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Genomic Insights into Climate Resilience: Tools and Strategies for Coffee...
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Genomic Insights into Climate Resilience: Tools and Strategies for Coffee Improvement

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 25 July 2026 | Viewed by 1965

Special Issue Editors

Dr. Marco Cristancho

E-Mail Website
Guest Editor
National Center for Coffee Research—CENICAFE, Chinchiná 173001, Colombia
Interests: plant sciences biochemistry; molecular biology genetics; heredity agriculture environmental sciences; ecology
Special Issues, Collections and Topics in MDPI journals
Dr. Jorge Berny

E-Mail Website
Guest Editor
World Coffee Research, Portland, OR 97225, USA
Interests: genetic resources; plant breeding; cultivar development

Special Issue Information

Dear Colleagues,

Genetic diversity is the cornerstone in building climate-resilient, high-yielding coffee systems. The strategic use of coffee genetic resources in breeding programs is critical in achieving this goal. Collecting, conserving, and characterizing coffee germplasm support crop improvement efforts, enabling the development of varieties that withstand drought, heat, pests, and diseases without compromising yield or quality. The efficient use of these genetic resources maximizes the impact of conservation investments, ensuring breeders have access to diverse, adaptable coffee genotypes for climate-smart development.

Advances in biotechnology—from genomics to metabolomics and pangenomics—are unlocking new insights into the genetic foundations of climate resilience in coffee. These cutting-edge tools accelerate the discovery of valuable traits, empowering targeted breeding for coffee varieties that can thrive in a changing climate.

This Special Issue, “Genomic Insights into Climate Resilience: Tools and Strategies for Coffee Improvement", highlights the latest research and innovations driving sustainable coffee production. We welcome contributions focusing on genomic tools, germplasm characterization, and breeding strategies that pave the way for climate-resilient coffee, securing the future of this vital crop amid global environmental challenges.

Dr. Marco Cristancho
Dr. Jorge Berny
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Horticulturae is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • climate-resilient coffee
  • genetic diversity
  • coffee germplasm
  • coffee breeding
  • genomics
  • sustainable
  • coffee production

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Published Papers (3 papers)

