Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [<i>Coffea arabica</i> L.] Genotypes Using ISSR Markers

Habtamu Gebreselassie; Bizuayehu Tesfaye; Andargachewu Gedebo; Yayis Rezene

doi:doi:10.11648/j.cbb.20251302.12

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Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers

Habtamu Gebreselassie^*

, Bizuayehu Tesfaye

, Andargachewu Gedebo, Yayis Rezene

Published in Computational Biology and Bioinformatics (Volume 13, Issue 2)

Received: 15 September 2025 Accepted: 29 September 2025 Published: 30 October 2025

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Abstract

Arabica coffee originated and diversified in Ethiopia, yet its considerable genetic diversity remains underutilized. This study assessed the genetic diversity and population structure of 50 Arabica coffee genotypes representing five populations (Sidama, Amaro, Jinka, Guji, and improved varieties) using inter-simple sequence repeat (ISSR) markers. The populations produced 74 distinct bands, with improved varieties showing the highest number of private bands (8) and lowest common bands (≤50%) at 6. Band frequency ranged from 8.62% (Guji) to 25.86% (improved varieties), averaging 17.93%. Genetic diversity parameters, including number of alleles per population, effective alleles, Shannon’s information index, observed diversity, and unbiased diversity, ranged from 0.276-0.672, 1.063-1.149, 0.052-0.12, 0.036-0.082, and 0.039-0.092, respectively. AMOVA revealed significant genetic variability, with 67% among populations and 33% within. Principal coordinate analysis explained 42.96% of total variation across three axes. UPGMA cluster analysis grouped the genotypes into four clusters (I-IV) containing 20%, 28%, 12%, and 40% of the genotypes, respectively, with genotypes from the same populations clustering together. Overall, the study demonstrated substantial genetic variation and population structure among South Ethiopian Arabica coffee genotypes, highlighting the potential for conservation and breeding efforts. Future studies should incorporate high-resolution markers and broader accession sets to better capture the genetic landscape of Ethiopian Arabica coffee.

Published in	Computational Biology and Bioinformatics (Volume 13, Issue 2)
DOI	10.11648/j.cbb.20251302.12
Page(s)	60-71
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2025. Published by Science Publishing Group

Keywords

Arabica Coffee, Genetic Polymorphism, Population Stracture, ISSR Markers

References

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Gebreselassie, H., Tesfaye, B., Gedebo, A., Rezene, Y. (2025). Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers. Computational Biology and Bioinformatics, 13(2), 60-71. https://doi.org/10.11648/j.cbb.20251302.12

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Gebreselassie, H.; Tesfaye, B.; Gedebo, A.; Rezene, Y. Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers. Comput. Biol. Bioinform. 2025, 13(2), 60-71. doi: 10.11648/j.cbb.20251302.12

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AMA Style

Gebreselassie H, Tesfaye B, Gedebo A, Rezene Y. Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers. Comput Biol Bioinform. 2025;13(2):60-71. doi: 10.11648/j.cbb.20251302.12

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@article{10.11648/j.cbb.20251302.12,
  author = {Habtamu Gebreselassie and Bizuayehu Tesfaye and Andargachewu Gedebo and Yayis Rezene},
  title = {Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers
},
  journal = {Computational Biology and Bioinformatics},
  volume = {13},
  number = {2},
  pages = {60-71},
  doi = {10.11648/j.cbb.20251302.12},
  url = {https://doi.org/10.11648/j.cbb.20251302.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20251302.12},
  abstract = {Arabica coffee originated and diversified in Ethiopia, yet its considerable genetic diversity remains underutilized. This study assessed the genetic diversity and population structure of 50 Arabica coffee genotypes representing five populations (Sidama, Amaro, Jinka, Guji, and improved varieties) using inter-simple sequence repeat (ISSR) markers. The populations produced 74 distinct bands, with improved varieties showing the highest number of private bands (8) and lowest common bands (≤50%) at 6. Band frequency ranged from 8.62% (Guji) to 25.86% (improved varieties), averaging 17.93%. Genetic diversity parameters, including number of alleles per population, effective alleles, Shannon’s information index, observed diversity, and unbiased diversity, ranged from 0.276-0.672, 1.063-1.149, 0.052-0.12, 0.036-0.082, and 0.039-0.092, respectively. AMOVA revealed significant genetic variability, with 67% among populations and 33% within. Principal coordinate analysis explained 42.96% of total variation across three axes. UPGMA cluster analysis grouped the genotypes into four clusters (I-IV) containing 20%, 28%, 12%, and 40% of the genotypes, respectively, with genotypes from the same populations clustering together. Overall, the study demonstrated substantial genetic variation and population structure among South Ethiopian Arabica coffee genotypes, highlighting the potential for conservation and breeding efforts. Future studies should incorporate high-resolution markers and broader accession sets to better capture the genetic landscape of Ethiopian Arabica coffee.
},
 year = {2025}
}

