Molecular diagnostics for Tilletia barclayana causing kernel smut of rice

ARADHIKA  TRIPATHI; JAMEEL  AKHTAR; VASIMALLA CELIA  CHALAM

doi:10.56093/ijas.v96i8.174410

Authors

ARADHIKA TRIPATHI ICAR-Indian Agricultural Research Institute, Regional Station, Katrain, Kullu Valley, Himachal Pradesh
JAMEEL AKHTAR ICAR-National Bureau of Plant Genetic Resources, New Delhi 110 012, India
VASIMALLA CELIA CHALAM ICAR-National Bureau of Plant Genetic Resources, New Delhi 110 012, India

https://doi.org/10.56093/ijas.v96i8.174410

Keywords:

Diagnostics, Paddy bunt, qPCR, Quarantine, Rice

Abstract

Kernel smut of rice, caused by fungal pathogen Tilletia barclayana has emerged as a serious challenge in rice (Oryza sativa L.) growing regions worldwide. The disease leads to considerable yield losses ranging from 5–20% during rice production and also adversely affects seed quality. In view of the importance of this pathogen of the most traded crop and the lack of a quick and reliable molecular detection protocol, the present study aimed to develop species-specific molecular markers for the direct detection and identification of T. barclayana from seeds in 2024. Two sets of specific primers, TbarF2&R2 and TbarF2&R3 were developed from partial sequences of internal transcribed spacer (ITS) DNA region. Species-specific fragments of 308 bp was produced using TbarF2&R2 and 328 bp was amplified with the primer, TbarF2&R3 in T. barclayana. No amplification was obtained from the DNA of other Tilletia spp. and several other unrelated fungal plant pathogens tested in the present work indicating the specificity of the primers for the detection of the target pathogen. The specific primers detected the presence of T. barclayana in infected rice samples received for quarantine clearance from different countries. This qPCR based diagnostic assay developed in the present study can be applied for the direct and rapid detection and identification of T. barclayana during quarantine processing and seed health testing to facilitate rice seed certification as well as quick quarantine clearance for international exchange of rice germplasm.

Downloads

Download data is not yet available.

References

Akhtar J, Kumar P, Kiran R, Meena B R and Ali A. 2022. Bio- efficacy of essential oils in eco-friendly management of Tilletia barclayana causing kernel smut in rice. Journal of Eco-friendly Agriculture 17(1): 162–65. https://doi.org/10.5958/2582-2683.2022.00034.x DOI: https://doi.org/10.5958/2582-2683.2022.00034.X

Allen T W, Growth D E, Wamishe Y A, Espino L, Jones G and Zhou X G. 2020. Disease loss estimates from the rice producing states in the United States. (In) 38th Proceedings of Rice Technical Working Group, Orange Beach, Alabama, February 24–27. 130p.

Brooks S A, Anders M M and Yeater K M. 2009. Effect of cultural management practices on the severity of false smut and kernel smut of rice. Plant Disease 93: 1202–08. https:// doi.org/10.1094/PDIS-93-11-1202 DOI: https://doi.org/10.1094/PDIS-93-11-1202

Carris L M, Castlebury L A and Goates B J. 2006. Nonsystemic bunt fungi - Tilletia indica and T. horrida: A review of history, systematics, and biology. Annual Review of Phytopathology 44: 113–33. https://doi.org/10.1146/annurev. phyto.44.070505.143402 DOI: https://doi.org/10.1146/annurev.phyto.44.070505.143402

Chahal S S. 2001. Epidemiology and management of two cereal bunts. Indian Phytopathology 54: 145–57.

Chen Y, Yang X, Yao J, Kyaw E P, Zhang A F, Li Y F, Gu C Y, Zang H Y and Gao T C. 2016. Simple and rapid detection of Tilletia horrida causing rice kernel smut in rice seeds. Scientific Reports 6: 33258. https://doi.org/10.1038/srep33258 DOI: https://doi.org/10.1038/srep33258

Cui D. 2021. Brief note on kernel smut. Journal of Rice Research 9: 251.

Dev U, Akhtar J, Chaudhury R, Kandan A, Chand D, Kumar J, Singh B and Agarwal P C. 2012. Survival of Colletotrichum capsici. Seed Research 40(1): 92–94.

Elshafey R A S. 2018. Biology of rice kernel smut disease causal organism Tilletia barclayana and its molecular identification. Journal of Phytopathology 5: 108–28.

EPPO. 2024. Tilletia barclayana (TILLBA). https://gd.eppo.int/ taxon/TILLBA

FAOSTAT 2022. World Food and Agriculture-Statistical Yearbook 2022. Food and Agriculture Organisations, Rome, Italy. 382p. https://doi.org/10.4060/cc2211en DOI: https://doi.org/10.4060/cc2211en

Khanal S, Antony-Babu S and Zhou X G. 2023a. Draft genome resources of seven strains of Tilletia horrida, causal agent of kernel smut of rice. PhytoFrontiers 3(3): 701–03 https://doi. org/10.1094/PHYTOFR-11-22-0139-A DOI: https://doi.org/10.1094/PHYTOFR-11-22-0139-A

Khanal S, Gaire S P and Zhou X G. 2023b. Kernel smut and false smut: The old-emerging diseases of rice-A review. Phytopathology 113(6): 931–44. https://doi.org/10.1094/phyto-06-22-0226-rvw DOI: https://doi.org/10.1094/PHYTO-06-22-0226-RVW

Khanal S, Antony-Babu S, Gaire S P and Zhou X G. 2022. Multilocus sequence analysis reveals diversity of the rice kernel smut populations in the United States. Frontiers Microbiology 13: 874120. https://doi.org/10.3389/fmicb.2022.874120 DOI: https://doi.org/10.3389/fmicb.2022.874120

Kumar A and Chordia N. 2015. In silico PCR primer designing and validation. (In)PCR Primer Design. Methods Molecular Biology, Vol 1275, pp. 143–51. Basu C (Ed). Humana Press, New York. https://doi.org/10.1007/978-1-4939-2365-6_10 DOI: https://doi.org/10.1007/978-1-4939-2365-6_10

Liu H. 2008. Research advance on Neovossia horrida in rice. Jiangxi Plant Protein 31(1): 3–6.

