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Population structure and virulence analysis of Alternaria carthami isolates of India using ISSR and SSR markers

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Abstract

Alternaria leaf spot caused by Alternaria carthami is one of the most devastating diseases of safflower. Diversity among 95 isolates of A. carthami was determined using virulence assays, enzyme assays, dominant (ISSR) and co-dominant (SSR) markers. Collections and isolations were made from three major safflower producing states of India. The virulence assays categorised the population into four groups based on level of virulence. Estimation of activities of cell wall degrading enzymes (CWDE) yielded concurrent results to virulence assays with maximum CWDE activities in most virulent group. Eighteen ISSR primers were used and 23 polymorphic microsatellite markers were developed to assess the genetic diversity and determine the population structure of A. carthami. Analysis of ISSR profiles revealed high genetic diversity (Nei’s Genetic diversity index; h = 0.36). Microsatellite markers produced a total of 56 alleles with an average of 2.43 alleles per microsatellite marker and Nei’s genetic diversity index as h = 0.43. Unweighted Neighbor-joining and population structure analysis using both the marker systems differently arranged the isolates into three clusters. Distance analysis of the marker profiles provided no evidence for geographical clustering of isolates, indicating that isolates are randomly spread across India, signifying high potential of the fungus to adapt to diverse regions. Microsatellite markers clustered the isolates in consonance to the virulence groups in the dendrogram. This implies that the fungus has a high potential to adapt to resistant cultivars or fungicides. The information can aid in the breeding and deployment of A. carthami resistant varieties, and in early blight disease management in all safflower growing regions of the world.

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Acknowledgements

The study was financially supported by Department of Science and Technology (DST-Purse II), Government of India. The authors gratefully acknowledge Dr. Charanjit Kaur, Department of Statistics, University of Delhi, Delhi and Dr. Ankita Bidalia for their help in statistical analyses. GA is grateful to University Grants Commission for providing fellowship as a Senior Research Fellow.

Funding

The study was financially supported by Department of Science and Technology (DST-Purse II), Government of India. GA performed the experiments and analysed the data. The work was designed and planned by RK.

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  1. Department of Botany, University of Delhi, New Delhi, 110007, India

    Garima Anand & Rupam Kapoor

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  1. Garima Anand
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Correspondence to Rupam Kapoor.

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Electronic supplementary material

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11274_2018_2524_MOESM1_ESM.pdf

Supplementary Figure 1: Map showing collection sites for A. carthami isolates from 24 districts of three major safflower producing states of India. The numerals in each district represent the number of isolates collected from the infected safflower fields of the region. (PDF 138 KB)

11274_2018_2524_MOESM2_ESM.jpg

Supplementary Figure 2: Activity of Pectin methyl esterases in (A) Different isolates of A. carthami. In all plots, data is presented as means ±S.D. (n=5); (B) Box-plot depicting the range of PME activity in A. carthami isolates. (JPG 72 KB)

11274_2018_2524_MOESM3_ESM.jpg

Supplementary Figure 3: Activity of Polygalacturonases in (A) Different isolates of A. carthami. In all plots, data are presented as means ±S.D. (n=5); (B) Box-plot depicting the range of PG activity in A. carthami isolates. (JPG 67 KB)

11274_2018_2524_MOESM4_ESM.jpg

Supplementary Figure 4: Activity of Exo-1,4 glucanases (C1) in (A) Different isolates of A. carthami. In all plots, data are presented as means ±S.D. (n=5) ; (B) Box-plot depicting the range of exo-1,4 glucanases activity in A. carthami isolates. (JPG 66 KB)

11274_2018_2524_MOESM5_ESM.jpg

Supplementary Figure 5: Activity of C, 1,4-endoglucanases (Cx) in (A) Different isolates of A. carthami. In all plots, data are presented as means ±S.D. (n=5); (B) Box-plot depicting the range of C, 1,4-endoglucanases activity in A. carthami isolates. (JPG 75 KB)

11274_2018_2524_MOESM6_ESM.jpg

Supplementary Figure 6: Average lesion area formed by A. carthami isolates on leaves of safflower. In all plots, data are presented as means ±S.D. (n=5). (JPG 177 KB)

Supplementary Figure 7: Distribution of major classes of microsatellites in A. carthami genome. (TIF 242 KB)

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Anand, G., Kapoor, R. Population structure and virulence analysis of Alternaria carthami isolates of India using ISSR and SSR markers. World J Microbiol Biotechnol 34, 140 (2018). https://doi.org/10.1007/s11274-018-2524-6

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