selection (MAS) technology and associative mapping to improve the efficiency of the breeding for disease resistance. Since 2015 she was manager of 6 projects funded by Ministry of Education and Science and Ministry of Agriculture. Under her supervision 1 PhD, 4 PhD-doctoral, 12 master’s theses defended;1 PhD-dissertation is carried out. Hirsch Index is 9 (https://apps.webofknowledge.com/CitationReport.do?product=UA&search_mode=CitationReport&SID=E4M3qrpPTX4Xbgyu2tf&page=1&cr_pqid=6&viewType=summary). She has 300 publications, including 20 works in WOS/Scopus databases. WOS-ID: M-6618-2015; ORCHID-ID:0002-0186-7832.
Research group:
Kumarbayeva M.T., MSci (6М081100 – Plant protection and quarantine), completed PhD (6D080100 -Агрономия), scientific researcher; h-index: 4; ResearcherID: AAQ-3647-2020; OrcID: 0000-0002-5588-6772 Scopus ID: 5721361957;
Keyshilov Zhenys Sovetkhanuly, MSci (6М081100 – Plant protection and quarantine); h-index: 4; ResearcherID: AAQ-3647-2020; OrcID: 0000-0002-5588-6772 Scopus; h-index: 2; ResearcherID: DWX-6746-2022; OrcID: 0000-0003-2126-6951; Scopus ID: 57221382183;
Zhanuzak Danna Komekkyzy, MSci (6М070100 – Biotechnology), ; h-index: 4; ResearcherID: AAQ-3647-2020; OrcID: 0000-0002-5588-6772 Scopus; junior scientific researcher, h-index: 1; ResearcherID: ABE-9520-2021; Scopus ID: 57226127734; OrcID: 0000-0002-2252-0870;
Bolatbekova A.A., MSci (6M060800 – Ecology); junior scientific researcher; h-index: 1; ResearcherID: CHB-6750-2022; Scopus ID: 57226105668;
Malysheva Angelina Alexandrovna, MSci (7M05109 — biotechnology); junior scientific researcher; h-index: 2; ResearcherID: ABE-9732-2021; OrcID: 0000-0002-9840-9570; Scopus ID: 57226102193;
Kokhmetova Asiya Myrzabekovna, (08.00.05 — economics of trade); assistant, OrcID: 0000-0003-0119-0849;
Bakhytuly Kanat, master (7M05109 — biotechnology); assistant, OrcID: 0000-0001-6084-0480
List
1. Kokhmetova A, Rsaliyev A, Malysheva A, Atishova M, Kumarbayeva M, Keishilov Z. 2021. Identification of Stripe Rust Resistance Genes in Common Wheat Cultivars and Breeding Lines from Kazakhstan // Plants. 10(11):2303. DOI: 10.3390/plants10112303 Scopus: percentile 56.
2. Kokhmetova A, Rsaliyev S, Atishova M, Kumarbayeva M, Malysheva A, Keishilov Z, Zhanuzak D, Bolatbekova A. 2021. Evaluation of Wheat Germplasm for Resistance to Leaf Rust (Puccinia triticina) and Identification of the Sources of Lr Resistance Genes Using Molecular Markers // Plants. 10(7):1484. DOI:10.3390/plants10071484 IF 3.935. WOS. Q1. Scopus: percentile 56.
3. Kokhmetova A., Kumarbayeva M., Atishova M. 2021. Identification of high-yielding wheat genotypes resistant to Pyrenophora tritici-repentis (tan spot) // Euphytica. 217:97. DOI:10.1007/s10681-021-02822-y IF 1.84. WOS. Q2. Scopus: percentile 71.
4.Madenova A.K., Kokhmetova A.M., Atishova M.N. et al. 2019. Identification of carriers of resistance to common bunt (Tilletia caries) of winter wheat // Research on Crops.20(4):782-790.DOI:10.31830/2348-7542.2019.115. Scopus, Q3. SJR 0.21. Scopus: percentile 18.
5.Kokhmetova A., Kremneva O.,Volkova G., Atishova M., Sapakhova Z. 2017. Evaluation of wheat cultivars growing in Kazakhstan and Russia for resistance to tan spot // Journal of Plant Pathology. 99(1):161-167. DOI:10.4454/jpp.v99i1.3812. IF 1.041. WOS. Q3. Scopus: percentile 31.
