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Genetic diversity and population structure analysis of bold type rice collection from Southern India

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Abstract

It is essential to elucidate genetic diversity and relationships among related varieties of origin and landraces for improving the breeding process. Since rice breeding has improved agronomic traits such as yield and eating quality during green revolution, modern rice varieties are originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in bold type rice varieties of southern India, we used a total of 81 rice genotypes by 100 simple sequence repeat markers composed of 36 improved varieties and 45 landraces, which are representative and important for bold type grain rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Clustering by Ward method was done to establish a relationship among the 81 rice genotypes. All the genotypes were clustered into mainly 5 clusters. Principle component analysis revealed that the first principal component revealed 42.87% variation, while the second component showed 14.01% variation. Among the eight morpho-physiological and plant production traits studied, the relative water content and spikelet fertility percentage contributed towards maximum diversity. Principle co-ordinate analysis evidently differentiated the genotypes to high yielding varieties with common ancestry. Population structure analysis also obviously classified the genotypes into high yielding susceptible and indigenous tolerant groups. These old varieties and landraces present in crop germplasm collections represent a strategic reserve of genetic variation that can be tapped for varieties and understanding of stress response and developing new varieties that are physiologically adapted to highly variable, climate-resilient environments.

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Acknowledgments

The authors thank Dean, College of Agriculture, Vellayani and Associate Director of Research, Regional Agricultural Research Station, Pattambi for extending full support in providing facilities for the research work.

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Authors and Affiliations

  1. Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala, 695522, India

    N. Nithya, R. Beena, Roy Stephen, R. V. Manju & M. M. Viji

  2. Department of Plant Breeding and Genetics, College of Agriculture, Kerala Agricultural University, Vellayani, Kerala, 695522, India

    V. G. Jayalekshmi

  3. Department of Plant Physiology, Regional Agricultural Research Station, Kerala Agricultural University, Thrissur, Kerala, India

    P. S. Abida

  4. ICAR-CTCRI, Thiruvannathapuram, Kerala, India

    J. Sreekumar

Authors
  1. N. Nithya
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  2. R. Beena
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  3. P. S. Abida
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  4. J. Sreekumar
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  5. Roy Stephen
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  6. V. G. Jayalekshmi
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  7. R. V. Manju
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  8. M. M. Viji
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Contributions

RB helped in conceptualization. NN, RB and JS contributed to data curation. JS helped in formal analysis. RB contributed to funding acquisition. RB and NN were involved in investigation. RB, JS, PSA, RS, MMV, VGJ and RVM was involved in methodology. SKP helped in project administration. RB, PSA, RS, MMV, VGJ and RVM contributed to resources. JS contributed to software. RB, PSA, RS, MMV, VGJ and RVM helped in supervision.

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Correspondence to R. Beena.

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All authors don’t have any conflict of interest regarding this article.

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Communicated by R. Chibbar.

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Nithya, N., Beena, R., Abida, P.S. et al. Genetic diversity and population structure analysis of bold type rice collection from Southern India. CEREAL RESEARCH COMMUNICATIONS 49, 311–328 (2021). https://doi.org/10.1007/s42976-020-00099-w

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  • DOI: https://doi.org/10.1007/s42976-020-00099-w

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