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TY  - JOUR
T1  - Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers

AU  - Habtamu Gebreselassie
AU  - Bizuayehu Tesfaye
AU  - Andargachewu Gedebo
AU  - Yayis Rezene
Y1  - 2025/10/30
PY  - 2025
N1  - https://doi.org/10.11648/j.cbb.20251302.12
DO  - 10.11648/j.cbb.20251302.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 60
EP  - 71
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20251302.12
AB  - Arabica coffee originated and diversified in Ethiopia, yet its considerable genetic diversity remains underutilized. This study assessed the genetic diversity and population structure of 50 Arabica coffee genotypes representing five populations (Sidama, Amaro, Jinka, Guji, and improved varieties) using inter-simple sequence repeat (ISSR) markers. The populations produced 74 distinct bands, with improved varieties showing the highest number of private bands (8) and lowest common bands (≤50%) at 6. Band frequency ranged from 8.62% (Guji) to 25.86% (improved varieties), averaging 17.93%. Genetic diversity parameters, including number of alleles per population, effective alleles, Shannon’s information index, observed diversity, and unbiased diversity, ranged from 0.276-0.672, 1.063-1.149, 0.052-0.12, 0.036-0.082, and 0.039-0.092, respectively. AMOVA revealed significant genetic variability, with 67% among populations and 33% within. Principal coordinate analysis explained 42.96% of total variation across three axes. UPGMA cluster analysis grouped the genotypes into four clusters (I-IV) containing 20%, 28%, 12%, and 40% of the genotypes, respectively, with genotypes from the same populations clustering together. Overall, the study demonstrated substantial genetic variation and population structure among South Ethiopian Arabica coffee genotypes, highlighting the potential for conservation and breeding efforts. Future studies should incorporate high-resolution markers and broader accession sets to better capture the genetic landscape of Ethiopian Arabica coffee.

VL  - 13
IS  - 2
ER  -

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Habtamu Gebreselassie

Crop Research Directorate, Wondo Genet Agricultural Research Center, Wondogenet, Ethiopia; Scool of Plant and Horticultural Science, Hawassa University, Hawassa, Ethiopia

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http://orcid.org/0000-0002-7495-8997
Bizuayehu Tesfaye

Scool of Plant and Horticultural Science, Hawassa University, Hawassa, Ethiopia

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http://orcid.org/0000-0002-4506-197X
Andargachewu Gedebo

Scool of Plant and Horticultural Science, Hawassa University, Hawassa, Ethiopia

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Yayis Rezene

Molecular Biology Research, Hawassa Agricultural Research Center, Hawassa, Ethiopia

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Gebreselassie, H., Tesfaye, B., Gedebo, A., Rezene, Y. (2025). Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers. Computational Biology and Bioinformatics, 13(2), 60-71. https://doi.org/10.11648/j.cbb.20251302.12

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Gebreselassie, H.; Tesfaye, B.; Gedebo, A.; Rezene, Y. Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers. Comput. Biol. Bioinform. 2025, 13(2), 60-71. doi: 10.11648/j.cbb.20251302.12