6. Galymbek K., Kokhmetova A.M., Akan K., Madenova A.K., Atishova M.N. 2017. Identification of germplasm of wheat on leaf rust (Puccinia recondita Rob. Ex Desm. F.sp. tritici)//Ecology, Environment and Conservation. 23(2):1211-1218. Scopus, Q4. SJR 0.14.
7. Кохметова А.М., Али С., Сапахова З., Атишова М.Н. 2018. Идентификация генотипов-носителей устойчивости к токсинам пиренофороза Ptr ToxA и Ptr ToxB Pyrenophora tritici-repentis в коллекции мягкой пшеницы//Вавиловский журнал генетики и селекции. 22(8):978¬-986. DOI:10.18699/VJ18.440. Scopus, Q4. SJR 0.15. 31-й процентиль.
8. A.Kokhmetova, M.Atishova, M.Kumarbayeva, Leonova I. 2019. Phytopathological screening and molecular marker analysis of wheat germplasm from Kazakhstan and CIMMYT for resistance to tan spot//Вавиловский журнал генетики и селекции. 23(7):879-886. DOI:10.18699/VJ19.562. Scopus, Q4. SJR 0.15. 31-й процентиль.
9.Kumarbayeva M., Kokhmetova A., Kovalenko N., Atishova M., Keishilov Zh., Aitymbetova K. Characterization of Pyrenophora tritici-repentis (tan spot of wheat) Races in Kazakhstan // Phytopathologia Mediterranea. – 2022(1). (Принята в печать) IF — 2.08, WOS. Q2, Scopus: процентиль 65.
10. Кеишилов Ж. С., Кохметова A.M., Кумарбаева M.T., Болатбекова A.A., Малышева A.A., Кохметова A.M. Жаздық бидайдың қоңыр тат (Puccinia recondita) ауруына солтүстік қазақстанда жүргізілген мониторингі 2019-2021 // Вестник науки Казахского агротехнического университета им. С. Сейфуллина. – 2022. – №. 1(112). – Б. 930. DOI: 10.51452/kazatu.2022.1(112).930 КОКСОН 10. Keishilov Zh.S., Kokhmetova A.M.,
11. Kumarbaeva M.T., Kokhmetova A.M., Keishilov Zh.S., Chudinov V., Zhanuzak D.K. 2022. Disease monitoring to determine the level of spread and development of the pathogen pyrenophora tritici-repentis in Kazakhstan // Herald of science of S. Seifullin KazATU. 1(112): 906. DOI:10.51452/kazatu.2022.1(112).906(КОКСОН).
12.Kumarbayeva M., Kokhmetova A., Kovalenko N., Atishova M., Keishilov Zh., Aitymbetova K. Characterization of Pyrenophora tritici-repentis (tan spot of wheat) Races in Kazakhstan // Phytopathologia Mediterranea. – 2022(1). (Принята в печать) IF — 2.08, WOS. Q2, Scopus: процентиль 65.
Results for 2022:
The response of wheat germplasm to resistance to races and host-specific toxins produced by the fungus S. nodorum was studied. Wheat germplasm resistant to S. nodorum races was identified. 107 genotypes (48.6%) resistant to the Sn2K race and 113 genotypes (51.4%) resistant to the Sn5K race were selected. A total of 154 ToxA toxin insensitive genotypes and 72 ToxB toxin resistant genotypes have been identified. A field assessment of wheat germplasm in 2 contrasting regions of Kazakhstan (Almaty and Kostanay regions) for the resistance of adult plants to S. nodorum was carried out. In the Kostanay region, 30 accessions of wheat with high field resistance to S. nodorum disease were isolated. In the Almaty region, on a natural background, 85 immune and 55 resistant genotypes were selected. Under an artificial background, the varieties Severyanka, KR12-9011, Almaly/GF92, Samgay proved to be immune, and resistant cultivars were Karaspan, Mereke 75, Saratovskaya 29, Stb-7, Yr2/Octyabrina, Bayandy, Mayra, Pamyati Azieva, Kokbiday.
Information on the achieved results of research for 2024 to fill out the Grants page of the Ministry of Education and Science of the Republic of Kazakhstan in the «Science» section for grant funding projects for 2022-2024
under the project AP14869967-OT-24 Mapping of genetic factors determining resistance to Septoria nodorum based on a genome-wide association study in a collection of hexaploid wheat (supervisor — Kokhmetova A.M.)
