Brief description of the project
(2023-2025)
Project title: AP19678215 «Metagenomic and population analysis of potato viruses and viroids and study of the mechanisms of their interaction with resistant potato varieties and hybrids».
Relevance.
This project is aimed at solving problems related to controlling the spread of potato viral infections, preventing the importation of dangerous strains and isolates of economically important viruses and viroids from other countries, and qualitatively increasing the breeding potential of varieties resistant to virus infection. Intensification of potato breeding in the country through cultivation of resistant local potato varieties and control over the spread of viruses and their vectors will make it possible to come to import substitution and dependence on foreign seed material. Molecular and genetic study of potato viruses and their interaction with potato varieties of local selection will prevent the spread of viruses in potato fields, especially seed farms.
The goal of the project:
The goal of the project is to investigate potato virome, study the genetic diversity of potato viruses and viroids distributed in Kazakhstan, as well as the mechanisms of interaction between natural isolates of viruses and viroids and resistant potato varieties, and identify new genes associated with the immune response to viral infection.
Expected results:
1) At least 500 potato samples will be collected from potato growing regions of the country (Northern and Almaty regions). Metagenomic analysis of potato virome, species identification of viruses and viroids common in potato growing fields of the country. Detection of new, quarantine and particularly dangerous viruses and viroids. Tubers and above-ground parts will be collected from plants showing signs of infestation as well as from asymptomatic plants. Tubers will be used as a source of virions for inoculation of resistant plants.
2) Full genome sequencing of detected PLRV, X, Y, S and M viruses and PSTVd potato viroid causing the greatest economic damage, detection of isolates and strains circulating in the country will be conducted. Development of a new vir-typing method for viruses to determine the genetic diversity of isolates in geographically distant populations. Comparison of the results of population analysis by vir-typing and full-genome sequencing. The new typing method will manifold reduce the cost of studying the population genetics of viruses. Identification of natural strains/isolates with significant mutations in the proteins responsible for amplification, movement and suppression of RNA interference, revealing the impact of mutations on virus biology by inoculation. Identification of the level of intraspecific and interspecific recombination. Identification of new recombinant forms. Whole-genome sequencing will identify conserved and variable patterns affecting the infectivity of the virus.
3) Identification of introgressed resistance genes to economically important potato viruses and viroids in 250 potato varieties and hybrids of Solanum tuberosum of local and foreign selection will be conducted. The selection of local potato varieties and hybrids involves a variety of source lines, which leads to a positive probability of identifying resistant alleles, as we have shown in the study of these varieties for the presence of resistance alleles to X and A potato viruses.
4) Selected potato varieties will be inoculated with different combinations of mutants in genes encoding proteins responsible for amplification, movement and suppression of RNA interference. Determination of the level of amplification and systemic movement of different virus isolates in plants carrying resistance genes. Determination of the relationship of activity of resistance genes in a specific genetic environment (different cultivars) to selected virus isolates. Detection of the influence of genetic environment on the activity of resistance genes. Identification of pathogenicity of selected isolates/ strains.
5) Transcriptomic analysis of potato varieties inoculated with virus isolates carrying significant mutations in target genes, identification of new genes involved in potato resistance to viral pathogens, including when inoculated with several viruses, will be conducted.
6) A bank of samples of new viral pathogens, strains and isolates will be created. Development of methods for breeders with description of genetic passports for resistance genes to economically important viruses and degree of resistance for each variety.
Scientific Supervisor of the project:
Dilyara Gritsenko
Research group:
Gritsenko D.A. — Head of Laboratory
Nizamdinova G.K. — senior researcher
Pozharsky A.S. — researcher
Taskuzhina A.K. — junior researcher
Kapytina A.I. — junior researcher
Kerimbek N.M- junior researcher
Kostyukova V.S.- junior researcher
Kolchenko M.V. — laboratory assistant
Abdrakhmanova A.B. — laboratory assistant
Adilbaeva K. — laboratory assistant
A.N.Makhambetov — laboratory assistant
List of publications of the project’s participants (2018-2022)
- Gritsenko, D., et al. Development of a “deconstructed” vector based on the genome of grapevine virus A // Plant Biotechnol Rep. -2019. Индекс цитирования – 2, Процентиль – 64, Квартиль- Q2, DOI: 10.1007/s11816-019-00528-1.
- Pozharskiy, A., Kostyukova, V., Nizamdinova, G., Kalendar, R., & Gritsenko, D. (2022). MLO proteins from tomato (Solanum lycopersicum L.) and related species in the broad phylogenetic context. Plants, 11(12), 1588.. DOI: 10.3390/plants11121588; WOS. Q1 (IF 4,827), Scopus: процентиль 71.
