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Introducing superior plants is one of the efforts to increase coffee produc- tivity in Indonesia. Three clones from France de Torino (FRT), FRT 07, FRT 09, and FRT 65, have been introduced to Indonesia. However, their cultivation is not widely distributed yet. Analysis of the responses of FRT clones against differences in climate and cultivation is needed to determine the right cultivation system to produce maximum growth and productivity. This study examines the vegetative growth of FRT clones introduced at some levels of shade. The study employed a split-plot design with 36 experimental units. The primary factor was the levels of shade consisting: without shade, 25% of shade, 50% of shade, and 100% of shade. The three introduced FRT clones (FRT 07, FRT 09, and FRT 65) were used as the subplot. Observations were done on several growth variables. The results showed that shade treatment affected all growth parameters and plant architecture. Clones significiantly affected plant height, orthotropic internode length, number of leaves, and average leaf area. Increased levels of shade caused an increase in internode length, branch angle, and crown diameter but decrease in number of internodes and leaves. A low level of shade (25%) produced an optimal value on parameters related to the productivity of FRT coffee plants, such as the number of plagiotropic internodes and the number of leaves. Parameters related to vegetative growth, such as plant height, stem diameter, and internode length, showed optimal values in a moderate level of shade (50%). Treatment without shade and a heavy shade resulted in impaired growth of FRT coffee. There was no interaction between levels of shade and clone treatment on most of the variables related to plant morphology, which indicated that the three introduced FRT clones gave relatively similar response to shade; thus, the three clones can be managed with the same shade management.

Leaf morphological traits and internode length significantly affect the adapt-ability and production of coffee plants, respectively. Therefore, genetic studies of these two characters can support the effectiveness of Robusta coffee breeding program for obtaining superior planting materials. This study aimed to determine the diversity and frequency distribution of F1 generation on internode length and leaf size of Robusta coffee crosses. The study involved six groups of F1 progeny and their reciprocals (F1R) resulted from a cross of three parents, namely BP 961, Q 121, and BP 409. Each cross combination was planted with 41–49 progenies singly side by side in Kaliwining Experimental Station, Jember, Indonesia. The observed traits were internode length and leaf size. Analysis results of progeny variation distribution showed that most of the F1 and F1R progenies from intraspecific Robusta crosses had shorter branches than both parents in all combinations of crosses, even in BP 961 × BP 409 crosses. In addition, all F1 and F1R progenies had shorter internodes than both parents. More than 50% of the progeny of Q 121 × BP 409 and BP 961 × BP 409 crosses showed leaf length trait between parents. This indicates the absence of dominance of one parent in the progeny. Less than 20.9% of the progeny had a narrower leaf size than Q 121 parent. Most of the F1 and F1R crosses had a leaf width between both parents. The leaf length and leaf width traits were incomplete dominance or recessive, while the internodelength was overdominant.&nbsp

Indonesia is the fourth largest coffee producer in the world, even though it is not the original plant. Efforts to increase coffee genetic diversity in Indonesia through the results of the introduction are also carried out to improve the quality and quantity of coffee in the international market. The aim is to obtain robusta coffee clones that are able to adapt in several agroclimates in Indonesia and have stable yield potential, so that they can be cultivated extensively. The analytical method is AMMI biplot with six clones are FRT04, FRT06, FRT07, FRT09, FRT23, FRT65, and six locations are Bangelan, Kalibendo, Kaliselogiri, Gumitir, Malangsari, Silosanen.Then the agroclimate is suitable for widespread cultivation. The results of the study based on observations made on the production of coffee plants, which are climate types, which are somewhat wet and are getting good production results in the locations of Bangelan, Kaliselogiri and Silosanen. FRT07and FRT09 clones is the best clone of production and able to adapt, has interaction between locations with clones tested annually.

