Coffee Genetic Diversity and Genomics: A Bibliometric Tropical Perspective
DOI:
https://doi.org/10.11594/Kata Kunci:
Coffea, Coffee genetics, Genomics, Tropical agriculture, VOSviewerAbstrak
Coffee genetic resources play a fundamental role in supporting sustainable production, crop improvement, and climate resilience. Over the past decades, rapid advances in molecular genetics and genomics have transformed coffee research; however, a comprehensive understanding of the intellectual development, thematic evolution, and future research directions of this field remains limited. This study aimed to systematically map the global landscape of coffee genetics and genomics research through a bibliometric analysis of 867 English-language journal articles indexed in the Scopus database and published between 1974 and 2024. Bibliometric analyses were conducted using Microsoft Excel, Harzing's Publish or Perish, and VOSviewer to evaluate publication trends, leading journals, countries, authors, citation networks, co-authorship, co-citation, and thematic evolution based on co-occurrence and overlay visualizations. The results demonstrate a substantial increase in scientific output over the past five decades, with France and Brazil emerging as the leading contributors to publication productivity and international collaboration. Co-citation analysis identified Philippe Lashermes and Bertrand B. as central figures shaping the intellectual structure of the field, while thematic analyses revealed a clear transition from studies emphasizing genetic diversity and phylogenetic characterization toward integrative genomics, functional genomics, molecular breeding, bioinformatics, and high-throughput sequencing. The overlay visualization further indicates an increasing emphasis on computational biology and genomics-driven approaches in recent years. Overall, this study provides a comprehensive bibliometric perspective on the evolution of coffee genetics and genomics research and identifies future research priorities, including multi-omics integration, artificial intelligence-assisted genomic prediction, genome editing, and expanded genomic characterization of wild Coffea species to support biodiversity conservation and the development of climate-resilient coffee cultivars in tropical production systems.
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Referensi
Abascal, F., Zardoya, R., & Telford, M. J. (2010). TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic acids research, 38(suppl_2), W7-W13. CrossRef
Abad, P., Gouzy, J., Aury, J. M., Castagnone-Sereno, P., Danchin, E. G., Deleury, E., ... & Wincker, P. (2008). Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incogni-ta. Nature biotechnology, 26(8), 909-915. CrossRef
Abdelwahab, S. I., Taha, M. M. E., Jerah, A. A., Aljahdali, I. A., Oraibi, B., Alfaifi, H. A., ... & Farasani, A. (2024). Coffee arabica research (1932–2023): Performance, thematic evolution and mapping, global landscape, and emerging trends. Heliyon, 10(16). CrossRef
Abrhám, J., Vošta, M., Čajka, P., & Rubáček, F. (2021). The specifics of selected agricultural com-modities in international trade. Agricultural and Resource Economics: International Scien-tific E-Journal, 7(2), 5-19. CrossRef
Alemayehu, D., Benti, T., Beksisa, L., Merga, D., Getaneh, A., Tefera, F., & Addisu, M. (2023). The exploration and utilization of coffee (Coffea arabica L.) genetic resource in its center of origin. Journal of Global Agriculture and Ecology. CrossRef
Anthony, F., Combes, M.-C., Astorga, C., Bertrand, B., Graziosi, G., & Lashermes, P. (2002). The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theoret-ical and Applied Genetics, 104(5), 894–900. CrossRef
Ariyoshi, C., de Oliveira, F. F., Shigueoka, L. H., da Silva, A. G., Arias, A. G., Villalta-Villalobos, J., ... & Pereira, L. F. P. (2022). Current challenges and genomic advances toward the develop-ment of coffee genotypes resistant to biotic stress. Genomic designing for biotic stress re-sistant technical crops, 159-189. CrossRef
Bergheaud, V., Audergon, J. M., Bellec, A., Delaunay, A., Duminil, J., Dussert, S., ... & Adam-Blondon, A. F. (2025). Organization of plant Biological Resource Centers for research in France: History, evolution and current status.
Bilen, C., El Chami, D., Mereu, V., Trabucco, A., Marras, S., & Spano, D. (2022). A systematic re-view on the impacts of climate change on coffee agrosystems. Plants, 12(1), 102.
