Identification of effector genes of Parastagonospora nodorum, P. pseudonodorum in Tambov populations and sensitivity genes to NEs in varieties and hybrid lines of spring soft wheat

Abstract

BACKGROUND: Parastagonospora nodorum and P. pseudonodorum are known for their ability to produce necrotrophic effectors that play an important role in micromycete pathogenicity. Fungal strains characterized by the presence of effector genes will be used to create artificial infectious backgrounds to identify sources and donors of resistance to fungal diseases. Selected varieties and lines that are donors of recessive alleles snn1 and snn3, which control plant resistance to fungal toxins PtrTox1 and PtrTox3, are recommended for inclusion in programs for breeding wheat for resistance to septoriosis pathogens.

AIM: The aim of the work is to assess the populations of the fungi Parastagonospora nodorum and P. pseudonodorum in 2023 based on the presence of effector genes, as well as to identify alleles of Snn1/snn1, Snn3/snn3 genes that control the sensitivity or resistance of wheat to PtrTox1 and PtrTox3 toxins.

MATERIALS AND METHODS: Infectious samples were collected in 2023 from spring wheat leaves. In addition, the material for the study was 2 varieties and 23 lines of spring soft wheat of local selection. Using the molecular markers Xfcp624 and Xcfd20, the presence of the Snn1 and Snn3-B1 alleles, which control sensitivity to the fungal toxins PtrTox1 and PtrTox3, was detected.

RESULTS: Using molecular screening, ToxA and Tox1 genes were identified in genotypes of P. pseudonodorum isolates; Tox3 and Tox267 in P. nodorum isolates. 2 varieties of spring soft wheat and 11 hybrid lines carry a recessive allele snn1, which protects against the phytopathogen toxin PtrTox1; wheat variety Tambovchanka and 2 hybrid lines carry the recessive allele snn3 on chromosome B1, which confers resistance to the fungal toxin PtrTox3.

CONCLUSIONS: The ToxA gene was found only among monoconidial isolates of P. pseudonodorum species obtained from leaves of spring soft wheat of Lebedushka variety. As a result of molecular screening, the Tox1 gene was identified among 70 P. pseudonodorum isolates (43,21% of those studied). The presence of the Tox3 and Tox267 genes was established in 30 isolates of P. nodorum species obtained from plant samples of spring durum wheat Donskaya Elegiya. Using the PCR method, donors of the snn1 and snn3 genes were identified.

Keywords

septoria of wheat / Tox1 / Tox267 / Tox3 / ToxA / molecular genetics testing / PCR / wheat

References

[1] Fones H, Gurr S. The impact of Septoria tritici blotch disease on wheat: An EU perspective. Fungal Genet Biol. 2015;79:3–7. doi: 10.1016/j.fgb.2015.04.004

[2] Fones H., Gurr S. The impact of Septoria tritici blotch disease on wheat: An EU perspective // Fungal Genet Biol. 2015. Vol. 79. P. 3–7. doi: 10.1016/j.fgb.2015.04.004

[3] Birr T, Hasler M, Verreet J-A, Klink H. Temporal changes in sensitivity of Zymoseptoria tritici field populations to different fungicidal modes of action. Agriculture. 2021;11(3):269. doi: 10.3390/agriculture11030269

[4] Birr T., Hasler M., Verreet J.-A., Klink H. Temporal changes in sensitivity of Zymoseptoria tritici field populations to different fungicidal modes of action // Agriculture. 2021. Vol. 11, N. 3. ID 269. doi: 10.3390/agriculture11030269

[5] Petit-Houdenot Y, Lebrun MH, Scalliet G. Understanding plant-pathogen interactions in Septoria tritici blotch infection of cereals. In: Oliver R, editor. Achieving durable disease resistance in cereals. London: Burleigh Dodds Science Publishing; 2021. P. 263–302. doi: 10.19103/AS.2021.0092.10

[6] Petit-Houdenot Y., Lebrun M.H., Scalliet G. Understanding plant-pathogen interactions in Septoria tritici blotch infection of cereals. В кн.: Oliver R., editor. Achieving durable disease resistance in cereals. London: Burleigh Dodds Science Publishing, 2021. P. 263–302. doi: 10.19103/AS.2021.0092.10

[7] Zeleneva YuV, Ablova IB, Sudnikova VP, et al. Species composition of wheat septoria pathogens in the European part of Russia and identifying SnToxA, SnTox1, and SnTox3 effector genes. Mycology and phytopathology. 2022;56(6):441–447. EDN: AEZUGR doi: 10.31857/S0026364822060113

