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Molecular Biology Reports

, Volume 42, Issue 6, pp 1107–1122 | Cite as

Morphological and comparative genomic analyses of pathogenic and non-pathogenic Fusarium solani isolated from Dalbergia sissoo

  • M. Arif
  • N. W. Zaidi
  • Q. M. R. Haq
  • Y. P. Singh
  • G. Taj
  • C. S. Kar
  • U. S. Singh
Article

Abstract

Sissoo or shisham (Dalbergia sissoo Roxb.) is one of the finest wood of South Asia. Fusarium solani is a causal organism of sissoo wilt, decline, or dieback. It is also a potential causal organism associated with other valuable tree species. Thirty-eight Fusarium isolates including 24 F. solani and 14 Fusarium sp., were obtained in 2005 from different geographical locations in India. All 38 (18 pathogenic and 20 non-pathogenic) isolates were characterized for genomic analysis, growth behaviour, pigmentation and sensitivity to carbendazim. Based on growth pattern, growth rate, pigmentation and sensitivity to carbendazim, all 38 isolates showed a wide range of variability, but no correlation with pathogenicity or geographical distribution. Three techniques were used for comparative genomic analysis: random amplified polymorphic DNA (RAPD); inter simple sequence repeats (ISSR); and simple sequence repeats (SSR). A total of 90 primers targeting different genome regions resulted a total of 1159 loci with an average of 12.88 loci per primer. These primers showed high genomic variability among the isolates. The maximum loci (14.64) per primer were obtained with RAPD. The total variation of the first five principal components for RAPD, ISSR, SSR and combined analysis were estimated as 47.42, 48.21, 46.30 and 46.78 %, respectively. Among the molecular markers, highest Pearson correlation value (r = 0.957) was recorded with combination of RAPD and SSR followed by RAPD and ISSR (r = 0.952), and SSR and ISSR (r = 0.942). The combination of these markers would be similarly effective as single marker system i.e. RAPD, ISSR and SSR. Based on polymorphic information content (PIC = 0.619) and highest coefficient (r = 0.995), RAPD was found to be the most efficient marker system compared to ISSR and SSR. This study will assist in understanding the population biology of wilt causing phytopathogen, F. solani, and in assisting with integrated disease management measures.

Keywords

RAPD ISSR SSR Morphological characterization Genetic variability 

Notes

Acknowledgments

We thank Trenna Blagden and Ian Moncrief (Oklahoma State University, Stillwater, OK), for reviewing this manuscript. This study was made possible through the financial support and fellowship to the first author from the Department of Biotechnology, Government of India.

Supplementary material

11033_2014_3849_MOESM1_ESM.tif (413 kb)
Three-dimensional plot (with vectors) of 38 isolates of Fusariumspecies generated by principal coordinate analysis (PCOORDA) using DCENTER andEIGEN modules of NTSYSpc. The numbers 1 to 38 plotted represents individual isolate andcorresponds to those listed as F1 to F38 in Table 1. (A) RAPD 3D plot, (B) ISSR 3D plot, (C)SSR 3D plot, and (D) combined RAPD+ISSR+SSR 3D plot
11033_2014_3849_MOESM2_ESM.tif (1.1 mb)
PCR amplicons profiles of different isolates of Fusarium sp. andFusarium solani obtained by agarose gel electrophoresis. Lane M is 100 bp ladder and lanes1 to 38 represents individual isolate and corresponds to those listed as F1 to F38 in Table 1.(A) RAPD profile obtained using primer P-132 (B) ISSR profile obtained using primer P-16,and (C) SSR profile obtained using primer P-309

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Centre of Advanced Studies in Plant PathologyG. B. Pant University of Agriculture & TechnologyPantnagarIndia
  2. 2.Department of BiosciencesJamia Millia IslamiaNew DelhiIndia
  3. 3.Forest Pathology DivisionForest Research InstituteDehradunIndia
  4. 4.Department of Molecular Biology and Genetic EngineeringG. B. Pant University of Agriculture & TechnologyPantnagarIndia
  5. 5.Central Research Institute for Jute and Allied FibresICARBarrackporeIndia
  6. 6.Department of Plant PathologyKansas State UniversityManhattanUSA
  7. 7.International Rice Research InstituteLos BanosPhilippines

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