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Coffee tree: Coffea canephora. (A) Tree carrying fruits. (B) Flowers. (C) Mature fruits.

Coffee tree: Coffea canephora. (A) Tree carrying fruits. (B) Flowers. (C) Mature fruits.

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Coffee is the second most valuable commodity exported by developing countries. The Coffea genus comprises over 103 species but coffee production uses only two species throughout the tropics: Coffea canephora, which is self-sterile and diploid and better known as Robusta, and C. arabica, which is self-fertile and tetraploid. With the arrival of new...

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... Statistics, 2004) but is the second most valuable commodity exported by developing countries, and more than 75 million people depend on coffee for all or most of their livelihood (Pendergrast, 2009). Coffee is currently produced throughout the tropics, the two main cultivated species being Coffea canephora (better known as Robusta) and C. arabica (Fig. ...

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... During the 1990's, the availability of DNA based molecular markers allowed a rapid progress in coffee genomics. As for other crops, early genomic studies in Coffea were mainly focused on assessing the genetic diversity and phylogenetic relationships, constructing genetic maps and identifying quantitative trait loci (QTLs) (reviewed by Lashermes et al. 2008;de Kochko et al. 2010). Genetic diversity was investigated from several molecular markers in wild Coffea species and, with a larger effort, in C. arabica and C. canephora. ...
... For C. canephora, the first genetic maps were constructed as soon as molecular markers became available for Coffea (reviewed by de Kochko et al. 2010). In 2014, the most complete genome sequence of C. canephora (accession number: PRJEB4211) was published along with a high-density genetic map constructed using several molecular markers and 3,230 loci distributed on 11 linkage groups, the same basic chromosome number of this species (x = 11). ...
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Main conclusion Coffea karyotype organization and evolution has been uncovered by classical cytogenetics and cytogenomics. We revisit these discoveries and present new karyotype data. Abstract Coffea possesses ~ 124 species, including C. arabica and C. canephora responsible for commercial coffee production. We reviewed the Coffea cytogenetics, from the first chromosome counting, encompassing the karyotype characterization, chromosome DNA content, and mapping of chromosome portions and DNA sequences, until the integration with genomics. We also showed new data about Coffea karyotype. The 2n chromosome number evidenced the diploidy of almost all Coffea, and the C. arabica tetraploidy, as well as the polyploidy of other hybrids. Since then, other genomic similarities and divergences among the Coffea have been shown by karyotype morphology, nuclear and chromosomal C-value, AT and GC rich chromosome portions, and repetitive sequence and gene mapping. These cytogenomic data allowed us to know and understand the phylogenetic relations in Coffea, as well as their ploidy level and genomic origin, highlighting the relatively recent allopolyploidy. In addition to the euploidy, the role of the mobile elements in Coffea diversification is increasingly more evident, and the comparative analysis of their structure and distribution on the genome of different species is in the spotlight for future research. An integrative look at all these data is fundamental for a deeper understanding of Coffea karyotype evolution, including the key role of polyploidy in C. arabica origin. The ‘Híbrido de Timor’, a recent natural allotriploid, is also in the spotlight for its potential as a source of resistance genes and model for plant polyploidy research. Considering this, we also present some unprecedented results about the exciting evolutionary history of these polyploid Coffea.
... Finally, a recent review provides an overview of cocoa production and recent advances in biotechnology for cocoa improvement (Wickramasuriya and Dunwell, 2019). The coffee story (De Kochko et al., 2010) is fairly similar to the cocoa one. The complete genome was reported and opened the way to further improvement strategies (Tran et al., 2016). ...
... Los marcadores moleculares se han utilizado en café para evaluar la diversidad genética de las especies y construir mapas genéticos (De-Kochko et al. 2010), así como para la evaluación de introgresión, determinación del modo de herencia de enfermedad y resistencia a plagas, evaluación de calidad de bebida y análisis e identificación de loci de rasgos cuantitativos (QTL), los cuales tienen implicaciones claves para el mejoramiento genético (Melese, 2016). ...