[8] Зеленева Ю.В., Аблова И.Б., Судникова В.П., и др. Видовой состав возбудителей септориозов пшеницы в европейской части России и идентификация генов-эффекторов SnToxA, SnTox1 и SnTox3 // Микология и фитопатология. 2022. Т. 56, № 6. С. 441–447. EDN: AEZUGR doi: 10.31857/S0026364822060113

[9] Zeleneva YuV, Gannibal PhB, Kazartsev IА, Sudnikova VP. Molecular identification, effector genes and virulence of isolates of Parastagonospora nodorum from Altai Krai (Russia). Mycology and phytopathology. 2023;57(5):362–371. EDN: EYWBIS doi: 10.31857/S0026364823050124

[10] Зеленева Ю.В., Ганнибал Ф.Б., Казарцев И.А., Судникова В.П. Молекулярная идентификация, гены-эффекторы и вирулентность изолятов гриба Parastagonospora nodorum из Алтайского края (Россия) // Микология и фитопатология. 2023. Т. 57, № 5. С. 362–371. EDN: EYWBIS doi: 10.31857/S0026364823050124

[11] Zhelezova SV, Pakholkova EV, Veller VE, et al. Hyperspectral non-imaging measurements and perceptron neural network for pre-harvesting assessment of damage degree caused by Septoria/Stagonospora blotch diseases of wheat. Agronomy. 2023;13(4):1045. doi: 10.3390/agronomy13041045

[12] Zhelezova S.V., Pakholkova E.V., Veller V.E., et al. Hyperspectral non-imaging measurements and perceptron neural network for pre-harvesting assessment of damage degree caused by Septoria/Stagonospora blotch diseases of wheat // Agronomy. 2023. Vol. 13, N. 4. ID 1045. doi: 10.3390/agronomy13041045

[13] Ficke A, Cowger C, Bergstrom G, Brodal G. Understanding yield loss and pathogen biology to improve disease management: Septoria nodorum blotch — a case study in wheat. Plant Dis. 2018;102(4):696–707. doi: 10.1094/PDIS-09-17-1375-FE

[14] Ficke A., Cowger C., Bergstrom G., Brodal G. Understanding yield loss and pathogen biology to improve disease management: Septoria nodorum blotch — a case study in wheat // Plant Dis. 2018. Vol. 102, N. 4. P. 696–707. doi: 10.1094/PDIS-09-17-1375-FE

[15] Haugrud ARP, Zhang Z, Friesen TL, Faris JD. Genetics of resistance to Septoria nodorum blotch in wheat. Theor Appl Genet. 2022;135(11):3685–3707. doi: 10.1007/s00122-022-04036-9

[16] Haugrud A.R.P., Zhang Z., Friesen T.L., Faris J.D. Genetics of resistance to Septoria nodorum blotch in wheat // Theor Appl Genet. 2022. Vol. 135, N. 11. P. 3685–3707. doi: 10.1007/s00122-022-04036-9

[17] Kariyawasam GK, Nelson AC, Williams SJ, et al. The necrotrophic pathogen Parastagonospora nodorum is a master manipulator of wheat defense. Mol Plant Microbe Interact. 2023;36(12):764–773. doi: 10.1094/MPMI-05-23-0067-IRW

[18] Kariyawasam G.K., Nelson A.C., Williams S.J., et al. The necrotrophic pathogen Parastagonospora nodorum is a master manipulator of wheat defense // Mol Plant Microbe Interact. 2023. Vol. 36, N. 12. P. 764–773. doi: 10.1094/MPMI-05-23-0067-IRW

[19] McDonald MC, Ahren D, Simpfendorfer S, et al. The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana. Mol Plant Pathol. 2018;19(2):432–439. doi: 10.1111/mpp.12535

[20] McDonald M.C., Ahren D., Simpfendorfer S., et al. The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana // Mol Plant Pathol. 2018. Vol. 19, N. 2. P. 432–439. doi: 10.1111/mpp.12535

[21] Navathe S, Yadav PS, Chand R, et al. ToxA–Tsn1 interaction for spot blotch susceptibility in Indian wheat: an example of inverse genefor-gene relationship. Plant Dis. 2020;104(1):71–81. doi: 10.1094/PDIS-05-19-1066-RE

[22] Navathe S., Yadav P.S., Chand R., et al. ToxA–Tsn1 interaction for spot blotch susceptibility in Indian wheat: an example of inverse genefor-gene relationship // Plant Dis. 2020. Vol. 104, N. 1. P. 71–81. doi: 10.1094/PDIS-05-19-1066-RE