- Gritsenko, D., Pozharskiy, A., Dolgikh, S., Aubakirova, K., Kenzhebekova, R., Galiakparov, N., Sadykov, S. Apple varieties from Kazakhstan and their relation to foreign cultivars assessed with RosBREED 10K SNP array. 2022. Eur.J.Hortic.Sci. 87 (1) 1-8, DOI: 10.17660/eJHS.2022/006. Индекс цитирования – 0, Процентиль – 62, Квартиль- Q2.
- Pozharskiy, A., Kostyukova, V., Taskuzhina, A., Nizamdinova, G., Kisselyova, N., Kalendar, R., Gritsenko, D. (2022). Screening a collection of local and foreign varieties of Solanum lycopersicum L. in Kazakhstan for genetic markers of resistance against three tomato viruses. Heliyon. DOI: 10.1016/j.heliyon.2022.e10095; WOS. Q2 (IF-3.7), Scopus: процентиль 82.
- Gritsenko, D., Zulfiya Kachiyeva, Gulzhan Zhamanbayev, Bakhytzhan DuisembekoV, Abai Sagitov. Detection of five potato viruses in Kazakhstan // IX International scientific agriculture symposium “AGROSYM 2018”., p. 611. 2018.
- Gritsenko D., Aubakirova K., Galiakrapov N. Simultaneous detection of five apple viruses by RT-PCR. International Journal of Biology and Chemistry (2020) v. 13, n. 1, p. 129-134. 2020. Индекс цитирования –0, doi: 10.26577/ijbch.2020.v13.i1.13.
- Gritsenko, D., et al. «Detection of Grapevine virus A in wild grape in Kazakhstan.» Phytopathology. Vol. 109. No. 11. 3340 Pilot Knob Road, St Paul, Mn 55121 Usa: Amer Phytopathological Soc, 2019.
- Gritsenko, D. A., K. P. Aubakirova, and A. S. Pozharskiy. «SSR profiling of potato cultivars resistant to pathogens.» Plant Genetics, Genomics, Bioinformatics, and Biotechnology. 2021.
- A.S. Pozharskiy, K. Aubakirova, D. Gritsenko, N. Galiakparov. Genotyping and morphometric analysis of Kazakhstani grapevine cultivars versus Asian and European cultivars // Genet. Mol. Res., 2020. Индекс цитирования – 0, DOI: 10.4238/gmr18482.
- A. Pozharskiy, D. Gritsenko // Prediction of Slmlo1 protein paralogs in Solanum l. Spp. using partially assembled genomic dat // IV. International Agricultural, Biological & Life Science Conference – 2022 – P.162.
- A. Kapytina, N. Kerimbek, A. Taskuzhina, G. Nizamdinova, K. Adilbayeva, S. Murzatayeva, Z. Kachiyeva // Detection and genetic investigation of potato leafroll virus in Kazakhstan // IV. International Agricultural, Biological & Life Science Conference – 2022 – P.165.
- Kerimbek N., Kapytina A., Pozharsky A., Khusnitdinova M., Gritsenko D. // Phylogenetic analysis of raspberry bush dwarf virus // Proceedings of the International Scientific and Practical Conference «Actual problems and prospects of science development in the field of fruit and vegetable growing» -2022 — P.139
Results for 2023:
Nucleotide sequences of the complete genome or individual regions were analyzed for PLRV in the amount of 296, PVX- 720, PVY- 632, PVS- 439, PVM- 276, PSTVd- 2864. The analysis identified at least 5 promising regions for primer design for each target pathogen. The variability within genomes ranged from 3.4 to 15.3%; within individual genes, the average variability did not exceed 4.7%. For primer design, a region was used whose conservation within species was at least 99.5% when analysing different strains and isolates; variability outside the species was at least 60%.
PLRV (11%), PVX (37%), PVY (29%) and Alfalfa mosaic virus (4%) were analyzed for the laboratory potato collection. Homology among isolates of each PLRV, PVX and PVY virus was 87 — 95% by full genomic analysis. Among PLRV isolates, the mutation frequency did not exceed 1.3 × 10-3 , for PVX 1.01 × 10-3 , for PVY virus 1.15 × 10-3 . The highest mutation frequency was observed in PLRV virus.
Metagenomic analysis of aboveground plant parts as well as potato tubers collected from the fields was performed. The analysis identified PLRV, X, Y, S viruses and viroid PSTVd. The northern region of the country is dominated by X and Y viruses, while the southern region (Narynkol) is dominated by X virus. In addition to the above viruses, Alfalfa mosaic virus was also detected.
Whole-genome analysis of PLRV, PVX and PVY viruses showed a high homology within each isolate population studied, which was 97 — 100%. Among PLRV isolates, the mutation frequency ranged from 0.95 × 10-3 to 1.19 × 10-3 , for PVX from 0.82 × 10-3 to 0.98 × 10-3 , and for PVY virus did not exceed 0.92 × 10-3.
Publications (2023):