Purpose of the work: Mapping genetic factors determining resistance to Septoria nodorum based on a genome-wide association study in a collection of hexaploid wheat”.
Research objects: 220 Kazakh and foreign varieties and lines of hexaploid wheat.
Genotyping of a collection of wheat samples was carried out using the next-generation sequencing technology DArTseq™ with SNP markers. Data were obtained from the results of genotyping and sequencing of a collection of wheat samples. The average genetic diversity index DI for 8486 SNPs in 220 samples was 0.43. The highest DI (0.49) was on chromosomes 2B and 1B (0.47). The average PIC value was 0.35. The LD for the whole genome was 4.6 cM. The largest number of markers were mapped in subgenomes A and B (44.3 and 47.5%, respectively). The presence of three subclusters in the genetic structure of the population was established. According to the region of origin, samples with K = 3 were distributed into three subpopulations.
The level of genetic diversity of Kazakh selection samples was higher than that of samples from Russia, Brazil and Canada, but lower compared to the diversity of germplasm from CIMMYT and Mexico. To identify the genetic diversity of the studied collection based on disease resistance, a search for effective carriers of Stb genes was conducted. 70 genotypes with Stb resistance genes were identified. The greatest genetic diversity for Stb genes was found in Kazakh wheat varieties (19.5%), and in samples from CIMMYT the frequency of Stb genes was 6.8%.
A search for marker-trait associations for septoria resistance was conducted in a panel of wheat varieties and lines based on response to SNB races and toxins and field disease resistance data. Based on a comparison of the whole-genome analysis of GWAS associations obtained using the results of the analysis of seedling resistance to SNB isolates and toxins and data on age-related resistance to the disease, the most informative markers were identified, and genomic regions were determined that were highly likely to contain genetic loci of resistance to SNB (Fig. 1). 6 marker-trait associations (MTAs) were identified.
Figure 1 – Graphical representation (Manhattan and QQ diagrams) of the association of SNP markers with resistance traits to isolates Pn ToxA_Russia, Pn Tox3_Russia and Sn2K_SNB_USA in a GWAS panel phenotyped under greenhouse conditions
Intergenic interactions with several quantitative trait loci (QTL) between associated SNPs were assessed (Fig. 2). Significant epistatic interactions were found between the associated loci for resistance to septoria isolates on chromosomes 1B and 6A, as well as on chromosomes 6A and 6B. The most preferred allelic combinations and promising wheat lines characterized by resistance to septoria have been identified. In the future, the selected QTLs and their allelic combinations can be used to develop breeding indices that will assist in the selection of promising wheat lines.
Figure 2 – Epistatic interactions between the resistance loci to isolates Pn ToxA_Russia (A), Pn Tox3_Russia (B) and AUDPC (B)
Recommendations for the implementation of research results: as promising material in breeding for resistance to septoria, it is recommended to use selected wheat genotypes with the best combinations of SNP alleles associated with resistance to isolates and toxins of septoria.
The work is distinguished by a high level of scientific development: complex, comprehensive experiments were carried out, including phytopathological and selection studies on a large amount of experimental material (220 wheat samples). The research is characterized by the completeness of the results. During the reporting period on the topic for 2022-2024, 1 article was published in a foreign publication indexed in the WOS Database — «Plants» (IF 4.5, quartile Q1, CiteScore 5.4, Scopus percentile 86); 1 article in the publication of the SHEQAC of MSHE of RK; 1 article in the proceedings of an international conference; 3 abstracts in proceedings of international conferences. Within the framework of the project, 1 doctoral dissertation was defended (Kumarbaeva M.T.).
The practical significance of the results and their prospects for further commercialization are confirmed by the selection of promising wheat lines with the best combinations of SNP alleles associated with resistance to isolates and toxins of septoria, which are considered as candidates for future varieties.
Application area: molecular genetics and plant breeding, phytopathology.
Cost effectiveness or value for money: Using disease-resistant wheat varieties will yield a profit equal to 20% of the cost of production.
Predictive assumptions about the development of the research object: it is necessary to continue research to confirm the results on independent genetic backgrounds so that the identified markers can be used in selection.
