Arabica Accessions Research Articles

Genetic Diversity of Yellow and Red Berries Arabica Coffee Populations Grown in a Mix Populations in Garut, West Java, Indonesia, Based on SSR Markers

Farmers in Garut, West Java, grow mixed varieties of Arabica coffee (Coffea arabica L.). Subsequently, they use harvested beans as seeds. Intercrossing among varieties may result in hybrid progenies and harvesting hybrid progenies as seed results in genetic variations. This research aims to evaluate the genetic diversity of Arabica coffee grown in a mixed population. Ninety-one Arabica coffees comprised 37 Arabica cv. “Ahernt GRT KN” (yellow-), 45 “Sigararutang” (red-), and nine “S795” (red berries) were sampled. Twenty SSR primer pairs were validated using 15 samples representing three varieties; six were polymorphic and used to genotype 91 Arabica accessions. Genetic data were analyzed using PowerMaker 3.25 and Darwin version 6 software. The results showed that the six SSR loci generated from 2 – 3 alleles, with an average of 2.17 alleles per locus. Genetic analysis of Arabica coffee from Garut, West Java, generated SSR markers with an average PIC of 0,33 across loci and varieties. The PIC within Arabica coffee cv. “Ahernt GRT KN” and “Sigararutang” were low, and within “S795” was moderate. Those PICs indicate the presence of more genetic diversity within “S795” than the other two cultivars. The Ho across Arabica coffee cv. “Sigararutang” and “S795” were lower than the He values, confirming their self-pollination nature. However, the Ho values of Arabica coffee cv. “Ahernt GRT KN” was larger than the others, indicating the presence of residual heterozygosity and a low percentage of recent outcrossing. The low Ho values of “Sigararutang” suggest that Arabica coffee is homozygous. Arabica coffee cv. “S795” also showed a low Ho value, but its moderate He value indicates the presence of more genetic diversity than the othercultivars.

Reaction of Gidami Coffee Collections against the Major Diseases

Ethiopia's largest export commodity is coffee arabica, one of the most significant goods that significantly contribute to the national economy. However, diseases including coffee berry, coffee leaf rust, and coffee wilt have been significantly reducing its yield. In order to assess Gidami coffee arabica accessions’ reaction to serious fungal infections, this study was started. The total of 100 genotypes was evaluated under Gera and Haru field situations for these major diseases. Whereas, 92 accessions with two checks were tested under greenhouse condition for coffee wilt. The results showed a highly significant variation (p<0.001) among genotypes in both conditions with 0–51%, 4–36%, and 0–100% disease severity ranges respectively. Except the four accessions namely G67/13, G71/13, G54/13, and G66/13, most of them showed susceptible reactions to CBD under Gera conditions. As well, 36 and 12 coffee accessions revealed <10% CLR reactivity at Haru and Gera conditions respectively. But none of the accessions had resistance levels higher than the two checks (Challa and 8136) at either of the locations. In other word, Gera had much greater levels of CBD and CLR pressure than Haru. On the other hand, only two accessions, G57 and G20, showed 100% CWD survival rate in greenhouse environments. This study showed how plant genetics and environmental variables affect diseases development and demonstrated that the response of Gidami coffee accessions to the major coffee diseases highly influenced by geographical and genetic variables. Therefore, continual and massive genotype screening across the locations must be taken into account in order to get resistance genotypes as the best disease mitigation to overcome the coffee diseases problem.

Multi-Omics Analyses Unravel Genetic Relationship of Chinese Coffee Germplasm Resources

