ArticlePlant biotechnology journal2018
Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.
Article in Plant biotechnology journal, 2018. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed, 66 citations in OpenAlex.
- Contrasting regulation of protein-coding genes and lncRNA homeologs in allotetraploid Coffea arabica.Planta · 2026Article
- Article
- Application and Progress of Genomics in Deciphering the Genetic Regulation Mechanisms of Plant Secondary Metabolites.Plants (Basel, Switzerland) · 2025Review
- Evolution of the biochemistry underpinning purine alkaloid metabolism in plants.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Genome-wide identification and expression analysis of the U-box gene family related to biotic and abiotic stresses in Coffea canephora L.BMC genomics · 2024Article
- The Genome of Vitis zhejiang-adstricta Strengthens the Protection and Utilization of the Endangered Ancient Grape Endemic to China.Plant & cell physiology · 2024Article
- A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm.Nature communications · 2024Article
- Hair Growth Promotion and Anti-Hair Loss Effects of By-Products Arabica Coffee Pulp Extracts Using Supercritical Fluid Extraction.Foods (Basel, Switzerland) · 2023Article
- Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes.BMC genomic data · 2023Article
- SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm.Molecular biology reports · 2022Article
- Transcriptome and carotenoid profiling of different varieties ofPlant diversity · 2022Article
- Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.Molecular biology and evolution · 2022Article
- Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern.BMC plant biology · 2022Article
- Genome-Wide Identification, Characterization, and Comparative Analysis ofFrontiers in plant science · 2022Article
- LysM receptors in Coffea arabica: Identification, characterization, and gene expression in response to Hemileia vastatrix.PloS one · 2022Article
- A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (GigaByte (Hong Kong, China) · 2022Article
- A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome.Genes · 2021Article
- Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis.Nature communications · 2021Article
- Omics Technologies to Enhance Plant Based Functional Foods: An Overview.Frontiers in genetics · 2021Review
- Functioning of PPR Proteins in Organelle RNA Metabolism and Chloroplast Biogenesis.Frontiers in plant science · 2021Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high- or low-caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long-read (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway-based analysis, 65 caffeine-associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee.
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