Results achieved in 2022:
No publications or other achievements in 2022
Results achieved in 2023:
- Кеишилов Ж.С., Кохметова А.М., Кумарбаева М.Т., Малышева А.А., Бахытұлы. Қ. Бидайдың септориоз (Septoria tritici) ауруына Алматы облысы бойынша 2022 жылы жүргізілген мониторингі // «Ізденістер, нәтижелер-Исследования, результаты». Алматы. – 2023. – № 2 . – С. 225-235. (kaz.)
- Малышева А.А., Кохметова А.М., Кумарбаева М.Т., Кейшилов Ж.С., Жанузак Д.К., Болатбекова А.А. Изучение реакции коллекции озимой пшеницы из Казахстана к Stagonospora Nodorum // «Экологическая генетика и здоровье населения: достижения и перспективы»: материалы международной научно-практической конференции. – Алматы, 2023. – С. 106 – 110. (rus.)
Participation in international conferences and meetings:
- A.Kokhmetova, B. Aynebekova, A. Bolatbekova, A. Malysheva, M. Kumarbayeva, Zh. Keishilov, K. Mukhametzhanov, As. Kokhmetova, K. Bakhytuly. Molecular identification of genes resistant to Septoria nodorum in wheat cultivars and breeding lines /36th International Conference on Ecological Agriculture, Biodiversity and Waste Management (EABWM-23)”, Bangkok, Thailand, 18-22.12.2023 g – UH1223304. (eng.)
Defense of dissertations, PhD/Master’s and diploma theses:
- Kumarbaeva M.T. – PhD dissertation defended. Specialty 6D080100 – “Agronomy”, Kazakh National Agrarian University.
Results achieved in 2024:
- Kokhmetova, A.; Bolatbekova, A.; Zeleneva, Y.; Malysheva, A.; Bastaubayeva, S.; Bakhytuly, K.; Dutbayev, Y.; Tsygankov, V. Identification of Wheat Septoria tritici Resistance Genes in Wheat Germplasm Using Molecular Markers. Plants 2024, 13, 1113. https://doi.org/10.3390/plants13081113. БД Web of Science, Q1, IF 4.5, CiteScore 5.4, percentile 86. (eng.)
- Kokhmetova A., Rathan N.D., Sehgal D., Kumarbayeva M., Bolatbekova A., Krishnappa G., Gultyaeva E., Kokhmetova As., Bakhytuly K. Mapping of QTL associated with resistance to leaf and yellow rust in populations of recombinant inbred wheat lines // Proc of International conference on plant biology and biotechnology (ICPBB 2024) June 3-6, 2024, Almaty, Kazakhstan. P.77. (eng.)
- Bolatbekova А., Kokhmetova A., Kumarbayeva M., Keishilov Zh., Kokhmetova As. Search for carriers of resistance to Septoria in the collection of wheat varieties and promising lines // Proc of International conference on plant biology and biotechnology (ICPBB 2024) June 3-6, 2024, Almaty, Kazakhstan. P.91. (eng.)
Participation in international conferences and meetings:
- Kokhmetova A., Rathan N.D., Sehgal D., Kumarbayeva M., Bolatbekova A., Krishnappa G., Gultyaeva E., Kokhmetova As., Bakhytuly K. Mapping of QTL associated with resistance to leaf and yellow rust in populations of recombinant inbred wheat lines // International conference on plant biology and biotechnology (ICPBB 2024) June 3-6, 2024, Almaty, Kazakhstan. Устный доклад. (eng.)
- Bolatbekova А., Kokhmetova A., Kumarbayeva M., Keishilov Zh., Kokhmetova As. Search for carriers of resistance to Septoria in the collection of wheat varieties and promising lines // International conference on plant biology and biotechnology (ICPBB 2024) June 3-6, 2024, Almaty, Kazakhstan. Постерное сообщение. (eng.)
- Kokhmetova A., Bolatbekova A., Kumarbayeva M., Keishilov Zh., Mukhametzhanov K., Kokhmetova As., Bakhytuly K. Study of Genetic Diversity of Wheat Collection Samples for Resistance to Septoria // European Biotechnology Congress, October 3rd – 5th 2024, Harbiye Military Museum, Istanbul, Türkiye. – P 197. (eng.)