CrossRef
Chawla, R. N., & Goyal, P. (2022). Emerging trends in digital transformation: a bibliometric anal-ysis. Benchmarking: An International Journal, 29(4), 1069-1112. CrossRef
Cahyono, A. A., Ardie, S. W., Rubiyo, R., & Sudarsono, S. (2024). Genetic Diversity of Yellow and Red Berries Arabica Coffee Populations Grown in a Mix Populations in Garut, West Java, In-donesia, Based on SSR Markers. Journal of Tropical Crop Science, 11(03), 207–216. Cross-Ref
Campuzano-Duque, L. F., Herrera, J. C., Ged, C., & Blair, M. W. (2021). Bases for the establishment of robusta coffee (Coffea canephora) as a new crop for Colombia. Agronomy, 11(12), 2550. CrossRef
Cortés, A. J., & Du, H. (2023). Molecular genetics enhances plant breeding. International Journal of Molecular Sciences, 24(12), 9977. CrossRef
Cudjoe, D. K., Virlet, N., Castle, M., Riche, A. B., Mhada, M., Waine, T. W., ... & Hawkesford, M. J. (2023). Field phenotyping for African crops: overview and perspectives. Frontiers in Plant Science, 14, 1219673. CrossRef
Davis, A. P., Chadburn, H., Moat, J., O’Sullivan, R., Hargreaves, S., & Nic Lughadha, E. (2019). High extinction risk for wild coffee species and implications for coffee sector sustainabil-ity. Science advances, 5(1), eaav3473. CrossRef
Dwivedi, S. L., Chapman, M. A., Abberton, M. T., Akpojotor, U. L., & Ortiz, R. (2023). Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of un-derutilized pulses. Frontiers in Genetics, 14, 1193780. CrossRef
Etienne, H., Breton, D., Breitler, J. C., Bertrand, B., Déchamp, E., Awada, R., ... & Ducos, J. P. (2018). Coffee somatic embryogenesis: how did research, experience gained and innova-tions promote the commercial propagation of elite clones from the two cultivated spe-cies?. Frontiers in Plant Science, 9, 1630. CrossRef
Ferrão, L. F. V., Caixeta, E. T., Souza, F. de F., Zambolim, E. M., Cruz, C. D., Zambolim, L., & Sa-kiyama, N. S. (2013). Comparative study of different molecular markers for classifying and establishing genetic relationships in Coffea canephora. Plant Systematics and Evolution, 299(1), 225–238. CrossRef
Góngora Orjuela, A. (2010). The importance of bibliometric studies. The Orinoquia case. Ori-noquia, 14(2), 121–122.
Guadalupe, G. A., Grandez-Yoplac, D. E., García, L., & Doménech, E. (2024). A comprehensive bib-liometric study in the context of chemical hazards in coffee. Toxics, 12(7), 526.
Gutiérrez-Salcedo, M., Martínez, M. Á., Moral-Munoz, J. A., Herrera-Viedma, E., & Cobo, M. J. (2018). Some bibliometric procedures for analyzing and evaluating research fields. Applied intelligence, 48(5), 1275-1287. CrossRef
Isfandyari-Moghaddam, A., Saberi, M. K., Tahmasebi-Limoni, S., Mohammadian, S., & Naderbeigi, F. (2023). Global scientific collaboration: A social network analysis and data mining of the co-authorship networks. Journal of Information Science, 49(4), 1126-1141. CrossRef
Kage, U., Kumar, A., Dhokane, D., Karre, S., & Kushalappa, A. C. (2016). Functional molecular markers for crop improvement. Critical reviews in biotechnology, 36(5), 917-930. CrossRef
Kakoulidou, I., Avramidou, E. V., Baránek, M., Brunel-Muguet, S., Farrona, S., Johannes, F., ... & Maury, S. (2021). Epigenetics for crop improvement in times of global change. Biology, 10(8), 766. CrossRef
Krishnan, S., Matsumoto, T., Nagai, C., Falconer, J., Shriner, S., Long, J., ... & Vega, F. E. (2021). Vulnerability of coffee (Coffea spp.) genetic resources in the United States. Genetic Re-sources and Crop Evolution, 68(7), 2691-2710. CrossRef
Krishnan, S. (2022). Coffee: Genetic diversity, erosion, conservation, and utilization. CrossRef
Kumar, M., Kumari, S., Guntipally, S. S., Chhabra, A., Kumar, A., & Kumar, P. (2024). A step-by-step guide of bibliometric study for healthcare and allied research. Journal of Pharmacy and Bioallied Sciences, 16(Suppl 4), S4114–S4116.