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AMA Style

Gebreselassie H, Tesfaye B, Gedebo A, Rezene Y. Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers. Comput Biol Bioinform. 2025;13(2):60-71. doi: 10.11648/j.cbb.20251302.12

Copy | Download

@article{10.11648/j.cbb.20251302.12,
  author = {Habtamu Gebreselassie and Bizuayehu Tesfaye and Andargachewu Gedebo and Yayis Rezene},
  title = {Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers
},
  journal = {Computational Biology and Bioinformatics},
  volume = {13},
  number = {2},
  pages = {60-71},
  doi = {10.11648/j.cbb.20251302.12},
  url = {https://doi.org/10.11648/j.cbb.20251302.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20251302.12},
  abstract = {Arabica coffee originated and diversified in Ethiopia, yet its considerable genetic diversity remains underutilized. This study assessed the genetic diversity and population structure of 50 Arabica coffee genotypes representing five populations (Sidama, Amaro, Jinka, Guji, and improved varieties) using inter-simple sequence repeat (ISSR) markers. The populations produced 74 distinct bands, with improved varieties showing the highest number of private bands (8) and lowest common bands (≤50%) at 6. Band frequency ranged from 8.62% (Guji) to 25.86% (improved varieties), averaging 17.93%. Genetic diversity parameters, including number of alleles per population, effective alleles, Shannon’s information index, observed diversity, and unbiased diversity, ranged from 0.276-0.672, 1.063-1.149, 0.052-0.12, 0.036-0.082, and 0.039-0.092, respectively. AMOVA revealed significant genetic variability, with 67% among populations and 33% within. Principal coordinate analysis explained 42.96% of total variation across three axes. UPGMA cluster analysis grouped the genotypes into four clusters (I-IV) containing 20%, 28%, 12%, and 40% of the genotypes, respectively, with genotypes from the same populations clustering together. Overall, the study demonstrated substantial genetic variation and population structure among South Ethiopian Arabica coffee genotypes, highlighting the potential for conservation and breeding efforts. Future studies should incorporate high-resolution markers and broader accession sets to better capture the genetic landscape of Ethiopian Arabica coffee.
},
 year = {2025}
}

Copy | Download

TY  - JOUR
T1  - Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers

AU  - Habtamu Gebreselassie
AU  - Bizuayehu Tesfaye
AU  - Andargachewu Gedebo
AU  - Yayis Rezene
Y1  - 2025/10/30
PY  - 2025
N1  - https://doi.org/10.11648/j.cbb.20251302.12
DO  - 10.11648/j.cbb.20251302.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 60
EP  - 71
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20251302.12
AB  - Arabica coffee originated and diversified in Ethiopia, yet its considerable genetic diversity remains underutilized. This study assessed the genetic diversity and population structure of 50 Arabica coffee genotypes representing five populations (Sidama, Amaro, Jinka, Guji, and improved varieties) using inter-simple sequence repeat (ISSR) markers. The populations produced 74 distinct bands, with improved varieties showing the highest number of private bands (8) and lowest common bands (≤50%) at 6. Band frequency ranged from 8.62% (Guji) to 25.86% (improved varieties), averaging 17.93%. Genetic diversity parameters, including number of alleles per population, effective alleles, Shannon’s information index, observed diversity, and unbiased diversity, ranged from 0.276-0.672, 1.063-1.149, 0.052-0.12, 0.036-0.082, and 0.039-0.092, respectively. AMOVA revealed significant genetic variability, with 67% among populations and 33% within. Principal coordinate analysis explained 42.96% of total variation across three axes. UPGMA cluster analysis grouped the genotypes into four clusters (I-IV) containing 20%, 28%, 12%, and 40% of the genotypes, respectively, with genotypes from the same populations clustering together. Overall, the study demonstrated substantial genetic variation and population structure among South Ethiopian Arabica coffee genotypes, highlighting the potential for conservation and breeding efforts. Future studies should incorporate high-resolution markers and broader accession sets to better capture the genetic landscape of Ethiopian Arabica coffee.

VL  - 13
IS  - 2
ER  -

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