Breeding for high yielding, pest and disease resistance, and good quality Arabica coffee is the direction of the coffee breeding program in Indonesia. Threeway cross-breeding method becomes the alternative method to improve plant genetics to achieve those goals. This research was aimed to evaluate the agronomic performance and grouping of Arabica coffee genotypes from three-way cross progeny. This study was conducted in Andungsari Experimental Station, Bondowoso, East Java from July until September 2021. A randomized complete block design with three replications was used as an experimental design. It consisted of eight Arabica genotypes resulting from three-way cross method and one check variety (Andungsari 1) as treatments. The tested genotypes were resulted from crossing parents i.e. S 1934, AB 3, RC, YC, S 795, and Catimor that was planted in 1997. The results of the agronomic performance evaluation showed that TWC (Tree Way Cross) 2 ((S 1934/AB 3 x AB 3) x AB 3) and TWC 3 (RC/S 795 x Catimor) had good agronomic characteristics i.e. weight of 100 cherries and cherry weight per tree. While grouping using heatmap clustering method showed that there were three groups of genotypes. One of the groups which consisted of TWC 1 ((S 1934/AB 3 x AB 3) x S 1934), TWC 2 ((S 1934/AB 3 x AB 3) x AB 3), and TWC 5 (S 1934/YC x S 1934) were categorized as moderate yield group.

Breeding for high yielding and good quality arabica coffee is the direction of the coffee breeding program in Indonesia. Hybridization becomes the important step to select promising genotypes from the genetic variability to achieve those goals. This research aimed to study heritability and combining ability of vegetative and yield characteristics of arabica coffee offspring. This research was conducted in randomized complete block design with three replications at Andungsari Experimental Station, East Java. The materials consisted of five parents of arabica coffee namely BP 542A(P1), P88(P2), S795(P3), HDT(P4), GEISHA(P5), and ten F1 hybrids as the offspring. The results showed that the narrow-sense heritability of leaf width was categorized as high. P3 and P5 varieties had the highest general combining ability (GCA) value for internode length, cluster number, and cherries number. These results indicated that both parental lines had potential as parents for the breeding program. The highest value of specific combining ability (SCA) for cherry size and leaf size was shown in crossing combination of P1×P3 and P2×P3. While, the crossing combination of P3×P4 showed the highest SCA value for cluster number, internode length, and cherries number per branch. From this crossing combination, high yielding promising lines can be obtained.

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species' global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda's native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vita

Coffee seeds are classified into intermediate seeds which require high moisture content during the storage and possess a short shelf life. Seed germination testing aims to determine the potential of a seed lot, evaluate seed quality during the storage and also to estimate the success of seedling in the nursery. This experiment aimed to determine the germination performance of several Arabica coffee varieties after being stored for six months at controlled temperature. Nine varieties of Arabica coffee, namely Abesinia-3, Andungsari-1, BLP, Gayo-2, Goiaba, Kartika-1, Kayumas, MP-3, and S-795 were used in this study. The seeds were harvested in the 2019 harvest season (September) and the germination was tested in April 2020. The germination test was carried out in laboratory by using petridish. The result showed that the tested Arabica coffee seeds still had a high germination percentage which was more than 85%. Only three varieties namely S-795, Abesinia-3, and Goiaba had low germination growth (<80%). Meanwhile, Kayumas, BLP, and Kartika-1 coffee varieties had the best germination growth with an average length of 34.19 mm; 39.79 mm and 39.41 mm, respectively. Kartika-1 variety needs 6–7 days to germinate; Kayumas, BLP, and Goiaba varieties took 7–8 days; S-795 and MP-3 took 10 days; as well as Andungsari-1, Abesinia-3, and Gayo-2 which took 10–12 days. Arabica coffee seeds that had a short germination time will had a high germination rate and otherwise. Each variety displayed a different germination performance. BLP, Kartika-1, Gayo-2 and MP-3 varieties had high potential germination, 86.67%; 89.17%; 86.67%, and 93.33%, respectively. Kayumas, BLP, and Kartika-1 varieties showed significantly longer germination, namely 34.19 mm; 39.79 mm and 39.41 mm, respectively. The fastest of average germination time was possessed by Kartika-1 variety (6.54 days) and the highest seed germination rate was also possessed by Kartika-1 variety (0.153 per day).&nbsp

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.

