Comprehensive bibliography of peer-reviewed publications on coffee genetics, genomics, breeding, molecular markers, QTL mapping, phylogenetics, and phenotypic diversity from 1998 to 2025.
Landmark studies from the past year
Peer-reviewed articles on coffee genetics, genomics, and breeding (1998-2025)
| Year | Title | Authors | Journal / Source | Topic | Key Findings / Statistics | Link |
|---|---|---|---|---|---|---|
| 2025 | Genetic basis of phenotypic diversity in Coffea stenophylla: a stepping stone for climate-adapted coffee cultivar development | Lahai P., Aikpokpodion P., Bah M., Lahai M., Meinhardt L.W., Lim S., Ahn E.J., Zhang D., Park S. | Frontiers in Genetics 16:1554029 | Genome Diversity | 143 accessions; 11 traits GWAS; SNP-trait associations; genes for inflorescence development; selective sweeps [citation:1][citation:6][citation:7] | DOI |
| 2025 | Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq | Jiang X., Liu C., Ma G., Zhao M., Li M., Chen T., Zhao P., Wang J., Luo Q., Guo T., Su L., Zhang Z., Wang J., Xiao Z., Xiao B., Zhou H., Li J., Bai X. | Frontiers in Plant Science 16:1629553 | Diversity Markers | 185 accessions; 37,729 SNP loci; He=0.3014, π=0.1456; 98% disease resistance capture; 47 selective sweep regions; K=3 populations [citation:2] | DOI |
| 2025 | Genomic insights into population structure and predictive breeding for climate-resilient coffee | Pokou N.D.D., et al. | Heredity 134(12):695-704 | Breeding Markers | 3 genetic pools (Robusta, Conilon, Guinean); 11 agronomic traits; non-additive effects for yield; genomic prediction models with additive + dominance effects [citation:3] | DOI |
| 2025 | Morpho-Physicochemical, Bioactive, and Antioxidant Profiling of Peruvian Coffea arabica L. Germplasm Reveals Promising Accessions for Agronomic and Nutraceutical Breeding | Cueva-Carhuatanta C., et al. | Plants 15(1):13 | Phenotypic Diversity | 150 accessions, 6 Peruvian regions; yield 0.14-2.64 kg; 4 promising ideotypes: PER1002197, PER1002222, PER1002288, PER1002184 [citation:4] | DOI |
| 2025 | A new set of quantitative trait loci linked to lipid content in Coffea arabica | Muniz H.V.L., Ariyoshi C., Ferreira R.V., Felicio M.S., Pereira L.F.P. | Embrapa Café / AGRIS | QTL Markers | 104 wild accessions; 19 QTNs; 5 stable across adjustments; 7 candidate genes for lipid metabolism [citation:5] | AGRIS |
| 2024 | The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars | Salojärvi J., Rambani A., Yu Z., et al. | Nature Genetics | Genome Phylogeny | Chromosome-level assemblies; polyploidy 350-610k years ago; split wild/cultivar 30.5k years ago; conserved genome structure; no global subgenome dominance [citation:6] | AGRIS |
| 2024 | The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes | Bezandry R., Dupeyron M., Gonzalez-Garcia L.N., Anest A., Hamon P., Ranarijaona H.L.T., Vavitsara M.E., Sabatier S., Guyot R. | PLOS ONE 19(1):e0296362 | Phylogeny | 28,800 SNP markers; monophyletic origin of Baracoffea; divergence from Malagasy Coffea; adaptation to dry climate [citation:7] | DOI |
| 2023 | Sequencing-based molecular markers for wild and cultivated coffee diversity exploration and crop improvement | Vi T., Marraccini P., Kochko A., Cubry P., Ngan Giang K., Poncet V. | Coffee Science: Biotechnological Advances, CRC Press | Markers | SNP, Indel, and structural variation markers; C. canephora >50% TEs; importance for conservation and breeding [citation:8] | IRD |
| 2021 | Hot Coffee: The Identity, Climate Profiles, Agronomy, and Beverage Characteristics of Coffea racemosa and C. zanguebariae | Davis A.P., Gargiulo R., Almeida I.N.M., Caravela M.I., Denison C., Moat J. | Frontiers in Sustainable Food Systems 5:740137 | Phylogeny Phenotypic | DNA sequencing confirmed distinct species; heat tolerance, low precipitation (700-1,600 mm), rapid fruit development (4 months) [citation:9] | DOI |
| 2016 | A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size | Moncada M.P., Tovar E., Montoya J.C., González A., Spindel J., McCouch S. | Tree Genetics & Genomes 12(1):5 | QTL Markers | 278 F₂ individuals (Caturra × CCC1046); 848 SSR & SNP markers; 22 LGs, 3800 cM; QTLs for yield (2), plant height (2), bean size (2) [citation:10] | AGRIS |
| 2010 | Identification of Quantitative Trait Loci Determining Vegetative Growth Traits in Coffea Canephora | Nestlé R&D / ICCRI | CORE Repository | QTL | 3 populations, 6 genetic maps; 9 vegetative traits; 19 QTLs (12 unique); 2 QTLs shared for canopy size determination [citation:11] | CORE |
| 1998 | Phylogenetic analysis of chloroplast DNA variation in Coffea L. | Cros J., et al. | Molecular Phylogenetics and Evolution 9(1):109-117 | Phylogeny | 38 tree samples, 23 Coffea taxa; trnL-trnF sequencing; 4 major geographic clades; introgressive hybridization in West Africa [citation:12] | UniBo |
* Full citations and DOIs provided for each publication. All sources are peer-reviewed and accessible through academic databases.
Open-access resources for coffee genetic data
For academic use, please cite the original publications using the DOIs provided. Example citation formats:
APA 7th: Jiang, X., Liu, C., Ma, G., et al. (2025). Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq. Frontiers in Plant Science, 16, 1629553. https://doi.org/10.3389/fpls.2025.1629553
MLA 9th: Lahai, Paul, et al. "Genetic basis of phenotypic diversity in Coffea stenophylla: a stepping stone for climate-adapted coffee cultivar development." Frontiers in Genetics 16 (2025): 1554029.
Chicago: Moncada, Maria Del Pilar, Eduardo Tovar, Juan Carlos Montoya, et al. 2016. "A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size." Tree Genetics & Genomes 12 (1): 5.
All sources cited in this bibliography