[23] Faris JD, Friesen TL. Plant genes hijacked by necrotrophic fungal pathogens. Curr Opin Plant Biol. 2020;56:74–80. doi: 10.1016/j.pbi.2020.04.003

[24] Faris J.D., Friesen T.L. Plant genes hijacked by necrotrophic fungal pathogens // Curr Opin Plant Biol. 2020. Vol. 56. P. 74–80. doi: 10.1016/j.pbi.2020.04.003

[25] Friesen TL, Faris JD. Characterization of effector-target interactions in necrotrophic pathosystems reveals trends and variation in host manipulation. Annu Rev Phytopathol. 2021;59:77–98. doi: 10.1146/annurev-phyto-120320-012807

[26] Friesen T.L., Faris J.D. Characterization of effector-target interactions in necrotrophic pathosystems reveals trends and variation in host manipulation // Annu Rev Phytopathol. 2021. Vol. 59. P. 77–98. doi: 10.1146/annurev-phyto-120320-012807

[27] Faris JD, Zhang Z, Lu H, et al. A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens. PNAS USA. 2010;107(30):13544–13549. doi: 10.1073/pnas.1004090107

[28] Faris J.D., Zhang Z., Lu H., et al. A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens // PNAS USA. 2010. Vol. 107, N. 30. P. 13544–13549. doi: 10.1073/pnas.1004090107

[29] Shi G, Zhang Z, Friesen TL, et al. The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease. Sci Adv. 2016;2(10):e1600822. doi: 10.1126/sciadv.1600822

[30] Shi G., Zhang Z., Friesen T.L., et al. The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease // Sci Adv. 2016. Vol. 2, N. 10. ID e1600822. doi: 10.1126/sciadv.1600822

[31] Richards JK, Kariyawasam GK, Seneviratne S, et al. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. New Phytol. 2022;233(1):427–442. doi: 10.1111/nph.17601

[32] Richards J.K., Kariyawasam G.K., Seneviratne S., et al. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat // New Phytol. 2022. Vol. 233, N. 1. P. 427–442. doi: 10.1111/nph.17601

[33] Friesen TL, Zhang Z, Solomon PS, et al. Characterization of the interaction of a novel Stagonospora nodorum host-selective toxin with a wheat susceptibility gene. Plant Physiol. 2008;146(2):682–693. doi: 10.1104/pp.107.108761

[34] Friesen T.L., Zhang Z., Solomon P.S., et al. Characterization of the interaction of a novel Stagonospora nodorum host-selective toxin with a wheat susceptibility gene // Plant Physiol. 2008. Vol. 146, N. 2. P. 682–693. doi: 10.1104/pp.107.108761

[35] Zhang Z, Running KLD, Seneviratne S, et al. A protein kinase-major sperm protein gene hijacked by a necrotrophic fungal pathogen triggers disease susceptibility in wheat. Plant J. 2021;106(3):720–732. doi: 10.1111/tpj.15194

[36] Zhang Z., Running K.L.D., Seneviratne S., et al. A protein kinase-major sperm protein gene hijacked by a necrotrophic fungal pathogen triggers disease susceptibility in wheat // Plant J. 2021. Vol. 106, N. 3. P. 720–732. doi: 10.1111/tpj.15194

[37] Abeysekara NS, Friesen TL, Keller B, Faris JD. Identification and characterization of a novel host-toxin interaction in the wheat–Stagonospora nodorum pathosystem. Theor Appl Genet. 2009;120(1):117–126. doi: 10.1007/s00122-009-1163-6

[38] Abeysekara N.S., Friesen T.L., Keller B., Faris J.D. Identification and characterization of a novel host-toxin interaction in the wheat–Stagonospora nodorum pathosystem // Theor Appl Genet. 2009. Vol. 120, N. 1. P. 117–126. doi: 10.1007/s00122-009-1163-6

[39] Friesen TL, Chu C, Xu SS, Faris JD. SnTox5–Snn5: a novel Stagonospora nodorum effector–wheat gene interaction and its relationship with the SnToxA–Tsn1 and SnTox3–Snn3–B1 interactions. Mol Plant Pathol. 2012;13(9):1101–1109. doi: 10.1111/j.1364-3703.2012.00819.x

[40] Friesen T.L., Chu C., Xu S.S., Faris J.D. SnTox5–Snn5: a novel Stagonospora nodorum effector–wheat gene interaction and its relationship with the SnToxA–Tsn1 and SnTox3–Snn3–B1 interactions // Mol Plant Pathol. 2012. Vol. 13, N. 9. P. 1101–1109. doi: 10.1111/j.1364-3703.2012.00819.x

[41] Pyzhikova GV, Sanina AA, Suprun LM, et al. Methods for assessing resistance of breeding material and wheat varieties to septoriosis: methodological guidelines. Moscow: All-Russian Research Institute of Phytopathology; 1989. 43 p. (In Russ.)