The low yield of Robusta coffee in Indonesia may be due to the use of planting materials derived from seeds. The research objective was to determine the variation of Robusta coffee yield wich local propagated by using seeds. The study was conducted in Kaliwining experimental Station of ICCRI (Indonesian Coffee andCocoa Research Institute). There were two populations observed. Number of progeny used in this study were 186 genotypes consisting of two groups from crossesBP 409 x Q 121 with 89 progenies and BP 961 x BP 409 with 81 progenies. The results showed that planting materials from seeds exhibit properties mixed results.Progeny that have the best results (yield more than 2 ton/ha) not more than 5% of the total population. In both populations there is a big difference between the progenythat has high and low yield. Highest yield B population could reach 2,500 kg/ha and the C population reached 2,200 kg/ha. The lowest yield can only produce coffee270 kg/ha in populations B and 120 kg/ha in population C.Key words: Coffea canephora, hybrid, variation, yield

Development of Robusta coffee clones needs special characteristics for rootstock. This research was aimed to study the characteristics of cutting growth of Robusta coffee as influenced by genetic factor. The research was conducted at Indonesian Coffee and Cocoa Research Institute using 269 progenies originated from reciprocal crossing populations among three parentals, namely BP 409, BP 961, and Q 121. BP 308 an easy cutting-propagated genotype was used as control. The research was arranged in three replications of randomized completely block design with 10 cuttings per replication. Each cutting was single planted in plastic polybag of 15 cm x 25 cm without any growth-regulator treatment. Cluster analysis procedure showed root growth characteristics which could be divided into three groups namely easy (85.3%, 3.82 and 6.68 cm), moderate (57.6%, 1.73 and 4.01 cm) and difficult (25.1%, 0.58 dan 1.44 cm) based on proportion of rooted cuttings, number of primary root and length of root, respectively. On the other side, growth of sprout showed good homogenous characteristic, mainly indicated by proportion of sprouted cuttings which generally achieved up to 98% in average. Study on shoot-root ratio of cuttings resulted in two groups of progenies, namely the first which tended to be dominant on sprout growth and the second which tended to balance their root and sprout growth. Based on proportion of sprouted cuttings which almost achieved up to 100% and various proportion of rooted cutting, it could be indicated that growth of cuttings was started and dominated by the growth of sprout. Key words: Coffee canephora, progeny, genetic variation, cutting, rooting, sprouting

Recently the use of molecular markers has been successfully applied for some crops. For coffee, new opportunities have been opened since Nestlé R&D Centre in collaboration with ICCRI completed the first genetic map of Coffea canephora. This study was aimed both to evaluate the phenotypic trait and also to identify the quantitative trait loci (QTLs) controlling the vegetative growth in Robusta coffee. Present study used three C. canephora populations and six genetic maps developed based on these populations using simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers. A total of 17 different quantitative data were used for the detection of QTLs on each of three populations. Present result showed that most of these traits were not heritable. The nine vegetative traits have been identified and distributed over seven different linkage groups. Due to some QTLs determining one given trait were overlapping on the same linkage group and were coming from the same favourable parent, a total of 19 QTLs detected for vegetative traits might finally be considered as only 12 QTLs involved. However, only two of them were shared for different traits. One involved for the number/length of primary branches and width of the canopy while the other for length of internodes and width of canopy. These two QTLs might determine the size of the tree canopy in this species. Key words: Coffea canephora, heridity, quantitative trait loci (QTLs), vegetative growth.

Bean characteristics in Robusta coffee (Coffea canephora) should be taken into considerations in coffee breeding. Beside genetic factor, environment has been known as an important factor in the formation and change of composition of bean characteristics. This research aimed to find out the effect of long dry season on changes of bean characteristics. The population observed consisted of 277 genotypes originated from reciprocal crossings of three parental namely BP 409, BP 961 and Q 121. Observation was conducted in Kaliwining Experimental Garden of ICCRI in Jember, East Java during two years with different drought intensity i.e. 2005—2006 and 2006—2007 production years. The result showed that long dry season decreased the range value of population of normal beans, pea beans and triage beans, and followed by decreasing in the mean value except for normal beans. Long dry season also influence the change of value range of empty bean to higher proportion, and followed by increasing in the mean value. Distribution pattern of normal beans tend in to remain at high proportion, in contrast to those of pea and triage beans. In other side, long dry season tended to change distribution pattern of empty beans to at high proportion. Correlation analysis among beans characteristics showed that normal beans had negative correlations with pea beans and empty beans. Pea beans had a positive correlation with empty beans. Long dry season decreased proportion of pea bean and triage bean, in contrast to those of empty beans. Increasing proportion of empty bean was caused by failure of growth to normal bean under stress condition. Key words : Coffee canephora, bean characteristics, long dry season, variation, correlation, composition.

