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Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers

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Abstract

Background

Upland cotton is one of the utmost significant strategic fiber crops, and play a vital role in the global textile industry.

Methods and results

A total of 128 genotypes comprised Gossypium hirsutum L, Gossypium barbadense L., and pure lines were used to examine genetic diversity using iPBS-retrotransposon markers system. Eleven highly polymorphic primers yielded 287 bands and 99.65% polymorphism was recorded. The mean polymorphism information content was estimated at 0.297 and the average diversity indices for the effective number of alleles, Shannon’s information index, and overall gene diversity were 1.481, 0.443, and 0.265, respectively. The analysis of molecular variance (AMOVA) revealed that 69% of the genetic variation was within the population. A model-based STRUCTURE algorithm divided the entire germplasm into four populations and one un-classified population, the genotypes G42 (originating in Egypt) and G128 (originating in the United States), showed the highest genetic distance (0.996) so these genotypes could be suggested for breeding programs as parental lines.

Conclusions

This is the first investigation using an iPBS-retrotransposon marker system to examine the genetic diversity and population structure of upland cotton germplasm. The rich diversity found in upland cotton germplasm could be exploited as a genetic resource when developing breeding programs and could also help with efforts to breed cotton around the world. These findings also show the applicability and effectiveness of iPBS-retrotransposons for the molecular characterization of cotton germplasm.

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Data Availability

The datasets used for the current study ıs provided in this manuscript.

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Acknowledgements

We would like to thank the Nazilli Cotton Research Institute and Prof. Dr. Mefhar Gültekin TEMİZ from the Faculty of Agriculture, University of Dicle (Diyarbakir, Turkey) for their assistance in supplying the cotton genetic materials used in this study.

Funding

Authors are grateful to Dicle University - Scientific Research Projects Coordinating Office for financial support (Project No: ZİRAAT.20.004).

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Authors and Affiliations

  1. Faculty of Applied Sciences, Department of Plant Production and Technologies, Mus Alparslan University, Mus, Turkey

    Nurettin Baran

  2. Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana, Turkey

    Flavien Shimira

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

    Muhammad Azhar nadeem, Muhammad Tanveer altaf & Faheem Shehzad Baloch

  4. Department of Plant and Animal Production, Organic Agriculture Program Batman, Batman University Sason Vocational School, Batman, Turkey

    Mehtap andirman

  5. Faculty of Agriculture, Department of Field Crops, Dicle University, Diyarbakır, Turkey

    Mefhar Gültekin Temiz

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  1. Nurettin Baran
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Correspondence to Faheem Shehzad Baloch.

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Baran, N., Shimira, F., nadeem, M.A. et al. Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers. Mol Biol Rep 50, 4799–4811 (2023). https://doi.org/10.1007/s11033-023-08399-0

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