[42] Пыжикова Г.В., Санина А.А., Супрун Л.М., и др. Методы оценки устойчивости селекционного материала и сортов пшеницы к септориозу: методические указания. Москва: ВНИИ фитопатологии, 1989. 43 с.

[43] Kolomiets TM, Pakholkova EV, Dubovaya LP. Selection of source material for creation of wheat varieties with long-term resistance to septoriosis. Moscow: Pechatny gorod; 2017. 56 p. (In Russ.)

[44] Коломиец Т.М., Пахолкова Е.В., Дубовая Л.П. Отбор исходного материала для создания сортов пшеницы с длительной устойчивостью к септориозу. Москва: Печатный город, 2017. 56 с.

[45] White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, editor. PCR protocols: A guide to methods and applications. San Diego: Academic Press; 1990. P. 315–322. doi: 10.1016/B978-0-12-372180-8.50042-1

[46] White T.J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. В кн.: Innis M.A., editor. PCR protocols: A guide to methods and applications. San Diego: Academic Press, 1990. P. 315–322. doi: 10.1016/B978-0-12-372180-8.50042-1

[47] Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. PNAS USA. 1977;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463

[48] Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors // PNAS USA. 1977. Vol. 74, N. 12. P. 5463–5467. doi: 10.1073/pnas.74.12.5463

[49] Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus. 1990;12(1):13–15.

[50] Doyle J.J., Doyle J.L. Isolation of plant DNA from fresh tissue // Focus. 1990. Vol. 12, N. 1. P. 13–15.

[51] Bertucci M, Brown-Guedira G, Murphy JP, Cowger C. Genes conferring sensitivity to Stagonospora nodorum necrotrophic effectors in Stagonospora nodorum blotch-susceptible U.S. wheat cultivars. Plant Dis. 2014;98(6):746–753. doi: 10.1094/PDIS-08-13-0820-RE

[52] Bertucci M., Brown-Guedira G., Murphy J.P., Cowger C. Genes conferring sensitivity to Stagonospora nodorum necrotrophic effectors in Stagonospora nodorum blotch-susceptible U.S. wheat cultivars // Plant Dis. 2014. Vol. 98, N. 6. P. 746–753. doi: 10.1094/PDIS-08-13-0820-RE

[53] Gao Y, Faris JD, Liu Z, et al. Identification and characterization of the SnTox6–Snn6 interaction in the Parastagonospora nodorum–wheat pathosystem. Mol Plant Microbe Interact. 2015;28(5):615–625. doi: 10.1094/MPMI-12-14-0396-R

[54] Gao Y., Faris J.D., Liu Z., et al. Identification and characterization of the SnTox6–Snn6 interaction in the Parastagonospora nodorum — wheat pathosystem // Mol Plant Microbe Interact. 2015. Vol. 28, N. 5. P. 615–625. doi: 10.1094/MPMI-12-14-0396-R

[55] Andrie RM, Pandelova I, Ciuffetti LM. A combination of phenotypic and genotypic characterization strengthens Pyrenophora tritici-repentis race identification. Phytopathology. 2007;97(6):694–701. doi: 10.1094/PHYTO-97-6-0694

[56] Andrie R.M., Pandelova I., Ciuffetti L.M. A combination of phenotypic and genotypic characterization strengthens Pyrenophora tritici-repentis race identification // Phytopathology. 2007. Vol. 97, N. 6. P. 694–701. doi: 10.1094/PHYTO-97-6-0694

[57] Zeleneva YV, Sudnikova VP, Afanasenko OS. Influence of agroclimatic conditions, life form, and host species on the species complex of wheat Septoria pathogens. Biol Bull. 2021;48(10):1806–1812. doi: 10.1134/S1062359021100277

[58] Zeleneva Y.V., Sudnikova V.P., Afanasenko O.S. Influence of agroclimatic conditions, life form, and host species on the species complex of wheat Septoria pathogens // Biol Bull. 2021. Vol. 48, N. 10. P. 1806–1812. doi: 10.1134/S1062359021100277

[59] Zeleneva YuV, Sudnikova VP, Kovalenko NM, Gusev IV. Resistance of spring bread wheat cultivars and lines to septoria leaf blotch, tan spot, and spot blotch pathogens. Proceedings on applied botany, genetics and breeding. 2023;184(3):196–206. EDN: KZBXQQ doi: 10.30901/2227-8834-2023-3-1-11