Kumar, R. (2025). Bibliometric analysis: comprehensive insights into tools, techniques, applica-tions, and solutions for research excellence. Spectrum of Engineering and Management Sci-ences, 3(1), 45-62. CrossRef
Liu, X., & Zhang, W. (2024). Bioinformatics in the age of big data: leveraging computational tools for biological discoveries. Computational Molecular Biology, 14. CrossRef
Madrid-Casaca, H., Salazar-Sepúlveda, G., Contreras-Barraza, N., Gil-Marín, M., & Vega-Muñoz, A. (2021). Global trends in coffee agronomy research. Agronomy, 11(8), 1471. CrossRef
Magos Brehm, J., Gaisberger, H., Kell, S., Parra‐Quijano, M., Thormann, I., Dulloo, M. E., & Maxted, N. (2022). Planning complementary conservation of crop wild relative diversity in southern Africa. Diversity and Distributions, 28(7), 1358-1372. CrossRef
Mohamad, M., Rahman, N. R. A., Nahar, H. S., & Alfi, C. F. (2023). what can we glean from the past seven decades of voluntary carbon emissions disclosure research?. International Journal of Energy Economics and Policy, 13(5), 83-97. CrossRef
Nasiro, K. (2024). Arabica coffee: Genetic diversity, conservation challenges, and breeding ap-proaches. International Journal of Food Science and Biotechnology, 9(4), 80–106. CrossRef
Ngure, G. M., & Watanabe, K. N. (2024). Coffee sustainability: leveraging collaborative breeding for variety improvement. Frontiers in Sustainable Food Systems, 8, 1431849. CrossRef
Notredame, C., Higgins, D. G., & Heringa, J. (2000). T-Coffee: A novel method for fast and accu-rate multiple sequence alignment. Journal of molecular biology, 302(1), 205-217. CrossRef
Pedrazzani, S., Maquia, I., Partelli, F. L., Ramalho, J. C., Marques, I. C. dos S. L., & Ribeiro-Barros, A. I. (2023). Genomic evaluation of Coffea arabica and its wild relative Coffea racemosa in Mozambique: Settling resilience keys for the coffee crop in the context of climate change. Plants, 12(10), 2044. CrossRef
Sabonsolin, J., & Lao, D. (2026). A comprehensive systematic literature review of multiple se-quence alignment algorithms. Discover Computing, 29(1), 33. CrossRef
Sallin, V. P., Lira, J. M. S., Falqueto, A. R., Arantes, L. D. O., & Dousseau-Arantes, S. (2024). Trends and findings in the rooting of conilon coffee: a bibliometric review. Ciência Rural, 55(02), e20240105. CrossRef
Santana, L. S., Ferraz, G. A. E. S., Teodoro, A. J. D. S., Santana, M. S., Rossi, G., & Palchetti, E. (2021). Advances in precision coffee growing research: A bibliometric review. Agronomy, 11(8), 1557.
Singh, R. K., Prasad, A., Muthamilarasan, M., Parida, S. K., & Prasad, M. (2020). Breeding and bio-technological interventions for trait improvement: status and prospects. Planta, 252(4), 54. CrossRef
Singh, R. K., Sood, P., Prasad, A., & Prasad, M. (2021). Advances in omics technology for improv-ing crop yield and stress resilience. Plant Breeding, 140(5), 719-731. CrossRef
Spinoso-Castillo, J. L., Corona-Torres, T., Escamilla-Prado, E., Morales-Ramos, V., Aguilar-Rincón, V. H., & García-de los Santos, G. (2021). Genetic diversity of Coffea arabica L.: A genomic approach. IntechOpen. CrossRef
Suryana, A. T., Saleh, Y., Dewi, T. G., & Rahayu, H. S. P. (2024). Global competitiveness of coffee products: A comparative study of Indonesia and Vietnam. CrossRef
Tapaça, I. D. P. E., Mavuque, L., Corti, R., Pedrazzani, S., Maquia, I. S., Tongai, C., ... & Ribeiro-Barros, A. I. (2023). Genomic evaluation of Coffea arabica and its wild relative Coffea race-mosa in Mozambique: Settling resilience keys for the coffee crop in the context of climate change. Plants, 12(10), 2044. CrossRef
Torok, A., Mizik, T., & Jambor, A. (2018). The competitiveness of global coffee trade. International Journal of Economics and Financial Issues, 8(5), 1.
Vegro, C. L. R., & de Almeida, L. F. (2020). Global coffee market: Socio-economic and cultural dynamics. In Coffee consumption and industry strategies in Brazil (pp. 3-19). Woodhead Publishing. CrossRef
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