Pannu P P S, Kaur G and Chahal S S. 2002. Variability in Tilletia barclayana, the causal organism of kernel smut of rice. The Journal of Mycology and Plant Pathology 32: 6–10.

Rush M C, Shahjahan A K M, Jones J P and Groth D E. 2000. Outbreak of false smut of rice in Louisiana. Plant Disease 84: 100. https://doi.org./10.1094/PDIS.2000.84.1.100D DOI: https://doi.org/10.1094/PDIS.2000.84.1.100D

Sharma A B, Singh B, Vikal Y, Singh A and Kaur S. 2021. Profiling of monosporidial populations of Tilletia barclayana causing kernel smut of rice. Indian Phytopathology 74: 681–89. https:// doi.org/10.1007/s42360-021-00367-7 DOI: https://doi.org/10.1007/s42360-021-00367-7

Sharma A B, Singh N and Singh T P. 2023. Alteration in the sowing time as an effective cultural management practice against kernel smut of rice. Journal of Phytopathology 171: 265–73 https:// doi.org/10.1111/jph.13180 DOI: https://doi.org/10.1111/jph.13180

Singh B, Akhtar J, Kandan A, Kumar P, Chand D, Maurya A K, Agarwal P C and Dubey S C. 2018. Risk of pathogens associated with plant germplasm imported into India from various countries. Indian Phytopathology 71(1): 91–102. https:// doi.org/10.1007/s42360-018-0014-2 DOI: https://doi.org/10.1007/s42360-018-0014-2

Tripathi A, Dubey S C, Akhtar J and Kumar P. 2023. Development of PCR-based assays to diagnose the major fungal pathogens infecting pulse crops, potential for germplasm health certification and quarantine processing. World Journal of Microbiology Biotechnology 39: 74. https://doi.org/10.1007/ s11274-023-03519-1 DOI: https://doi.org/10.1007/s11274-023-03519-1

USDA. 2020. Rice Yearbook 2020. U S Department of Agriculture, Economic Research Service. https://www.ers.usda.gov/data- products/rice-yearbook/

Wang A, Shu X, Xu D, Jiang Y, Liang J, Yi X, Zhu J, Yang F, Jiao C, Zheng A, Yin D and Li P. 2022. Understanding the rice fungal pathogen Tilletia horrida from multiple perspectives. Rice 15: 64. https://doi.org/10.1186/s12284-022-00612-1 DOI: https://doi.org/10.1186/s12284-022-00612-1

Wang A J, Jiang B, Fu R, Wang N, Yin D S, Li P, Zhang J and Zheng A P. 2018. Identification and pathogenicity of pathogen causing kernel smut on rice. Acta Phytophylacica Sinica 48(3): 297–304.

Wang A, Zha Z, Yin D, Shu X, Li M, Wang L, Li P and Zheng A. 2020. Comparative transcriptome analysis of Tilletia horrida infection in resistant and susceptible rice (Oryza sativa L.) male sterile lines reveals potential candidate genes and resistance mechanisms. Genomics 112: 5214–26. https://doi.org/10.21203/rs.2.16204/v1 DOI: https://doi.org/10.1016/j.ygeno.2020.09.036

Wang L, Nysetvold E and Zhou X. 2021. Culture media promoting sporulation of rice kernel smut fungus Tilletia barclayana. European Journal of Plant Pathology 161: 629–35. https://doi.org/10.1007/s10658-021-02348-y DOI: https://doi.org/10.1007/s10658-021-02348-y

Webster R K. 2005. Being at the right place, at the right time, for the right reasons-plant pathology. Annual Review of Phytopathology 43: 1–24. https://doi.org./10.1146/annurev. phyto.43.040204.140209 DOI: https://doi.org/10.1146/annurev.phyto.43.040204.140209

Webster R K and Gunnell P S. 1992. Compendium of Rice Diseases. APS Press. 62p.

Whitney N G and Cartwright R D. 2018. Kernel smut in compendium of rice diseases and pests, 2nd edn. The American Phytopathological Society, St. Paul, Minnesota, USA.

Whitney N G. 1989. Taxonomy of the fungus causing kernel smut of rice. Mycology 81: 468–71. https://doi.org/10.1080/00275514.1989.12025771 DOI: https://doi.org/10.1080/00275514.1989.12025771

Zhou X G, Khanal S and Imran M. 2021. Severe outbreaks of kernel smut in 2021. Agfax. https://agfax.com/2021/09/10/ texas-rice-severe-outbreaks-of-kernelsmut-in-2021

Zhu J Q, Zhou K D and Tao J F. 1998. Cytological study on Neovossia horrida infection in male sterile lines of rice. Southwest China Journal of Agricultural Sciences 11(1): 67–72.