[60] Зеленева Ю.В., Судникова В.П., Коваленко Н.М., Гусев И.В. Устойчивость сортов и линий яровой мягкой пшеницы к возбудителям септориозной, пиренофорозной и темно-бурой пятнистостей // Труды по прикладной ботанике, генетике и селекции. 2023. Т. 184, № 3. С. 196–206. EDN: KZBXQQ doi: 10.30901/2227-8834-2023-3-1-11

[61] Mironenko NV, Kovalenko NM, Baranova OA. Characteristics of the geographically distant populations of Pyrenophora tritici-repentis in terms of virulence and ToxA and ToxB toxin-forming gene. Plant protection news. 2019;(1):24–29. EDN: ZERIBN doi: 10.31993/2308-6459-2019-1(99)-24-29

[62] Мироненко Н.В., Коваленко Н.М., Баранова О.А. Характеристика географически отдаленных популяций Pyrenophora tritici-repentis по вирулентности и генам токсинообразования ToxA и ToxB // Вестник защиты растений. 2019. № 1. С. 24–29. EDN: ZERIBN doi: 10.31993/2308-6459-2019-1(99)-24-29

[63] Kokhmetova AM, Kovalenko NM, Kumarbaeva MT. Pyrenophora tritici-repentis population structure in the republic of Kazakhstan and identification of wheat germplasm resistant to tan spot. Vavilov Journal of Genetics and Breeding. 2020;24(7):722–729. EDN: ADNKBJ doi: 10.18699/VJ20.666

[64] Кохметова А.М., Коваленко Н.М., Кумарбаева М.Т. Структура популяции Pyrenophora tritici-repentis в Республике Казахстан и идентификация устойчивой к пиренофорозу гермоплазмы пшеницы // Вавиловский журнал генетики и селекции. 2020. Т. 24, № 7. С. 722–729. EDN: ADNKBJ doi: 10.18699/VJ20.666

[65] Kokhmetova A, Kumarbayeva M, Atishova M, et al. Identification of high-yielding wheat genotypes resistant to Pyrenophora tritici-repentis (tan spot). Euphytica. 2021;217:97. doi: 10.1007/s10681-021-02822-y

[66] Kokhmetova A., Kumarbayeva M., Atishova M., et al. Identification of high-yielding wheat genotypes resistant to Pyrenophora tritici-repentis (tan spot) // Euphytica. 2021. Vol. 217. ID 97. doi: 10.1007/s10681-021-02822-y

[67] Zeleneva YuV, Konkova EA. Soft wheat cultivars grown in the Saratov Region and their resistance to septoria blotch. Vavilov Journal of Genetics and Breeding. 2023;27(6):582–590. EDN: PJPYLM doi: 10.18699/VJGB-23-70

[68] Зеленева Ю.В., Конькова Э.А. Устойчивость сортов мягкой пшеницы, возделываемых на территории Саратовской области, к возбудителям септориозных пятнистостей // Вавиловский журнал генетики и селекции. 2023. Т. 27, № 6. С. 582–590. EDN: PJPYLM doi: 10.18699/VJGB-23-70

[69] Kovalenko NM, Zeleneva YuV, Sudnikova VP. Characterization of Pyrenophora tritici-repentis, Parastagonospora nodorum, and Parastagonospora pseudonodorum in the Tambov Oblast for the presence of effector genes. Russian Agricultural Sciences. 2023;49(3):285–291. doi: 10.3103/S1068367423030114

[70] Kovalenko N.M., Zeleneva Yu.V., Sudnikova V.P. Characterization of Pyrenophora tritici-repentis, Parastagonospora nodorum, and Parastagonospora pseudonodorum in the Tambov Oblast for the presence of effector genes // Russian Agricultural Sciences. 2023. Vol. 49, N. 3. P. 285–291. doi: 10.3103/S1068367423030114

[71] Nuzhnaya T, Veselova S, Burkhanova G, et al. novel sources of resistance to Stagonospora nodorum and role of effector-susceptibility gene interactions in wheat of Russian breeding. Int J Plant Biol. 2023;14(2):377–396. doi: 10.3390/ijpb14020031

[72] Nuzhnaya T., Veselova S., Burkhanova G., et al. novel sources of resistance to Stagonospora nodorum and role of effector-susceptibility gene interactions in wheat of Russian breeding // Int J Plant Biol. 2023. Vol. 14, N. 2. P. 377–396. doi: 10.3390/ijpb14020031

Funding

Российский научный фондRussian Science Foundation(19-76-30005)

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