Plant Protect. Sci., 2023, 59(1):31-47 | DOI: 10.17221/76/2022-PPS

Genetic diversity and pathotype profiling of Xanthomonas oryzae pv. oryzae isolates from diverse rice growing ecosystems of Karnataka state of IndiaOriginal Paper

Adke Raghunandana1, Devanna Pramesh1*, Gururaj Sunkad2, Chittaragi Amoghavarsha1, Manoj K. Yadav3, Umakanta Ngangkham4, H.D. Pushpa5, M.K. Prasannakumar6, B.T. Raghavendra2, Harischandra R. Naik7, Siddepalli E. Manjunatha1, S.T Yenjerappa2
1 Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
2 Department of Plant Pathology, University of Agricultural Sciences, Raichur, India
3 ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, India
4 ICAR-Research Complex for North-Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
5 ICAR-Indian institute of oilseeds research, Rajendranagar, Hyderabad, India
6 Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
7 Department of Agriculture Entomology, University of Agricultural Sciences, Raichur, India

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the significant constraints for rice production. A study was carried out to analyze the virulence, genetic diversity, and population structure of Xoo isolates collected from different rice ecosystems of Karnataka, India. The taxonomic identity of all 54 isolates was confirmed using a Xoo-specific PCR assay. The virulence assay on a set of twenty-eight near-isogenic differentials identified nine pathotype groups (KPthX-1 to KPthX-9). Among them, KPthX-6 was highly virulent, whereas KPthx-2 was less virulent. Differentials with four and five resistance (R) genes (Xa4+xa5+xa13+Xa21, Xa4+Xa7+xa13+Xa21, and Xa4+xa5+Xa7+xa13+Xa21) were effective against all the pathotypes. Further, genetic diversity was deduced using a universal marker set, JEL-1, and JEL-2, complementary to a conserved repetitive sequence IS1112. The amplicon size and numbers varied from 100 bp to 3 Kb and 1 to 25. Based on the amplicon counts, Jaccard’s co-efficient and phylogenetic analyses were carried out and categorized the 54 isolates into three clusters (I to III). Cluster-II contains the maximum number of isolates (27), followed by cluster-I (23 isolates) and cluster-III (one isolate). The structure analysis categorized the isolates into five subgroups, viz. SG1, SG2, SG3, SG4, and SG5 indicate the existence of five subpopulations. The present study has identified the genetic and virulence diversity of the Xoo population and reported the effective R gene/s for different rice ecosystems, which can be used in the breeding program for the eco-specific management of BLB of rice.

Keywords: Rice, Xanthomonas oryzae pv. oryzae, ecosystem, pathotypes, virulence, R genes, diversity

Received: July 11, 2023; Accepted: January 5, 2023; Published: January 31, 2023  Show citation

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Raghunandana A, Pramesh D, Sunkad G, Amoghavarsha C, Yadav MK, Ngangkham U, et al.. Genetic diversity and pathotype profiling of Xanthomonas oryzae pv. oryzae isolates from diverse rice growing ecosystems of Karnataka state of India. Plant Protect. Sci. 2023;59(1):31-47. doi: 10.17221/76/2022-PPS.
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    References