Selection of superior genotypes of robusta coffee (Coffea canephora) to improve its important agronomic characters should be conducted continuously to get better planting productivity. The aim of this research was to select superior genotypes of Robusta coffee for high yield and high proportion of large bean. Selection was conducted on controlled hybrid populations, developed from three crossing parental clones, i.e. BP 961 x Q 121 (A), BP 409 x Q 121 (B) and BP 961 x BP 409 (C). Selection was done by applying cluster analysis with complete linkage and Euclidean distance as the clustering method. The result of the research showed that the selection was successful to identify superior genotypes of Robusta coffee for high yield and high proportion of large bean. The parameters used (cherries weight/tree, bean weight/tree, bean size percentage > 6.5 mm and 100 cherries weight) were effective in clustering the superior genotypes, indicated by increased minimum and average value of population. Yield potential and percentage of bean size > 6.5 mm of those genotypes were having better performance than the control genotype and its parent. The selection code A 95, B 28, B 62, B 66, B 74 and C 38 were considered as promising superior genotypes of Robusta coffee, respectively. Key words: Coffea canephora, selection, bean size, yield, cluster analysis

The version of record of this article, first published in Metabolomics, is available online at Publisher’s website: https://doi.org/10.1007/s11306-023-02051-5, Introduction: The cupping test is a widely used method for quality assessment of Arabica coffee. However, the cupping test is limited by the low number of certified panelists and the low throughput. Therefore, an analytical-based quality assessment may be a promising tool to complement the cupping test. A present, there is no report investigating quality marker candidates, focusing only on “specialty” grade Arabica coffee from Indonesia. Objective: This study identified the potential quality marker(s) in Arabica Specialty coffee at different stages (green beans, roasted beans, and brewed coffee. Methods: The metabolite profiles of ten different Arabica specialty-grade coffees were analyzed with different cup scores using gas chromatography–mass spectrometry (GC/MS). From the ten samples, green coffee beans, roasted coffee beans, and brewed coffee were selected. In addition, an orthogonal projection to latent structure (OPLS) regression analysis was conducted to obtain a potential quality marker based on the variable importance in projection (VIP). The potential quality marker(s) were validated by GC/MS metabolome profiling and OPLS analysis of different sets of samples consisting of 35 Arabica specialty-grade coffee samples. Results: In Arabica coffee samples, the OPLS model of the three stages showed galactinol to have a high VIP score. Galactinol showed a consistent positive correlation with cup scores at all stages of coffee production (green beans, roasted beans, and brewed coffee). The correlation suggests galactinol is a potential quality marker after further validation using different samples. Conclusion: GC/MS combined with OPLS regression analysis suggested galactinol as a quality marker and provide an early screening method for Arabica coffee quality that complements the cupping test performed by certified panelists.

The version of record of this article, first published in Metabolomics, is available online at Publisher’s website: https://doi.org/10.1007/s11306-023-02051-5, Introduction: The cupping test is a widely used method for quality assessment of Arabica coffee. However, the cupping test is limited by the low number of certified panelists and the low throughput. Therefore, an analytical-based quality assessment may be a promising tool to complement the cupping test. A present, there is no report investigating quality marker candidates, focusing only on “specialty” grade Arabica coffee from Indonesia. Objective: This study identified the potential quality marker(s) in Arabica Specialty coffee at different stages (green beans, roasted beans, and brewed coffee. Methods: The metabolite profiles of ten different Arabica specialty-grade coffees were analyzed with different cup scores using gas chromatography–mass spectrometry (GC/MS). From the ten samples, green coffee beans, roasted coffee beans, and brewed coffee were selected. In addition, an orthogonal projection to latent structure (OPLS) regression analysis was conducted to obtain a potential quality marker based on the variable importance in projection (VIP). The potential quality marker(s) were validated by GC/MS metabolome profiling and OPLS analysis of different sets of samples consisting of 35 Arabica specialty-grade coffee samples. Results: In Arabica coffee samples, the OPLS model of the three stages showed galactinol to have a high VIP score. Galactinol showed a consistent positive correlation with cup scores at all stages of coffee production (green beans, roasted beans, and brewed coffee). The correlation suggests galactinol is a potential quality marker after further validation using different samples. Conclusion: GC/MS combined with OPLS regression analysis suggested galactinol as a quality marker and provide an early screening method for Arabica coffee quality that complements the cupping test performed by certified panelists.