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Agro-morphological and genetic diversity studies in Rice (Oryza sativa L.) germplasm using microsatellite markers

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Abstract

Background

Knowledge of the genetic diversity and population structure of germplasm collections is an important foundation for crop improvement. Rice production across a broad range of rice-growing environments results in a diverse array of local rice varieties. Many rice varieties have been lost as a result of biodiversity loss and are now grown in Pakistan.

Methods and results

To protect the biodiversity of rice varieties, an experiment was carried out to check the genetic and morphological variations between 8 exotic and 7 local rice genotypes, using 5 different SSR markers, i.e., RM3, RM259, RM341, RM520, and RM11943. The analysis of morphological and quality traits of rice observed significant variation across genotypes. The results revealed that genotype Irri-Pak attained the highest plant height and primary branch plant-1, while genotype Mushkan produced a higher number of productive tillers and obtained a higher fertility factor (%). Similarly, the highest value for panicle length was observed for genotype Faker-e-Malakand, 1000-grains weight in genotype Calmochi, and maximum days to maturity was noticed in genotype Swati-2014. Moreover, the genotype Brio attained the highest value of stem diameter, while maximum seed length was noted in the genotype Sug Dasi. The highest number of primary branches plant−1 in genotype Ibge-I and secondary branches plant−1 in genotype Calmochi were noticed. A higher concentration of sodium and potassium was observed for the genotype Marte, while the genotype Muskan attained the maximum content of copper. Moreover, the highest concentration of iron in genotype Originario, zinc in genotype JP-5, and cadmium content were noticed in genotype Ibge. Similarly, the dendrogram analysis for quantitative parameters showed three clusters at 74.13% similarities. Whereas all the genotypes of European origin formed a separate cluster. A set of 5 simple sequence repeat primers, covering four chromosomes, amplified a total of 14 alleles and showed 100% polymorphism with an average PIC value ranging from 0.39 to 0.91. The UPGMA cluster analysis separated the 15 rice genotypes into 3 main groups based on 32.5% similarities and the highest genetic distance (45.1%) was observed between two genotypes (Fakher-e-malakand and Musa), having different geographical origins. There was no genetic distance between the genotypes Marte and Brio, irrespective of having the same origin.

Conclusions

The maximum genetic distances were noted for genotype, Fakhre-e-Malakand and Musa having a different origin, while the minimum genetic distance was shown by genotypes, Marte and Onice, from the same origin.

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Data availability

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Abbreviations

AFLPs:

Amplified fragment length polymorphisms

CTAB:

Cetyltrimethylammonium bromide

ISSR:

Inter simple sequence repeat

PCR:

Microsatellite-primed PCR

RAPD:

Random amplified polymorphic DNA

SSRs:

Simple sequence repeats

ISSRs:

Inter simple sequence repeats

SNPs:

Single nucleotide polymorphisms

EDTA:

Ethylenediaminetetraacetic acid

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Authors and Affiliations

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

    Shiraz Mehmood, Israr Ud Din & Syed Saad Hussain Shah

  2. Department of Horticulture, The University of Agriculture, Peshawar, Pakistan

    Izhar Ullah & Abdul Basit

  3. Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, Egypt

    Heba I. Mohamed

  4. Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan

    Mudassar Nawaz Khan

  5. Horticulture Technologies Production System Unit, Natural Resources Institute (Luke), Toivonlinnantie 518, 21500, Piikkiö, Finland

    Attiq ur Rehman

  6. Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, 00790, Helsinki, Finland

    Attiq ur Rehman

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  1. Shiraz Mehmood
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  2. Israr Ud Din
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  4. Heba I. Mohamed
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Contributions

SM, IUD, IU, AB, MNK, SS, AR: conceived and designed the experiments, SM, IUD, IU, AB, MNK, SS, AR: performed the experiments, SM, IUD, IU, AB, MNK, SS, AR: analyzed the data, SM, IUD, IU, AB, MNK, SS, AR: contributed to materials, tools, and wrote the manuscript, HIM: reviewed and editing the manuscript.

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Correspondence to Israr Ud Din or Heba I. Mohamed.

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Mehmood, S., Ud Din, I., Ullah, I. et al. Agro-morphological and genetic diversity studies in Rice (Oryza sativa L.) germplasm using microsatellite markers. Mol Biol Rep 48, 7179–7192 (2021). https://doi.org/10.1007/s11033-021-06710-5

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