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La roya del cafeto (Hemileia vastatrix) es una de las enfermedades de mayor importancia para el cultivo del café, por lo que se dispone de referencia documental de estudios realizados para su manejo y alternativas de control integral. Millones de caficultores en todo el mundo y sobre todo de países en Centroamérica, enfrentan los brotes de la roya del café. Un alto número de asociaciones y cooperativas de caficultores, gobiernos locales y nacionales, técnicos, investigadores, programas y organismos internacionales buscan respuestas frente a los impactos que trae consigo esta enfermedad con consecuencias adversas en la economía y seguridad alimentaria de un gran número de familias en las regiones donde se produce café. Por esta razón este documento surgió como alternativa de apoyo a los procesos que buscan hacer frente a la roya del café (Hemileia vastatrix), ya que la dinámica de comportamiento histórico de este hongo ha mostrado que son ciclos de epidemias que se repiten a lo largo del tiempo y cada uno con sus particularidades, por lo que es importante estar permanentemente preparados para establecer medidas preventivas o de control que sean oportunas y efectivas. Es indispensable plasmar una línea teórica base que permita reconocer a detalle el comportamiento de la enfermedad de la propagación de la roya en las plantaciones de café. El contenido del Manual fue desarrollado a partir del trabajo de seguimiento a la Plataforma Técnica Regional de la Roya del Café, apoyada por el programa PROCAGICA desde el 2018 y que contó con la participación de especialistas de ANACAFÉ (Guatemala), CENTA CAFÉ/Consejo Salvadoreño del Café (El Salvador), INDOCAFE (República Dominicana), ICAFE (Costa Rica), IHCAFE (Honduras), INTA (Nicaragua), MIDA-IDIAP (Panamá), CIRAD (FRANCIA), UFV (Brasil).
... Since the development of EST sequencing projects (for reviews, see Lashermes et al. 2008;de Kochko et al. 2010de Kochko et al. , 2017and Tran et al. 2016), RT-qPCR experiments, using either SYBR Green fluorochrome or specific TaqMan probes, are nowadays used in routine to study coffee gene expression. In order to quantify the expression levels, these experiments require the use of endogenous reference genes (as internal controls) which must be previously validated for particular tissues (Bustin 2002;Bustin et al. 2009). ...
Chapter
Coffee is cultivated in more than 70 countries of the intertropical belt where it has important economic, social and environmental impacts. As for many other crops, the development of molecular biology technics allowed to launch research projects for coffee analyzing gene expression. In the 90s decade, the first expression studies were performed by Northern-blot or PCR, and focused on genes coding enzymes of the main compounds (e.g., storage proteins, sugars, complex polysaccharides, caffeine and chlorogenic acids) found in green beans. Few years after, the development of 454 pyrosequencing technics generated expressed sequence tags (ESTs) obviously from beans but also from other organs (e.g., leaves and roots) of the two main cultivated coffee species, Coffea arabica and C. canephora. Together with the use of real-time quantitative PCR, these ESTs significantly raised the number of coffee gene expression studies leading to the identification of (1) key genes of biochemical pathways, (2) candidate genes involved in biotic and abiotic stresses as well as (3) molecular markers essential to assess the genetic diversity of the Coffea genus, for example. The development of more recent Illumina sequencing technology now allows large-scale transcriptome analysis in coffee plants and opens the way to analyze the effects on gene expression of complex biological processes like genotype and environment interactions, heterosis and gene regulation in polypoid context like in C. arabica. The aim of the present review is to make an extensive list of coffee genes studied and also to perform an inventory of large-scale sequencing (RNAseq) projects already done or on-going.
... C. arabica is the only known tetraploid (allotetraploid, 2n ¼ 4x ¼ 44) in Coffea, formed from two diploid species, C. canephora (paternal) and Coffea eugenioides (maternal) (Lashermes et al., 1999). The genome size of C. arabica is close to 1.3 Gb, while C. canephora is around 710 Mb (Noirot et al., 2003;De Kochko et al., 2010). ...
... SNP loci associated with pathways of caffeine and trigonelline biosynthesis were first discovered in C. arabica using extreme phenotyping GWAS. Other studies have mainly used the mining of expressed sequence tags (ESTs) or transcriptome data for SNP discovery (Combes et al. 2013;Kochko et al. 2010;Vidal et al. 2010;Yuyama et al. 2016;Zhou et al. 2016). QTL mapping for quality traits has been conducted for C. canephora only (reviewed by Tran et al. 2016). ...
