Investigating the virulence and genetic diversity of Colletotrichum lindemuthianum populations distributed in the North Western Himalayan hill states

  • Naiya Sharma
  • Nidhi Kumari
  • Surinder Kumar Sharma
  • Bilal Ahmad Padder
  • Prem Nath SharmaEmail author
Original Article


Bean anthracnose caused by Colletotrichum lindemuthianum is one of the devastating diseases in common beans possessing wide genetic and pathogenic variability. Sixty isolates of C. lindemuthianum collected from three North-Western Himalayan States were characterized on differential bean cultivars and analyzed by random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR). Based on pathogenicity tests and CIAT-defined binary race-classification system, 60 isolates belonged to 27 races. Out of 27 races, 19 races were identified from Himachal Pradesh, three from Jammu and Kashmir (J&K) and 13 from Uttrakhand. Predominant races present in North Western Himalayas were 17 and 503, although 25.9% (7 out of 27) of the races were detected repeatedly. In addition, this is the first study on characterization of C. lindemuthianum races from J&K and Uttrakhand. The virulence analysis on differential cultivars from Andean and Mesoamerican gene pool suggested four interaction types in accordance with the genetic origin of the cultivars that were attacked by a particular race. The interaction type I with race 0 isolates was avirulent on all the differential cultivars, while the races placed in interaction type IV attacked the genotypes from both the gene pools, thereby complicating the designing of resistance breeding strategies in this part of the world. The genetic diversity analysis using RAPD and ISSR markers revealed higher polymorphism with RAPD markers compared to ISSRs. The population STRUCTURE analysis revealed that most of the isolates from three States shared unique haplotypes based on Bayesian clustering. The RAPD and ISSR markers based analysis of C. lindemuthianum isolates grouped in different races revealed a very low level of similarity coefficient and thus their correlation with pathogenic races could not be established.


Anthracnose Variability Virulence Physiologic races Molecular markers 



The corresponding author is thankful to the Department of Biotechnology, New Delhi, Government of India for financial support (award letter no. BT/PR12099/AGII/106/979/2014). The authors are also grateful to the unknown reviewers for their critical review of the manuscript.


This study was funded by Department of Biotechnology, New Delhi, Government of India for financial support (award letter no. BT/PR12099/AGII/106/979/2014).

Compliance with ethical standards

Conflict of interest

The corresponding author declares no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

42161_2019_269_Fig8_ESM.png (638 kb)
Fig. S1

Electrophoretic analysis of amplification products obtained with RAPD OPA-13 and with ISSR SSR 814 The first lane to 1 kb plus ladder and isolates as 1-CL.202, 2-CL.203, 3-CL.204, 4-CL.205, 5-CL.206, 6-CL.207, 7-CL.208, 8-CL.209, 9-CL.210, 10-CL.211, 11-CL.212, 12-CL.213, 13-CL.214, 14-CL.215, 15-CL.216, 16-CL.217, 17-CL.218, 18-CL.219, 19-CL.220, 20- CL.221, 21-CL.222, 22-CL.223, 23-CL.224, 24-CL.225, 25-CL.226, 26-CL.227, 27-CL.228. second lane to 1 kb plus ladder isolates as 28-CL.229, 29- CL.230, 30-CL.231, 31-CL.232, 32-CL.233, 33-CL.234, 34-CL.235, 35-CL.236, 36-CL.237, 37-CL.238, 38-CL.239, 39-CL.240, 40-CL.241, 41-CL.242, 42-CL.243, 43-CL.244, 44-CL.245, 45-CL.246, 46-CL.247, 47- CL.248, 48-CL.249, 49-CL.250, 50-CL.251, 51-CL.252, 52-CL.253, 53-CL.254, 54-CL.255,. Third lane 1 kb plus ladder and isolates as 55-CL.256, 56-CL.257, 57-CL.258, 58-CL.259, 59- CL.260, 60-CL.261 (PNG 637 kb)

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Copyright information

© Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2019

Authors and Affiliations

  1. 1.Molecular Plant Pathology Laboratory, Department of Plant Pathology, College of AgricultureCSK HP Agricultural UniversityPalampurIndia
  2. 2.Mountain Agriculture Research and Extension CentreCSK HP Agricultural UniversitySangla, KinnaurIndia
  3. 3.Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant PathologySKUAST-KashmirShalimar SrinagarIndia

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