    1. Adhikari T.B., Cruz V.C.M., Zhang Q., Nelson R.J., Skinner D.Z., Mew T.W., Leach J.E. (1995): Genetic diversity of Xanthomonas oryzae pv. oryzae in Asia. Applied and Environmental Microbiology, 61: 966-971. Go to original source... Go to PubMed...
    2. Adhikari T.B., Mew T.W., Leach J.E. (1999): Genotypic and pathotypic diversity in Xanthomonas oryzae pv. oryzae in Nepal. Phytopathology, 89: 687-694. Go to original source... Go to PubMed...
    3. Amoghavarsha C., Pramesh D., Naik G.R., Naik M.K., Yadav M.K., Ngangkham U., Chidanandappa E., Raghunandana A., Sharanabasav H., Manjunatha S.E. (2021): Morpho-molecular diversity and avirulence genes distribution among the diverse isolates of Magnaporthe oryzae from Southern India. Journal of Applied Microbiology, 132: 1275-1290. Go to original source... Go to PubMed...
    4. Chen X., Wei S., Yan Q. (2019): Virulence and DNA fingerprinting analysis of Xanthomonas oryzae pv. oryzae identify a new pathotype in Guangxi, South China. Journal of Basic Microbiology, 59: 1082-1091. Go to original source... Go to PubMed...
    5. Cruz C.V., Ardales E., Skinner D., Talag J., Nelson R., Louws F., Leung H., Mew T., Leach J. (1996): Measurement of haplotypic variation in Xanthomonas oryzae pv. oryzae within a single field by rep-PCR and RFLP analyses. Phytopathology, 86: 1352-1359.
    6. Earl D.A., VonHoldt B.M. (2012): STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4: 359-361. Go to original source...
    7. Evanno G., Regnaut S., Goudet J. (2005): Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14: 2611-2620. Go to original source... Go to PubMed...
    8. Fang C.T., Ren H.C., Chen T.Y., Chu Y.K., Faan H.C., Wu S.C. (1957): A comparison of the rice bacterial leaf blight organism of rice and Leersia hexandra Swartz. Acta Phytopathologica Sinica, 3: 99-124.
    9. Fiyaz R.A., Shivani D., Chaithanya K., Mounika K., Chiranjeevi M., Laha G.S., Viraktamath B.C., Rao L.S., Sundaram R.M. (2022): Genetic improvement of rice for bacterial blight resistance: Present status and future prospects. Rice Science, 29: 118-132. Go to original source...
    10. George M.L.C., Bustamam M., Cruz W.T., Leach J.E., Nelson R.J. (1997): Movement of Xanthomonas oryzae pv. oryzae in Southeast Asia detected using PCR-based DNA fingerprinting. Phytopathology, 87: 302-309. Go to original source... Go to PubMed...
    11. Gonzalez C., Szurek B., Manceau C., Mathieu T., Sere Y., Verdier V. (2007): Molecular and pathotypic characterization of new Xanthomonas oryzae strains from West Africa. Molecular Plant Microbe Interactions, 20: 534-546. Go to original source... Go to PubMed...
    12. Hu J., Zhang Y., Qian W., He C. (2007): Avirulence gene and insertion element-based RFLP as well as RAPD markers reveal high levels of genomic polymorphism in the rice pathogen Xanthomonas oryzae pv. oryzae. Systematic and Applied Microbiology, 30: 587-600. Go to original source... Go to PubMed...
    13. IRRI (2013): Standard Evaluation System for Rice. Manila, International Rice Research Institute.
    14. Islam M.R., Alam M.S., Khan A.I., Hossain I., Adam L.R., Daayf F. (2016): Analyses of genetic diversity of bacterial blight pathogen, Xanthomonas oryzae pv. oryzae using IS1112 in Bangladesh. Comptes Rendus Biologies, 339: 399-407. Go to original source... Go to PubMed...
    15. Kauffman H.E., Reddy A.P.K., Hsieh S.P.Y., Nerca S.D. (1973): An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Disease Report, 56: 537-541.
    16. Kumar I., Maravi A.K., Kumar L. (2018): Evaluation of near isogenic lines and pyramids against Xoo isolates collected from three different geographical location of Chhattisgarh. Journal of Pharmacology and Phytochemistry, 1: 1306-1313.