The genetic relationships between Coffea arabica resources were analyzed via specific length amplified fragment sequencing (SLAF-seq) and transcriptome sequencing to provide the theoretical basis for breeding new varieties. Twenty C. arabica accessions were used to analyze genetic diversity on the basis of SNPs identified in SLAFs and the transcriptome data. For the SLAF-seq analysis of 20 C. arabica accessions, two Coffea canephora accessions, one Coffea liberica accession, and one Coffea racemosa accession, the number of reads ranged from 2,665,424 to 7,210,310, with a GC content of 38.49%–40.91% and a Q30 value of 94.99%–96.36%. A total of 3,347,069 SLAF tags were obtained, with an average sequencing depth of 13.90×. Moreover, the 1,048,575 SNPs identified in the polymorphic SLAFs were filtered, then the remaining 198,955 SNPs were used to construct a phylogenetic tree, perform a principal component analysis, and characterize the population structure. For the transcriptome analysis, 128.50 Gb clean reads were generated for the 20 C. arabica accessions, with a GC content of 44.36%–51.09% and a Q30 value of 94.55%–95.40%. Furthermore, 25,872 genes’ expression levels were used for the correlation analysis. The phylogenetic relationships as well as the results of the principal component analysis, population structure analysis, and correlation analysis clearly distinguished C. arabica Typica-type accessions from the C. arabica Bourbon-type accessions. Notably, several C. arabica local selections with unknown genetic backgrounds were classified according to all four clustering results.

Comprehensive analysis of quality characteristics in main commercial coffee varieties and wild Arabica in Kenya.

Coffee flavor is a complex commercial trait and its generation mechanisms remain largely unclear. Here, we investigated non-volatile and volatile compounds in the AA grade coffee beans of cultivated and wild Coffea arabica accessions in Kenya. An increased accumulation of trigonelline and sucrose along with a decreased accumulation of caffeine and 5-caffeoylquinic acid or chlorogenic acid (CGA) relative to wild Arabica contribute to the improved flavor of commercial varieties. Trigonelline was strongly associated with attributes of coffee brews such as pH, aroma intensity and antioxidant activity, suggesting that it is one of the main flavor precursors. Partial least squares discriminant analysis (PLS-DA) identified 18 volatiles that could potentially define flavor quality of coffee brews, with pyrazines and thiols as the major coffee flavor determinants.

Genetic diversity and population structure of a Peruvian Coffea arabica L. collection

Peru is an important producer of specialty coffee beans in the world, however the genetic of their coffee plant populations is unknown. Therefore, the genetic diversity and population structure of a Peruvian germplasm collection of plant coffee was analyzed to ascertain its potential use in plant breeding and conservation. In this work 54 DNA genotypes from 17 Coffea arabica L. and one C. canephora Pierre ex A. Froehner accessions were analyzed by microsatellite and sequence-related amplified polymorphism (SRAP) markers. In the assessment of molecular markers both systems were adequate to perform C. arabica germplasm collection genetic analysis. The obtained genetic diversity estimators were similar to germplasm assessments from other plant breeding programs. In the population structure analysis, the genetic differentiation (GST = 0.6584) and genetic flow (Nm = 0.2594) estimators were high. In analysis of molecular variance (AMOVA), total variation was divided 43.05% between accessions and 56.95% within accessions. In the Bayesian analysis with STRUCTURE software using admixed model for K = 2, the C. arabica and C. canephora accessions were separated, while for K = 7, the C. arabica accessions were grouped similarly to what obtained by the unweighted pair group method with arithmetic mean (UPGMA) dendrogram. The high genetic differentiation and genetic structuring of the accessions would indicate that the cultivars, from which the accessions were originated, have been preserved over time. The genetic diversity of Peruvian coffee might be the consequence of a long history of introductions of cultivars from different origins

Assessment of the Genetic Diversity of Philippine Arabica Coffee (Coffea arabica L.) Using SSR Markers

