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Assessment and comparison of AFLP and SSR based molecular genetic diversity in Indian isolates of Ascochyta rabiei, a causal agent of Ascochyta blight in chickpea (Cicer arietinum L.)

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Abstract

Ascochyta blight (AB), caused by Ascochyta rabiei (Pass.) Labr. (anamorph), is the most damaging disease of chickpea (Cicer arietinum L.) and is a serious biotic stress constraint for chickpea production. To understand the molecular diversity in A. rabiei populations of India, a total of 64 isolates collected from AB-infected chickpea plants from different agroclimatic regions in the North Western Plain Zone (NWPZ) of India were analyzed with 11 AFLP (amplified fragment length polymorphism) and 20 SSR (simple sequence repeat) markers. A total of 9 polymorphic AFLP primer pairs provided a total of 317 fragments, of which 130 were polymorphic and showed an average PIC value 0.28. Of the SSR markers, 12 showed polymorphism and provided a total of 29 alleles with an average PIC value 0.35. To the best of our knowledge, this is the first report on a comparison of AFLP and SSR diversity estimates in A. rabiei populations. The dendrogram developed based on AFLP and SSR data separately, as well as on the combined marker dataset, grouped the majority of AB isolates as per geographic regions. Model based population structure analysis revealed four distinct populations with varying levels of ancestral admixtures among 64 isolates studied. Interestingly, several AFLP primer combinations and SSR markers showed the locus/allele specific to AB isolates of certain regions, e.g., Hisar, Sriganganagar, Gurdaspur, and Sundarnagar. Genetic variability present in AB isolates of the NWPZ of India suggests the continuous monitoring of changes in A. rabiei population to anticipate the breakdown of AB resistance in chickpea cultivars grown in India.

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References

  • Ambardar VK, Singh SK (1996) Identification and elucidation of Ascochyta rabiei isolates of chickpea in Jammu. Indian J Mycol Plant Pathol 26:4–8

    Google Scholar 

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrels ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186. doi:10.1139/g93-024

    Article  PubMed  CAS  Google Scholar 

  • Barve MP, Santra DK, Ranjekar PK, Gupta VS (2004) Genetic diversity analysis of a world-wide collection of Ascochyta rabiei isolates using sequence tagged microsatellite marker. World J Microb Biot 20:735–741. doi:10.1007/s11274-004-1550-8

    Article  CAS  Google Scholar 

  • Basandrai AK, Pande S, Kishore GK, Crouch JH, Basandrai D (2005) Cultural, morphological and pathological variation in Indian isolates of Ascochyta rabiei, the chickpea blight pathogen. Plant Pathol J 21:207–213

    Google Scholar 

  • Chongo G, Gossen BD, Buckwaldt L, Adhikari T, Rimmer SR (2004) Genetic diversity of Ascochyta rabiei in Canada. Plant Dis 88:4–10. doi:10.1094/PDIS.2004.88.1.4

    Article  Google Scholar 

  • Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 8:55. doi:10.1186/1471-2229-8-55

    Article  PubMed  Google Scholar 

  • Geistlinger J, Maqbool S, Kaiser WJ, Kahl G (1997) Detection of microsatellite fingerprint markers and their Mendelian inheritance in Ascochyta rabiei. Mycol Res 101:1113–1121. doi:10.1017/S0953756297004231

    Article  CAS  Google Scholar 

  • Geistlinger J, Weising K, Winter P, Kahl G (2000) Locus-specific microsatellite markers for the fungal chickpea pathogen Didymella rabiei (anamorph) Ascochyta rabiei. Mol Ecol 9:1939– 1941. doi:10.1046/j.1365-294x.2000.01092-13.x

    Article  PubMed  CAS  Google Scholar 

  • Gowen SR, Orton M, Thurley B, White A (1989) Variation in pathogenicity of Ascochyta rabiei on chickpeas. Trop Pest Manage 35:180–186. doi:10.1080/09670878909371353

    Article  Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185. doi:10.1023/A:1003910819967

    Article  CAS  Google Scholar 

  • Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8:460. doi:10.1186/1471-2105-8-460

    Article  PubMed  Google Scholar 

  • Jamil JJ, Sarwar N, Sarwar M, Khan JA, Geistlinger J, Kahl G (2000) Genetic and pathogenic diversity within Ascochyta rabiei (Pass.) Lab. population in Pakistan causing blight of chickpea (Cicer arietinum). . Physiol Mol Plant Pathol 57:243–254. doi:10.1006/pmpp.2000.0303

    Article  CAS  Google Scholar 

  • Morjane H, Geistlinger J, Harrabi M, Weising K, Kahl G (1994) Oligonucleotide fingerprinting detects genetic diversity among Ascochyta rabiei isolates from a single chickpea field in Tunisia. Curr Genet 26:191–197. doi:10.1007/BF00309547

