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Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers

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Abstract

Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-à-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer’s varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI’s Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grou** indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.

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Acknowledgements

This study was carried out under the project ‘Marker Assisted Creation of Heterotic Pools and Diversification of Male Sterility and Fertility Restoration System for Hybrid Seed Production in Rice’ funded by the Council of Scientific and Industrial Research (CSIR), Government of India, under The New Millennium Indian Technology Leadership Initiative (NMITLI).

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Authors and Affiliations

  1. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110 012, India

    SHEEL YADAV, ASHUTOSH SINGH, NITIKA GOEL & A. K. SINGH

  2. Post Graduate College, Ghazipur, 233 001, India

    M. R. SINGH

  3. Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, 612 101, India

    K. K. VINOD

  4. Central Rice Research Institute, Cuttack, 753 006, India

    T. MOHAPATRA

  5. Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India

    SHEEL YADAV

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  1. SHEEL YADAV
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  2. ASHUTOSH SINGH
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  3. M. R. SINGH
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  4. NITIKA GOEL
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  5. K. K. VINOD
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  6. T. MOHAPATRA
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Correspondence to A. K. SINGH.

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[Yadav S., Singh A., Singh M. R., Goel N., Vinod K. K., Mohapatra T. and Singh A. K. 2013 Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers. J. Genet. 92, xx–xx]

Sheel Yadav and Ashutosh Singh contributed equally to this work.

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YADAV, S., SINGH, A., SINGH, M.R. et al. Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers. J Genet 92, 545–557 (2013). https://doi.org/10.1007/s12041-013-0312-5

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