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Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers

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Abstract

Background

Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems.

Materials and methods

In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification.

Results

The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin.

Conclusions

A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.

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Acknowledgements

We would like to thank the Scientific and Technological Research Council of Turkey (TUBITAK; Project IDs: 115R042, 109O163 and 119R013), USDA-ARS Germplasm Resources Information Network (GRIN), Research Institutes of the Republic of Turkey Ministry of Agriculture and Forestry, and commercial companies for supplying plant materials used in this study. The authors are grateful to Bolu Abant Izzet Baysal University Scientific Research Projects Coordination Unit (2021.10.06.1495 and 2021.10.07.1518).

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Authors and Affiliations

  1. Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey

    Mehmet Zahit Yeken, Orkun Emiralioğlu & Vahdettin Çiftçi

  2. Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey

    Harun Bayraktar & Gülsüm Palacioğlu

  3. Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey

    Göksel Özer

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  1. Mehmet Zahit Yeken
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  2. Orkun Emiralioğlu
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  3. Vahdettin Çiftçi
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  5. Gülsüm Palacioğlu
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  6. Göksel Özer
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Contributions

Investigation, G.Ö., M.Z.Y., O.E.; Methodology, writing-review and editing G.Ö., M.Z.Y.; Statistical analysis, G.Ö., G.P., H.B.; Visualization, V.Ç., H.B.; Resources, V.Ç. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Göksel Özer.

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Yeken, M.Z., Emiralioğlu, O., Çiftçi, V. et al. Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers. Mol Biol Rep 49, 3839–3847 (2022). https://doi.org/10.1007/s11033-022-07229-z

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