    17. Ladha D.L., Rabindran R. (2012): Molecular variability in Xanthomonas oryzae pv. oryzae isolates of Tamil Nadu. Indian Journal of Plant Protection, 40: 123-128.
    18. Lang J.M., Hamilton J.P., Diaz M.G.Q., Van Sluys M.A., Burgos M.R.G., Vera Cruz C.M., Buell C.R., Tisserat N.A., Leach J.E. (2009): Genomics-based diagnostic marker development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. Plant Disease, 94: 311-319. Go to original source... Go to PubMed...
    19. Leach J.E., White F.F., Rhoads M.L., Leung H. (1990): A repetitive DNA sequence differentiates Xanthomonas campestris pv. oryzae from other pathovars of X. campestris. Molecular Plant Microbe Interactions, 3: 238-246. Go to original source...
    20. Leach J.E., Rhoads M.L., Cruz C.V., White F.F., Mew T.W., Leung H. (1992): Assessment of genetic diversity and population structure of Xanthomonas oryzae pv. oryzae with a repetitive DNA element. Applied and Environmental Microbiology, 58: 2188-2195. Go to original source... Go to PubMed...
    21. Lore J.S., Vikal Y., Hunjan M.S., Goel R.K., Bharaj T.S., Raina G.L. (2011): Genotypic and pathotypic diversity of Xanthomonas oryzae pv. oryzae, the cause of bacterial blight of rice in Punjab State of India. Journal of Phytopathology, 159: 479-487. Go to original source...
    22. Louws F.J., Fulbright D.W., Stephens C.T., Fjde B. (1995): Differentiation of genomic structure by rep-PCR fingerprinting to rapidly classify Xanthomonas campestris pv. vesicatoria. Phytopathology, 85: 528-536. Go to original source...
    23. McKinney H.H. (1923): A new system of grading plant diseases. Journal of Agricultural Research, 26: 195-218.
    24. Mishra D., Vishnupriya M.R., Anil M.G., Konda K., Raj Y., Sonti R.V. (2013): Pathotype and genetic diversity amongst Indian isolates of Xanthomonas oryzae pv. oryzae. PLoS One, 8: 57-65. Go to original source... Go to PubMed...
    25. Mizukami T., Wakimoto S. (1969): Epidemiology and control of bacterial leaf blight of rice. Annual Review of Phytopathology, 7: 51-72. Go to original source...
    26. Mondal K.K., Meena B.R., Junaid A., Verma G., Mani C., Majumder D., Banik S. (2014): Pathotyping and genetic screening of type III effectors in Indian strains of Xanthomonas oryzae pv. oryzae causing bacterial leaf blight of rice. Physiological and Molecular Plant Pathology, 86: 98-106. Go to original source...
    27. Mondal K.K., Mani C., Verma G. (2015): Emergence of bacterial panicle blight caused by Burkholderia glumae in North India. Plant Disease, 99: 1268. Go to original source...
    28. Muniraju K.M., Pramesh D., Mallesh S.B., Mallikarjun K., Guruprasad G.S. (2017): Disease severity and yield losses caused by false smut disease of rice in different rice ecosystems of Karnataka. International Journal of Microbiology Research, 9: 955-958.
    29. Noda T., Li C., Li J., Ochiai H., Ise K., Kaku. H. (2001): Pathogenic diversity of Xanthomonas oryzae pv. oryzae strains from Yunnan province, China. Japan Agricultural Research Quarterly: JARQ, 35: 97-103. Go to original source...
    30. Noer Z., Hasanuddin, Lisnawita, Suryanto D. (2018): Pathotype profile of Xanthomonas oryzae pv. oryzae isolates from North Sumatera. IOP Conference Series, Earth and Environmental Science, 122: 012142. doi: 10.1088/1755-1315/122/1/012142 Go to original source...
    31. Ochiai H., Horino O., Miyajima K., Kaku H. (2000): Genetic Diversity of Xanthomonas oryzae pv. oryzae strains from Sri Lanka. Phytopathology, 90: 415-421. Go to original source... Go to PubMed...
    32. Ou S.H. (1985): Rice Diseases. Kew, Commonwealth Mycological Institute. 61-96.
    33. Pritchard J.K., Stephens M., Donnelly P. (2000): Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. Go to original source... Go to PubMed...
