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Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India

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Abstract

This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate collections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies.

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Acknowledgments

This project was supported by the Indian Council of Agricultural Research (ICAR) and the Gus R. Douglass Institute of West Virginia State University. We declare that we have no conflicts of interest. The authors thank the National Agricultural Innovation Project, ICAR, for sponsoring visits of N.V. Singh, D. Ramajayam and Ravinder Kumar.

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Authors and Affiliations

  1. Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA

    Venkata Lakshmi Abburi, Thangasamy Saminathan, Robert Cantrell, Padma Nimmakayala & Umesh K. Reddy

  2. ICAR-National Research Center on Pomegranate, Kegaon, Solapur, Maharashtra, 413255, India

    Nripendra Vikram Singh, Ram Chandra, Kuldeep Kumar Sharma, Jyotsana Sharma, K. Dhinesh Babu & Ram Krishna Pal

  3. ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari, Andhra Pradesh, 534450, India

    D. Ramajayam

  4. ICAR-Sugarcane Breeding Institute’s Regional Centre, Karnal, Haryana, 132 001, India

    Ravinder Kumar

  5. MGM’s Institute of Biosciences and Technology, Aurangabad, Maharashtra, 431 003, India

    Dhananjay M. Mundewadikar & Umesh K. Reddy

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  1. Nripendra Vikram Singh
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  2. Venkata Lakshmi Abburi
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  3. D. Ramajayam
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  4. Ravinder Kumar
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  5. Ram Chandra
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  6. Kuldeep Kumar Sharma
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  7. Jyotsana Sharma
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  8. K. Dhinesh Babu
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  9. Ram Krishna Pal
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  11. Thangasamy Saminathan
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  12. Robert Cantrell
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  13. Padma Nimmakayala
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  14. Umesh K. Reddy
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Correspondence to Umesh K. Reddy.

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Communicated by S. Hohmann.

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Fig S1: Skree plot of individual and cumulative proportions vs. principal component to infer variation that can be explained by principal component analysis.

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Singh, N.V., Abburi, V.L., Ramajayam, D. et al. Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India. Mol Genet Genomics 290, 1393–1402 (2015). https://doi.org/10.1007/s00438-015-1003-0

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