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Single nucleotide polymorphism based assessment of genetic diversity in local and exotic onion genotypes

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Abstract

Background

Onion is an economically important vegetable cultivated worldwide on a large scale. Liberal exchange of germplasm and frequent selection caused narrow genetic diversity in most crops, including onion. Thus, it is essential to estimate and understand genetic diversity before launching of any breeding program. The current study was conducted to explore genetic diversity among 39 short-day onion genotypes (indigenous and exotic).

Methods and Results

All the genotypes were evaluated for various phenotypic traits by using single nucleotide polymorphism (SNP) genotyping based on KASPar assays. Principal component analysis (PCA) was performed to determine the variability among genotypes. The four principal components with eigenvalue greater than 1 accounted for 67.5656% variability for quantitative traits, whereas first five principal components with eigenvalue greater than 0.7 accounted for 86.24% variation among the genotypes for qualitative traits. The principal component analysis identified diverse traits including bulb weight, bulb diameter, plant height, number of survived plants and vitamin C. These traits were further analyzed through ANOVA (Analysis of Variance) following augmented block design to describe genotypic variability for selected traits. Onion genotypes showed significant variation for bulb weight, bulb diameter and Vitamin C. Genotypic clustering based on PCA showed that 15 indigenous genotypes were clustered with exotic genotypes (14) while remaining indigenous genotypes (10) were distant. A total of 30 SNPs were used for assessment of genetic diversity out of these, 24 SNPs were detected with polymorphic loci (0.8%, heterozygosity), while only six markers were with monomorphic sites (0.2% heterozygosity). Subsequently, population structure analysis revealed three different populations indicating significant variability.

Conclusion

Conclusively, a significant similarity between exotic and a group of indigenous genotypes indicates direct adoption of exotic genotypes or their sister lines. A further broadening of the genetic base is required and could be done by crossing distant genotypes.

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Acknowledgements

The authors extend their appreciation to Taif University for funding current work by Taif University Researchers Supporting Project number (TURSP-2020/85), Taif University, Taif, Saudi Arabia.

Funding

The current work was funded by Taif University Researchers Supporting Project number (TURSP-2020/85), Taif University, Taif, Saudi Arabia.

Author information

Authors and Affiliations

  1. Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan

    Najma Tabussam, Rashid Mehmood Rana, Fahad Masoud Wattoo & Sunny Ahmar

  2. Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan

    Azeem Iqbal Khan

  3. Institute of Food &, Nutritional Sciences PMAS-Arid Agriculture University, Rawalpindi, Pakistan

    Rai Muhammad Amir

  4. College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Talha Javed

  5. Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia

    Eldessoky S. Dessoky

  6. Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt

    Nader R. Abdelsalam

Authors
  1. Najma Tabussam
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  2. Rashid Mehmood Rana
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  3. Fahad Masoud Wattoo
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  4. Azeem Iqbal Khan
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  7. Sunny Ahmar
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by NT, FWM,  AIK, SA, TJ, ESD and NRA. The first draft of the manuscript was written by RMR and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Rashid Mehmood Rana.

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Tabussam, N., Rana, R.M., Wattoo, F.M. et al. Single nucleotide polymorphism based assessment of genetic diversity in local and exotic onion genotypes. Mol Biol Rep 49, 5511–5520 (2022). https://doi.org/10.1007/s11033-022-07431-z

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  • DOI: https://doi.org/10.1007/s11033-022-07431-z

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