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Population Structure and Genetic Diversity in Popular Rice Varieties of India as Evidenced from SSR Analysis

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Abstract

We report here on the phylogenetic analysis, population substructure, and identification of molecular tags of 25 popular rice varieties and four landraces from different ecological belts of India employing a set of 52 simple sequence repeat (SSR) markers. Genetic analysis using the SSR markers categorized the genotypes into two major clusters, distributed according to their pedigree. Population structure analysis suggested that the optimum number of subpopulations was three (K = 3) in the popular varieties and landraces. At K = 5 the allelic distribution was much more similar to the phylogenetic dendrogram. The molecular diversity and population structure analysis indicated that there is not much variation among the popular rice cultivars of India. The study has identified SSR markers producing unique alleles, which should aid in the precise identification, maintenance, and genetic purity analysis of rice varieties.

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Authors and Affiliations

  1. Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221 005, India

    Priti Upadhyay

  2. Directorate of Rice Research, Rajendra Nagar, Hyderabad, 500 030, India

    Priti Upadhyay, C. N. Neeraja & Vikas Kumar Singh

  3. Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

    C. Kole

  4. Molecular Marker Lab II, Rice Section, Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110 012, India

    Vikas Kumar Singh

Authors
  1. Priti Upadhyay
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  2. C. N. Neeraja
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  3. C. Kole
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  4. Vikas Kumar Singh
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Correspondence to Vikas Kumar Singh.

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Upadhyay, P., Neeraja, C.N., Kole, C. et al. Population Structure and Genetic Diversity in Popular Rice Varieties of India as Evidenced from SSR Analysis. Biochem Genet 50, 770–783 (2012). https://doi.org/10.1007/s10528-012-9519-z

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  • DOI: https://doi.org/10.1007/s10528-012-9519-z

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