    34. Que H., Chen H., Wu M., He C. (2011): Rep-PCR analysis of genotypic diversity of Xanthomonas oryzae pv. oryzae strains from North China. Acta Agricultural University, Jiangxiensis, 33: 482-487.
    35. Rademaker J.L., Hoste B., Louws F.J., Kersters K., Swings J., Vauterin L., Vauterin P., de Bruijn F.J. (2000): Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. International Journal of Systematic and Evolutionary Microbiology, 50: 665-677. Go to original source... Go to PubMed...
    36. Rao P.S., Kauffman H.E. (1977): Potential yield losses in dwarf rice varieties due to bacterial blight in India. Journal of Phytopathology, 90: 281-284. Go to original source...
    37. Reddy P.R., Nayak P., Sridhar R. (1978): Physiology of bacterial leaf blight of rice: Influence of light intensity on some biochemical changes associated with the disease development (India). Indian Phytopathology, 30: 51-54.
    38. Reddy L.J., Sirisha C., Rao K.R.S.S. (2009): Assessment of genetic and pathogenic diversity of Xanthomonas oryzae pv. oryzae on high yielding local variety, tella hamsa, from farmer fields in Gagillapur and Kompaly, Andhra Pradesh. Taiwania, 54: 241-247.
    39. Saha S., Garg R., Biswas A., Rai A.B. (2015): Bacterial diseases of rice: An overview. Journal of Pure and Applied Microbiology, 9: 725-736.
    40. Sandhu A.F., Khan J.A., Ali S., Arshad H.I., Saleem K. (2018): Molecular characterization of Xanthomonas oryzae pv. oryzae isolates and its resistance sources in rice germplasm. PSM Microbiology, 3: 55-61.
    41. Shankara K. (2015): Geographic profiling and pathotype analysis of bacterial leaf blight (Xanthomonas oryzae pv. oryzae) of rice in southern India [PhD thesis]. Raichur, University of Agricultural Sciences.
    42. Shankara K., Patil M.B., Pramesh D., Sunkad G., Yenjerappa S.T., Ibrahim M., Rajesh N.L., Chikkannaswamy (2017): Characterization of Xanthomonas oryzae pv. oryzae isolates from rice growing regions of southern India. International Journal of Pure and Applied Biosciences, 5: 452-461. Go to original source...
    43. Shanti M.L., George M.L.C., Cruz C.V., Bernardo M.A., Nelson R.J., Leung H., Sridhar R. (2001): Identification of resistance genes effective against rice bacterial blight pathogen in eastern India. Plant Disease, 85: 506-512. Go to original source... Go to PubMed...
    44. Sharanabasav H., Pramesh D., Prasannakumar M.K., Chidanandappa E., Yadav M.K., Ngangkham U., Parivallal B., Raghavendra B.T., Manjunatha C., Sharma S.K., Karthik N. (2021): Morpho-molecular and mating-type locus diversity of Ustilaginoidea virens: An incitant of false smut of rice from Southern parts of India. Journal of Applied Microbiology, 131: 2372-2386. Go to original source... Go to PubMed...
    45. Singh S., Sodhi M., Vikal Y., George M.L.C., Bala G.S., Mangat G.S., Garg M., Sindhu J.S., Dhaliwal H.S. (2003): DNA fingerprinting and virulence analysis of Xanthomonas oryzae pv. oryzae isolates from Punjab, Northen India. Euphytica, 130: 107-115. Go to original source...
    46. Sundaram R.M., Vishnupriya M.R., Biradar S.K., Laha G.S., Shobharani N., Sarma M.P., Sonti R.V. (2008): Marker assisted introgression of bacterial blight resistance in Sambha Mahsuri, an elite indica rice variety. Euphytica, 160: 411-422. Go to original source...
    47. Yugander A., Sundaram R.M., Ladhalakshmi D., Hajira S.K., Prakasam V., Prasad M.S., Sheshumadhav M., Babu V.R., Laha G.S. (2017): Virulence profiling of Xanthomonas oryzae pv. oryzae isolates, causing bacterial blight of rice in India. European Journal of Plant Pathology, 149: 171-191. Go to original source...
    48. Zhang Q., Leach J.E., Nelson R.J., Mew T.W. (1997): Genetic structure of rice bacterial blight pathogen population in China. Zuo Wu Xue Bao, 23: 150-158.

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