Arabica coffee (Coffea arabica L.) plays a significant contribution to the Philippine coffee industry. Many important genes are continuously lost due to an increase in population, urbanization, and the promotion of registered and popular varieties in the country. This study was conducted to assess the genetic diversity of 27 Philippine C. arabica accessions currently maintained at the Cavite State University – National Coffee Research, Development and Extension Center (CvSU-NCRDEC) field genebank using 19 simple sequence repeat (SSR) markers. Around 80% of the markers used showed polymorphism. A total of 56 alleles were detected, 47 of which were polymorphic. The average number of alleles per locus (3.7) and the polymorphism information content (PIC) (~ 0.40) found in this study were higher than those reported in the literature. Duplicate accessions were identified despite their striking morphological differences, and differentiation of synonymous accessions was also noted. The average genetic similarity was 0.83 and ranged from 0.64–1.0. Overall, the genetic diversity of Philippine C. arabica collection was low. Nonetheless, the higher number of alleles and PIC obtained provide more information in the selection of materials that can be used as parents in hybridization works. Cluster analysis showed three major clusters: Cluster I consisted of most of the accessions from Benguet State University (BSU), while Cluster II consisted of all accessions from the Bureau of Plant Industry (BPI) except Yellow Bourbon. MCA and Yellow Bourbon banded in Cluster III. The cluster analysis offers valuable information in the selection of parents for the development of vigorous F1 hybrids. Further, the results obtained in this study can be utilized in developing strategies to widen the low genetic variability of C. arabica through proper management of the country’s coffee genetic resources, development of effective breeding and selection programs, and varietal registration and identification.

Performance of arabica coffee accessions from the active germplasm bank of Minas Gerais, Brazil as a function of dry and wet processing: a sensory approach

The post-harvest processing of coffee is one of the most important factors in obtaining a superior quality product with differentiated attributes in the cup. The objective of this study was to evaluate the influence of wet and dry postharvest processing on beverage quality and on the sensory profile of 49 Coffea arabica accessions from the Active Germplasm Bank of Minas Gerais. For this purpose, the sensory analysis was applied based on the protocols of the Specialty Coffee Association, and the data were analyzed by Principal Component Analysis. Some coffee accessions were separated by the final score according to the type of processing used. However, the influence of the processing method was most evident in the individual scores for sensory attributes. Regardless of the processing method, some accessions presented stability for the notes of taste, acidity, fragrance, body, aftertaste, balance, global impression as well as for the final score. The Coffea arabica accessions of the Active Germplasm Bank of Minas Gerais presented variability in the sensory profile of the beverage according to the type of postharvest processing used.

Chloroplast Genome Sequence Variations and Development of Polymorphic Markers in Coffea arabica

Coffee is a popular beverage in the world and a valuable agricultural export commodity for several developing countries. Coffea arabica is one of the widely cultivated species and is believed to have originated from Ethiopia. Currently, a large number of C. arabica accessions are conserved ex situ in field gene banks in Ethiopia. However, there is no useful molecular barcoding to identify the conserved accessions, which presents a challenge to sustainable utilization of this economic species. To identify polymorphic chloroplast markers for the use in various studies, the complete chloroplast genome sequences of 24 C. arabica accessions were assembled and screened for variable regions in this study. The total length of the individual chloroplast genome sequence varied from 155,059 to 155,192 bp. Genome annotation revealed a total of 114 unique genes, consisting of 80 protein-coding, 30 tRNA, and four rRNA genes in all the 24 genomes. Twenty-four polymorphic regions were identified and developed. Most (71%) of the variable regions were found in non-coding sequence, and 54% of the variations detected are single base pairs. Three non-synonymous SNPs were found in accD, rpoA, and ycf1 genes. The markers developed were able to cluster the majority of the coffee accessions according to their geographical regions of collection. Five out of 24 newly developed markers were validated by assessing the diversity levels that were assessed in five original regions. The southwest region displayed the highest genetic diversity (HE = 0.224; I = 0.370) and might become a potential coffee genetic resource bank. Overall, the polymorphic markers developed and validated in this study could be a useful genomic resource for molecular breeding, identification, and biogeography studies of this commercially important crop.

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma’s D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

Genetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers

Population genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei’s gene diversity (He) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora, with Fst values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the Fst value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise (Fst) index and Nei’s standard genetic distance tests. The Fst outlier test for deviation from expected distribution between Fst and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies.