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Research

24 pages, 7544 KB  
Article
F1 Coffee Hybrids: Combining High Productivity with Genetic Resistance to Coffee Berry Borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae)
by Carmenza E. Góngora, Juan Carlos Arias-Suarez, Marisol Giraldo-Jaramillo, Rubén Medina-Rivera, Roosevelt Escobar and Claudia Patricia Flórez-Ramos
Horticulturae 2026, 12(6), 704; https://doi.org/10.3390/horticulturae12060704 (registering DOI) - 6 Jun 2026
Abstract
To identify Coffea arabica genotypes with enhanced resistance to the coffee berry borer (CBB), Hypothenemus hampei, two wild accessions (C306 and C534) and their derived hybrids were evaluated. Four F1 genotypes—H1 (CU1842 × C306), H2 (CX2385 × C534), H3 (CX2385 × C306), [...] Read more.
To identify Coffea arabica genotypes with enhanced resistance to the coffee berry borer (CBB), Hypothenemus hampei, two wild accessions (C306 and C534) and their derived hybrids were evaluated. Four F1 genotypes—H1 (CU1842 × C306), H2 (CX2385 × C534), H3 (CX2385 × C306), and H4 (CX2848 × C534)—were generated and subsequently mass-propagated in vitro via somatic embryogenesis. In the original F1 hybrids, laboratory bioassays using artificial coffee diets showed that while CBB mortality in susceptible controls (Var. Caturra and maternal lines) did not exceed 15%, paternal lines induced 31–49%, and hybrids H1 and H3 reached 26%. Population suppression was further quantified in infested parchment coffee, where these hybrids exhibited intermediate CBB numbers between parents. Subsequent field evaluations in Caldas, Colombia, confirmed that H1 and H3 maintained CBB populations up to 43% lower than maternal lines (p < 0.05). To verify the stability of the resistance trait after clonal multiplication, a five-year field study was conducted in Risaralda, Colombia, using in vitro-propagated clones. These regenerated hybrids (H1, H2, and H3) demonstrated stable phenotypic expression, achieving up to a 70% reduction in CBB populations in the field compared to commercial varieties. Specifically, H1 and H3 clones induced significantly higher insect mortality (up to 47%) and superior population suppression. Furthermore, by manifesting hybrid vigor, cumulative production was significantly higher in all four hybrids than in commercial controls, with H3, H1, and H4 exhibiting the highest yields. Based on the dual criteria of useful heterosis for yield and stable pest resistance, these results identify the most promising hybrid combinations which integrate elite agronomic traits with stable resistance, providing a strategic genetic resource for sustainable coffee production under climatic change conditions. Full article
(This article belongs to the Special Issue Genomic Insights into Climate Resilience: Tools and Strategies for Coffee Improvement)
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19 pages, 841 KB  
Article
Genetic Diversity and Structure in Coffea canephora Genotypes from the Amazon Region
by Shayenne Hevelyn Farias Fernandes, Caroline de Souza Bezerra, Santiago Linorio Ferreyra Ramos, Ricardo Lopes, Marcelo Curitiba Espíndula, Thaynara Silva Ramos, Rodrigo Rodrigues Matiello, Maria José Marques, Carlos Henrique Salvino Gadelha Meneses and Maria Teresa Gomes Lopes
Horticulturae 2026, 12(2), 250; https://doi.org/10.3390/horticulturae12020250 - 20 Feb 2026
Cited by 1 | Viewed by 850
Abstract
Coffea canephora is economically and socially important for small-scale agriculture in Northern Brazil. To identify genotypes adapted to Amazonian edaphoclimatic conditions, clones of the species have been evaluated across multiple locations in Amazonas. Introducing genetically selected materials into comparable environments may promote consistent [...] Read more.
Coffea canephora is economically and socially important for small-scale agriculture in Northern Brazil. To identify genotypes adapted to Amazonian edaphoclimatic conditions, clones of the species have been evaluated across multiple locations in Amazonas. Introducing genetically selected materials into comparable environments may promote consistent productivity gains in the short and medium term. In this context, the aim of this study was to assess the genetic diversity of different C. canephora genotypes using microsatellite markers, which will support the development of superior genotypes adapted to Amazon conditions. A total of 43 C. canephora genotypes were analyzed. Leaves were collected for genomic DNA extraction and were standardized and amplified by PCR using microsatellite primers. Genotyping was performed via capillary electrophoresis, allowing for the determination of allele sizes. Genetic structure was inferred, and genetic diversity parameters were estimated. The average observed heterozygosity (HO = 0.64) exceeded the expected heterozygosity (HE = 0.53), and the average inbreeding coefficient (f = −0.19) indicated an excess of heterozygotes. The results revealed high genetic variability among the evaluated genotypes. These findings highlight the broad genetic diversity of C. canephora, reinforcing its potential as a genetic basis for selection and the development of cultivars adapted to the environmental conditions of the Amazon. Full article
(This article belongs to the Special Issue Genomic Insights into Climate Resilience: Tools and Strategies for Coffee Improvement)
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20 pages, 4152 KB  
Article
Selection of High-Yielding Genotypes of Coffea canephora at Transitional Altitude: Adaptability and Stability and Impacts of Water Management
by Tafarel Victor Colodetti, Wagner Nunes Rodrigues, João Felipe de Brites Senra, Marcelo Curitiba Espindula, José Francisco Teixeira do Amaral, José Domingos Cochicho Ramalho and Marcelo Antonio Tomaz
Horticulturae 2026, 12(2), 207; https://doi.org/10.3390/horticulturae12020207 - 7 Feb 2026
Cited by 1 | Viewed by 701
Abstract
Expanding Coffea canephora cultivation to transitional altitudes offers a promising strategy to sustain coffee production under climate change. This study evaluated 27 genotypes cultivated under two water management regimes (fully and minimally irrigated) at 650 m altitude in Espírito Santo, Brazil, over eight [...] Read more.
Expanding Coffea canephora cultivation to transitional altitudes offers a promising strategy to sustain coffee production under climate change. This study evaluated 27 genotypes cultivated under two water management regimes (fully and minimally irrigated) at 650 m altitude in Espírito Santo, Brazil, over eight harvests (2018–2025). A split-plot design was analyzed using a three-way mixed model (REML/BLUP) to estimate genetic parameters and predicted genotypic values. Adaptability and stability were assessed using the harmonic mean of relative performance of genotypic values (HMRPGV) and weighted average of absolute scores (WAASB) and integrated into a multi-trait selection index. Significant genotypic and temporal effects were detected, while the interaction between genotypes and water management regimes was non-significant, indicating consistent performance under different water regimes. Broad-sense heritability was moderate, with high selective accuracy. Genotypes 108 and 203 achieved the highest predicted yields (91.4 and 86.8 bags ha−1) and superior adaptability. The multi-trait index identified six outstanding genotypes—108, 203, 201, 306, 303, and 302—combining high yield, broad adaptability, and temporal stability, resulting in an expected genetic gain of 8.17% in relation to the original population. These findings demonstrate that selected C. canephora genotypes are well adapted to transitional altitudes, supporting breeding programs for climate-resilient and high-yielding crops. Full article
(This article belongs to the Special Issue Genomic Insights into Climate Resilience: Tools and Strategies for Coffee Improvement)
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