ArticlePlant biotechnology journal2019
Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.
Article in Plant biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Farmers' indigenous knowledge in the management of coffee berry disease caused by Colletotrichum kahawae and its status assessment.Journal of ethnobiology and ethnomedicine · 2026Article
- Uncovering the historic genetic diversity of Ugandan Robusta coffee germplasm: a foundation for core collection design.BMC plant biology · 2026Article
- Molecular marker applications and functional genomics of drought tolerance in Coffea canephora: a comprehensive review.Molecular biology reports · 2026Review
- Genomic discrimination of the botanical groups conilon and robusta of Coffea canephora.Scientific reports · 2026Article
- Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressedFrontiers in plant science · 2026Article
- Genomic insights into population structure and predictive breeding for climate-resilient coffee.Heredity · 2025Article
- Article
- Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq.Frontiers in plant science · 2025Article
- Coffee Breeding and Stress Biology.Plants (Basel, Switzerland) · 2024Article
- Identification of SNP Markers and Candidate Genes Associated with Major Agronomic Traits inPlants (Basel, Switzerland) · 2024Article
- Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo.Annals of botany · 2024Article
- The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.Nature genetics · 2024Article
- Convention on Biological Diversity (CBD) and the Nagoya Protocol: Implications and Compliance Strategies for the Global Coffee Community.Foods (Basel, Switzerland) · 2024Article
- Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity.PloS one · 2024Article
- Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee.Genome biology and evolution · 2023Article
- Article
- Intraspecific variation in growth response to drought stress across geographic locations and genetic groups inEcology and evolution · 2023Article
- Multiplex CRISPR/Cas9-mediated knockout of the phytoene desaturase gene in Coffea canephora.Scientific reports · 2022Article
- SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm.Molecular biology reports · 2022Article
- A review of the indigenous coffee resources of Uganda and their potential for coffee sector sustainability and development.Frontiers in plant science · 2022Article
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24 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
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