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Genetic characterization of coarse and basmati rice (Oryza sativa L.) through microsatellite markers and morpho-agronomic traits

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Abstract

Knowledge of genetic diversity is necessary for designing future breeding programs and deriving desired genotypes. The current study was designed to explore the genetic diversity between 37 coarse and basmati rice genotypes by using 15 agro-morphological traits and 35 SSR markers. Mahalanobis’ generalized distance (D2) and principal component analysis (PCA) were used to evaluate the data for agronomical traits. Of the information in the raw data for the yield-related traits, 67.28% was represented by two principal components. Five different clusters were revealed by cluster analysis (D2): Cluster I had up to 6 genotypes, followed by 17, 5, 8, and 1 genotypes in clusters II, III, IV, and V, respectively. Greater genetic diversity among the genotypes was signified by a greater inter-cluster than intra-cluster distance. The maximum inter-cluster distance was observed between clusters II and V (80.88). The highest (33.080) and lowest (12.745) intra-cluster distances were observed for Cluster IV and Cluster II, respectively. Tall-growing and long grain basmati genotypes were grouped into Cluster II, while Cluster IV contained all the coarse rice genotypes. The minimum intra-cluster distance (12.745) of Cluster II indicated a narrow genetic base for the basmati rice. Molecular-based exploration of genetic diversity produced genetic similarity coefficients and clustered the genotypes into two major clusters. The total number of polymorphic alleles was 69, with an average of 1.97 alleles per SSR locus. In this study, a maximum of 5 alleles were revealed by marker RM16. The highest and lowest polymorphic information content (PIC) values were observed for markers RM6 (0.92) and RM10 (0.36), respectively. The coefficient of genetic similarity ranged between 0.45 and 1 for all basmati and coarse rice genotypes. Two pairs of coarse rice genotypes, Nagina/RD25 and Nagina/SUB-1, showed maximum divergence (0.42), with a similarity index of 0.58 for both pairs. In contrast, the maximum divergence (0.18) between three pairs of basmati rice genotypes—EF52/sup-23 and Super basmati, Sup/1138-2 and Lpa-56-3, and Sup/1138-2 and Basmati515—had a similarity index of 0.82. The similarity coefficient ranges showed a narrower genetic base for basmati rice genotypes as compared to coarse rice genotypes. Clustering based on agronomic and molecular analysis showed the clear differentiation of coarse and basmati rice into different groups, except in a few lines—Lpa-66-3-1, KSK-133, Nagina, SUB-4, and Sup1138/2—which showed some deviation from the trend. The study of genetic differences concluded that the genotypes of Cluster II and Cluster V are complementary for maximum desirable traits and could be selected for use in hybridization programs to develop promising F1 hybrids or transgressive segregants in subsequent generations.

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Acknowledgements

The authors extend their appreciation to the Researchers Supporting Project number (RSP-2023R369), King Saud University, Riyadh, Saudi Arabia.

Funding

No specific funding has been received to conduct present research.

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Authors and Affiliations

  1. NIAB-C, Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan

    Tahira Luqman, Zia-ul Qamar, Aqsa Tabasum, Amjad Hameed & Zahra Maryum

  2. Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan

    Zia-ul Qamar, Aqsa Tabasum & Amjad Hameed

  3. Rice Research Department, Agriculture Research Center, Field Crops Research Institute, Giza, Egypt

    Wael. H. El-Kallawy

  4. Centre for Agriculture and Bioscience International (CABI), Rawalpindi, 46000, Punjab, Pakistan

    Talha Nazir

  5. Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan

    Safira Attacha

  6. Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan

    Sajid Fiaz

  7. Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 5810, Sivas, Turkey

    Muhammad Azhar Nadeem

  8. Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-Ku, Niigata, 950-2181, Japan

    Itoh Kimiko

  9. Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia

    Kotb Attia

Authors
  1. Tahira Luqman
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  2. Zia-ul Qamar
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  3. Aqsa Tabasum
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  4. Wael. H. El-Kallawy
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  5. Talha Nazir
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  6. Safira Attacha
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  7. Sajid Fiaz
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  8. Muhammad Azhar Nadeem
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  9. Amjad Hameed
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  10. Zahra Maryum
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  11. Itoh Kimiko
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  12. Kotb Attia
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Contributions

Conceptualization, TL and ZQ; Data curation, TN, AT and AH; Formal analysis, TL and ZM; Methodology, TL; Resources, ZQ, WHE and IK; Writing—original draft, KA, TN, SF, MAN, SA and AT; Writing—review & editing, KA, ZM, AH and ZQ. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Sajid Fiaz or Zahra Maryum.

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This article does not contain any studies with human/animals performed by any of the authors.

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Research ethics

We also took appropriate permission from the farm or field owner during specimens’ collection and experimentation. We confirm that during the collection and execution of the experiment authors have complied with the IUCN Statement on Research Involving Species at Risk of Extinction and the Convention on the Trade in Endangered Species of Wild Fauna and Flora. All methods were performed in accordance with the relevant guidelines/regulations/legislation.

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Luqman, T., Qamar, Zu., Tabasum, A. et al. Genetic characterization of coarse and basmati rice (Oryza sativa L.) through microsatellite markers and morpho-agronomic traits. Genet Resour Crop Evol 70, 2307–2320 (2023). https://doi.org/10.1007/s10722-023-01620-w

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