Multiple resistance to bacterial halo blight and bacterial leaf spot in Coffea spp.*

ABSTRACT Breeding for genetic resistance is an important method of crop disease management, due to the numerous benefits and low cost of establishment. In this study, progenies of 11 Coffea species and 16 wild C. arabica accessions were tested for their response to Pseudomonas syringae pv. garcae, the causal agent of bacterial halo blight, a widespread disease in the main coffee-producing regions of Brazil and considered a limiting factor for cultivation in pathogen-favorable areas; and also to P. syringae pv. tabaci, causal agent of bacterial leaf spot, a highly aggressive disease recently detected in Brazil. Separate experiments for each disease were carried out in a greenhouse, with artificial pathogen inoculations and ideal moisture conditions for disease development. The results showed that C. canephora, C. congensis, C. eugenioides, C. stenophylla, and C. salvatrix progenies, the wild C. arabica accessions Dilla & Alghe and Palido Viridis, and cultivar IPR 102 contain satisfactory levels of simultaneous resistance against bacterial halo blight and bacterial leaf spot. These results are useful in breeding programs for durable resistance to multiple biotic agents, providing new combinations of resistance alleles by hybridization, as well as for phytopathological studies, to identify infraspecific variability of the pathogens.

Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.

Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.).

Allopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora, one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.

Chemical partitioning and antioxidant capacity of green coffee (Coffea arabica and Coffea canephora) of different geographical origin

Green coffee beans of Coffea arabica and Coffea canephora accessions from different geographical origin (Brazil, Colombia, Ethiopia, Honduras, Kenya, Mexico, Peru, Uganda and Vietnam) were extracted and the extracts analyzed by HPLC–ESI-MS/MS for the identification and quantification of chlorogenic acids and caffeine content. Principal component and cluster analyses were used to identify chemical patterns separating the different species and accessions based on their geographical origin. C. canephora showed always a higher caffeine content with respect to C. arabica, whereas the C. arabica accessions from Kenya showed a higher chlorogenic acids and a lower caffeine content. The antioxidant capacity of green coffee extracts was assayed by the reducing power and DPPH assays. The antioxidant capacity correlated with the chlorogenic acids content. The results show that the C. arabica from Kenya possesses the highest chlorogenic acids/caffeine ratio and, among the C. arabica accessions, the highest antioxidant capacity. Therefore, the C. arabica from Kenya is the most suitable green coffee source for nutraceutical applications because of its high antioxidant capacity and low caffeine content.

Genetic characterization of an elite coffee germplasm assessed by gSSR and EST-SSR markers

Coffee is one of the main agrifood commodities traded worldwide. In 2009, coffee accounted for 6.1% of the value of Brazilian agricultural production, generating a revenue of US$6 billion. Despite the importance of coffee production in Brazil, it is supported by a narrow genetic base, with few accessions. Molecular differentiation and diversity of a coffee breeding program were assessed with gSSR and EST-SSR markers. The study comprised 24 coffee accessions according to their genetic origin: arabica accessions (six traditional genotypes of C. arabica), resistant arabica (six leaf rust-resistant C. arabica genotypes with introgression of Híbrido de Timor), robusta (five C. canephora genotypes), Híbrido de Timor (three C. arabica x C. canephora), triploids (three C. arabica x C. racemosa), and racemosa (one C. racemosa). Allele and polymorphism analysis, AMOVA, the Student t-test, Jaccard's dissimilarity coefficient, cluster analysis, correlation of genetic distances, and discriminant analysis, were performed. EST-SSR markers gave 25 exclusive alleles per genetic group, while gSSR showed 47, which will be useful for differentiating accessions and for fingerprinting varieties. The gSSR markers detected a higher percentage of polymorphism among (35% higher on average) and within (42.9% higher on average) the genetic groups, compared to EST-SSR markers. The highest percentage of polymorphism within the genetic groups was found with gSSR markers for robusta (89.2%) and for resistant arabica (39.5%). It was possible to differentiate all genotypes including the arabica-related accessions. Nevertheless, combined use of gSSR and EST-SSR markers is recommended for coffee molecular characterization, because EST-SSRs can provide complementary information.

Variations in Leaf Water Potential in the Wild Ethiopian Coffea arabica Accessions under Contrasting Nursery Environments

Variations in Leaf Water Potential in the Wild Ethiopian Coffea arabica Accessions under Contrasting Nursery Environments

Polymorphic information content of SSR markers for Coffea spp.