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Amer Naturalist 106:283–292. doi:10.1086/282771

    Article  Google Scholar 

  • Nene YL (1984) A review of Ascochyta blight of chickpea (Cicer arietinum L.). In: Saxena MC, Singh KB (eds) Ascochyta blight and winter sowing of chickpea. Proceedings of the Workshop on Ascochyta Blight and Winter Sowing of Chickpeas. Junk, The Hague, The Netherlands, pp 17–34

    Google Scholar 

  • Pande S, Siddique KHM, Kishore GK, Baaya B, Gaur PM, Gowda CLL, Bretag T, Crouch JH (2005) Ascochyta blight of chickpea (Cicer arietinum L.): a review of biology, pathogenicity, and disease management. Aust J Agric Res 56:317–332. doi:10.1071/AR04143

    Article  Google Scholar 

  • Peever TL, Salimath SS, Su G, Kaiser WJ, Muehlbauer FJ (2004) Historical and contemporary multilocus population structure of Ascochyta rabiei (teleomorph: Didymella rabiei) in the Pacific Northwest of the United States. Mol Ecol 13:291–309. doi:10.1046/j.1365-294X.2003.02059.x

    Article  PubMed  CAS  Google Scholar 

  • Powell W, Margenta M, Andre C, Hanfrey M, Vogel J, Tingey S, Rafalsky A (1996) The utility of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238. doi:10.1007/BF00564200

    Article  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Punithalingam E, Holliday P (1972) Ascochyta rabiei. In Descriptions of pathogenic fungi and bacteria. Commonwealth Mycological Institute: Kew, England. Vol 34 p 337

  • Roldán-Ruiz I, Dendauw J, Van Bockstæle E, Depicker A, DeLoose M (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6:125–134. doi:10.1023/A:1009680614564

    Article  Google Scholar 

  • Santra DK, Singh G, Kaiser WJ, Gupta VS, Ranjekar PK, Muehlbauer FJ (2001) Molecular analysis of Ascochyta rabiei (Pass.) Labr., the pathogen of ascochyta blight in chickpea. Theor Appl Genet 102:676–682. doi:10.1007/s001220051696

    Article  CAS  Google Scholar 

  • Singh KB, Reddy MV (1991) Advances in disease-resistance breeding in chickpea. Adv Agron 45:191–222. doi:10.1016/S0065-2113(08)60041-3

    Article  Google Scholar 

  • Singh KB, Reddy MV (1996) Improving chickpea yield by incorporating resistance to Ascochyta blight. Theor Appl Genet 92:509–515. doi:10.1007/BF00224552

    Article  Google Scholar 

  • Spooner DM, Tivang J, Nienhuis J, Miller JT, Douches DS, Contreras MA (1996) Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe). Theor Appl Genet 92:532–540. doi:10.1007/BF00224555

    Article  CAS  Google Scholar 

  • Swofford DL (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts

  • Tegelstrom H (1992) Detection of mitochondrial DNA fragments. In: Hoelzel AR (ed) Molecular genetic analysis of populations: a practical approach. IRL Press, Oxford, pp 89–114

    Google Scholar 

  • Udupa SM, Weigand F, Saxena MC, Kahl G (1998) Genotyping with RAPD and microsatellite markers resolves pathotype diversity in the ascochyta blight pathogen of chickpea. Theor Appl Genet 97:299–307. doi:10.1007/s001220050899

    Article  CAS  Google Scholar 

  • Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649. doi:10.1016/j.plantsci.2007.08.010

    Article  CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407

    Article  PubMed  CAS  Google Scholar 

  • Weising K, Kaemmer D, Epplen JT, Weigand F, Saxena MC, Kahl G (1991) DNA fingerprinting of Ascochyta rabiei with synthetic oligodeoxynucleotides. Curr Genet 19:483–489. doi:10.1007/BF00312740

    Article  CAS  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535. doi:10.1093/nar/18.22.6531

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This work, in part, was supported by Generation Challenge Programme (http://www.generationcp.org). Thanks are due to Mr A. Gafoor, Research Technician, for his help in some experiments.

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  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India

    Rajeev Varshney, Suresh Pande, Seetha Kannan, Thudi Mahendar, Mamta Sharma, Pooran Gaur & Dave Hoisington

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  1. Rajeev Varshney
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  2. Suresh Pande
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Correspondence to Rajeev Varshney.

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Varshney, R., Pande, S., Kannan, S. et al. Assessment and comparison of AFLP and SSR based molecular genetic diversity in Indian isolates of Ascochyta rabiei, a causal agent of Ascochyta blight in chickpea (Cicer arietinum L.). Mycol Progress 8, 87–97 (2009). https://doi.org/10.1007/s11557-008-0581-1

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