Article
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Association analysis was performed at the whole genome level to identify loci affecting the caffeine and trigonelline content of Coffea arabica beans. DNA extracted from extreme phenotypes was bulked (high and low caffeine, and high and low trigonelline) based on biochemical analysis of the germplasm collection. Sequencing and mapping using the combined reference genomes of C. canephora and C. eugenioides (CC and CE) identified 1351 non-synonymous SNPs that distinguished the low- and high-caffeine bulks. Gene annotation analysis with Blast2GO revealed that these SNPs corresponding to 908 genes with 56 unique KEGG pathways and 49 unique enzymes. Based on KEGG pathway-based analysis, 40 caffeine-associated SNPs were discovered, among which nine SNPs were tightly associated with genes encoding enzymes involved in the conversion of substrates (i.e. SAM, xanthine and IMP) which participate in the caffeine biosynthesic pathways. Likewise, 1060 non-synonymous SNPs were found to distinguish the low- and high-trigonelline bulks. They were associated with 719 genes involved in 61 unique KEGG pathways and 51 unique enzymes. The KEGG pathway-based analysis revealed 24 trigonelline-associated SNPs tightly linked to genes encoding enzymes involved in the conversion of substrates (i.e. SAM, L-tryptophan) which participate in the trigonelline biosynthesis pathways. These SNPs could be useful targets for further functional validation and subsequent application in arabica quality breeding.
... Arabica has the genome size estimated at 1.3 Gb (Kochko et al., 2010) which is fairly large compared to other common genome species such as Arabidopsis, rice, grape and sorghum (Michael and VanBuren, 2015). A large and complex genome has large repetitive elements and covers a large fraction of the genome resulting in ambiguities in the scaffolding step (Madoui et al., 2016). ...
Article
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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 1,448 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 1,444 non-synonymous SNPs associating with caffeine content. Based on KEGG 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.
... The markers used to detect DNA-level polymorphisms were RFLPs (Restriction Fragment Length Polymorphisms), RAPDs (Random Amplified Polymorphic DNAs), AFLPs (Amplified Fragment Length Polymorphisms) and, more recently, ISSRs (Inter-Simple Sequence Repeats), SSRs (Single Sequence Repeats), COS (Conserved Orthologue Set) and SNPs (Single Nucleotide Polymorphisms). Most of these pioneer works on molecular markers in coffee have already been reviewed elsewhere (Hendre and Aggarwal, 2007;Lashermes, Andrade and Etienne, 2008;Kochko et al., 2010;Priyono and Putranto, 2014) and our focus will be on large-scale genotyping platforms. ...
... In the last years, great efforts have been implemented in genomics to attempt to understand the genetic determinism of tolerance to environmental stresses, biotic and abiotic, especially in species models (Umezawa et al., 2006;Ashraf, 2010). The same applies to the case of coffee on which the recent progress in genome sequencing resulted in thousands of EST sequences Poncet et al., 2006;Vieira et al., 2006;, for the construction of genetic maps (Lefebvre-Pautigny et al., 2010;Leroy et al., 2011), improvement of genetic transformation techniques (Ribas et al., 2011) and complete genome sequencing of coffee (De Kochko et al., 2010). These scientific advances have paved the way for studies of genetic determinism and molecular drought tolerance in this plant. ...
... Using the recent advances in coffee genomics (De Kochko et al. 2010), our study set out to (1) identify the different coffee nsLTP homeologs corresponding to the C. canephora and C. eugenioides ancestor sub-genomes of C. arabica and (2) evaluate the expression of these alleles during bean development. We also report on the cloning of an nsLTP promoter that was tested in transgenic tobacco for analyzing its ability to control the expression of the uidA reporter gene in seeds. ...