Thirty-three coffee SSR primers from enriched genomic library with (GT)15 and (AGG)10 repeats were analyzed in 24 coffee tree accessions. Twenty-two primers were polymorphic among accessions; the number of alleles ranged from 2 to 13, with the mean number of 5.1 alleles per primer. PIC values ranged from 0.08 to 0.79. The highest mean PIC values were found for C. canephora (0.46), and the lowest values for C. arabica (0.22) and triploids (0.22) accessions. The polymorphic SSR markers used in this study were useful for genetic fingerprinting in the coffee tree, especially in the C. canephora and the leaf rust resistant arabica cultivars.

Genetic variability of Coffea arabica L. accessions from Ethiopia evaluated with RAPDs

The genetic diversity of 50 wild and semi-wild accessions of the Coffea arabica L. germplasm collection, gathered by the FAO and ORSTOM missions to Ethiopia, and maintained in Colombia by CENICAFE, was evaluated with RAPD markers. The evaluation was carried out in two phases: In phase one, the polymorphism of 8 Ethiopian accessions of different geographic origin, plus the cultivated variety 'Caturra' was assessed with the RAPD technique with forty-two 10-mer oligonucleotides. In phase two, 51 accessions were assessed with a set of 5 polymorphic primers that reproduced, with a correlation of 95%, the groups generated by the 24 polymorphic primers found in phase one. Principal Coordinate Analysis of molecular data revealed that a closely related group consisting of 86% of the Ethiopian C. arabica accessions evaluated are significantly different from the Caturra variety and could be used in a genetic breeding initiative to increase the variability of cultivated varieties. The results also indicate that a larger polymorphism is present in the Colombian replica of FAO Ethiopian coffee germplasm collection than previously reported.

Detection by simple sequence repeat markers of introgression from Coffea canephora in Coffea arabica cultivars

AbstractMicrosatellites or simple sequence repeats (SSR) were used to assess polymorphism among 16 Coffea arabica and four Coffea canephora accessions, and to identify DNA introgression fragments from C. canephora in four C. arabica lines. Thirty‐one primer pairs allowed for the identification of 92 polymorphic alleles distributed over 37 loci. The C. arabica accessions derived from the genetic bases ‘Typica’ and ‘Bourbon’ were grouped separately according to their genetic origin. Two genotypes derived from a spontaneous hybrid (C arabica×C. canephora) were classified with the C. canephora accessions from Central Africa. Coffea canephora from West Africa were separated from the other accessions studied. Four alleles related to introgression (i.e. present in C. canephora and introgressed lines, and absent in C. arabica) were identified. The SSR markers were used successfully for characterization of a particular cultivar (‘Veranero’) from Costa Rica, which is known for its late maturity.

Resistance of cultivated coffee ( Coffea arabica and C. canephora) trees to corky-root caused by Meloidogyne arabicida and Fusarium oxysporum, under controlled and field conditions.

The coffee disease complex known as corky-root, composed of the root-knot nematode Meloidogyne arabicida and Fusarium oxysporum, causes serious damage to Coffea arabica in Costa Rica. Resistance to Meloidogyne arabicida alone and to the field population ( M. arabicida, M. exigua, F. oxysporum) was evaluated under controlled and field conditions. The studied material consisted of subspontaneous-derived C. arabica accessions, C. canephora accessions, introgression lines derived from the interspecific Timor Hybrid ( C. arabica× C. canephora) and F1 hybrids from crosses between subspontaneous-derived accessions and cultivars. Accessions resistant to M. arabicida and to the field population were identified at varying frequencies in the different groups of study materials. The results showed that resistance to corky-root is heritable and that genetic resistance to M. arabicida is an effective strategy against corky-root disease. By using C. canephora rootstocks, it was possible to substantially reduce mortality in the field and reduce by half the number of plants with corky-root symptoms. The results were used to define appropriate strategies for the sustainable management of coffee corky-root disease resistance.