Thesis
Abscisic acid (ABA) is a phytohormone universally conserved in land plants which coordinates several aspects of the plant response to water deficit such as root architecture, seed dormancy and regulation of stomatal closure. A mechanism of ABA signal transduction has been proposed, evolving intracellular ABA receptors (PYR/PYL/RCARs) interacting with PP2Cs phosphatases and SnRK2 protein kinases regulating this tripartite protein system. The goal of this study was to identify and characterize for the first time the orthologs genes of this tripartite system in Coffea. For this purpose, protein sequences from Arabidopsis, citrus, rice, grape, tomato and potato were chosen as query to search orthologous genes in the Coffee Genome Hub (http://coffee-genome.org/). Differential expression in tissues as leaves, seeds, roots and floral organs was checked through in silico analyses. In vivo gene expression analyses were also performed by RT-qPCR in leaves and roots of drought-tolerant (DT 14, 73 and 120) and drought-susceptible (DS 22) C. canephora Conilon clones submitted (or not) to drought. The expression profiles of the tripartite system CcPYL-PP2C-SnRK2 genes were also analyzed in leaves of C. arabica (Ca) and C. canephora (Cc) plants grown under hydroponic condition and submitted to exogenous ABA treatment (500 µM). This approach allowed the identification and characterization of 24 candidate genes (9 PYL/RCARs, 6 PP2Cs and 9 SnRK2s) in Cc genome. The protein motifs identified in the predict coffee sequences enabled characterize these genes as family’s members of PYL/RCARs receptors, PP2Cs phosphatases or SnRK2 kinases of the ABA-dependent response pathway. These families were functionally annotated in the Cc genome. In vivo analyses revealed that eight genes were up-regulated under drought conditions in both leaves and roots tissues. Among them, three genes coding phosphatases were expressed in all (DT and DS) clones therefore suggesting that they were activated as a general response to cope with drought stress. However, two other phosphatase coding genes were up-regulated only in the DT clones, suggesting that they constitute key-genes for drought tolerance in these clones. The DT clones also showed differential gene expression profiles for five other genes thus reinforcing the idea that multiple biological mechanisms are involved in drought tolerance in Cc. In response to exogenous ABA, 17 genes were expressed in leaves of Cc and Ca plants. Several genes were differentially expressed in the DT clone 14 either in control condition or after 24h with ABA treatment. Under control condition, five genes were higher expressed as in the Cc as in Ca DT plants. The kinase CcSnRK2.6 was highlighted as a gene specifically expressed in the Cc plants (DT and DS) after 72h of ABA treatment. Overall, it was observed that ABA signaling pathway is delayed in the DS C. arabica Rubi. Those molecular evidences corroborated with microscopies analyses which showed that the DT clone 14 was more efficient to control the stomatal closure than other coffee plants in response to ABA treatment. All these evidences will help us to identify the genetic determinism of drought tolerance through ABA pathway essential to obtain molecular markers that could be used in coffee breeding programs
... All species of Coffee are diploid (2n =2x=22 chromosomes) and self-incompatible, excepting Coffea arabica which is a self pollinated and allotetraploid (2n = 4x = 44 chromosomes) derived from hybridization between Coffea canephora and Coffea eugenioides (Lashermes et al 1999). The genome size of the two main domesticated coffee species has been predestined to be 1.3 Gb for C. arabica (Kochko et al 2010) and 710 Mb for C. canephora (Denoeud et al 2014) and the DNA content of the Coffea arabica was 2.47 pg while canephora was 1.43 pg. Many of the previous studies suggest that the origin of Arabica coffee and its primary centre of genetic diversity in highlands of South West Ethiopia (Sylvain 1955), also there are records of wild Arabica coffee in the Boma Plateau of Sudan and Mount Marsabit of Kenya (Thomas 1942 andAnthony et al 1987). ...
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This study was carried out to determine the genetic diversity degree and genetic relationships among seventeen genotypes involving 16 commercial cultivars and one accession of Yemeni coffee (Coffea arabica L.) germplasm collected from different Governorates in Yemen, and analysis of the DNA fingerprinting data for creating molecular IDs for conservation and protection of these genotypes. These goals were done using 15 previously described SSR primer pairs, in addition, evaluating of the efficiency and performance of these loci to achieve these objectives. The SSR loci were very highly polymorphic with an average of 100% polymorphism, the scored alleles were high and ranged from 4 to 25 with a mean value of 10.7 per locus. Heterozygosity values per locus and per genotype were low with an average of 0.21., the (PIC) values or gene diversity differed from 0.57 to 0.98. Also, the discriminating power for all loci was high with a mean value of 0.81; the most informative primer pairs was gSSRCa 021 with DP value of 0.94. However, the probability of matching fingerprints was low with an average value of 0.19. In this study, it was impossible to obtain identical DNA fingerprints for any of genotype pairs at all loci, even the genotypes with the same name but were collected from different geographical regions. However, the 15 SSR loci could differentiate between 17 Yemeni coffee genotypes through detecting of 86 clear specific/exclusive alleles. All Cultivars and accessions had unique alleles to that genotype alone with a mean value of 5.06. The cluster analysis grouped the 17 genotypes into three main clusters with a genetic similarity degree ranged from 0.00 to 0.486 with an average of 0.243. The genotypes also were classified according to fruit color and geographical regions. Results of this study confirmed the presence of genetic diversity among Yemeni coffee genotypes ranging between a moderate to high, indicating their importance as source of genetic variability for the purposes of coffee improvement, especially with the suffering of Arabica coffee from the narrowness of its genetic base