Genetic Analysis of Yield and Yield Components Based on the Three Controlled Hybrid Populations in the Robusta Coffee （Coffea canephora Pierre）

Genetic analysis of yield and yield components were carried out on three parental clones of Coffea canephora Pierre and their controlled hybrid progenies. There is a possibility to estimate coffee yield capabilities in simply via the easier measuring traits of yield components since significant correlation between them were detected. We found that among parental show very few significantly differences of all observed characters and even not found between the overall mean of the descendants and their donor parents, whereas some particular descendants show higher values rather than their donor parent in one or more characters. Increased value between the best parent to the best descendent were detected varies from zero to 102%. This situation suggests the difficulty to find out the optimum yield in a single plant by accumulating all of yield components that actually can increase 143% to 278% from actual to potential yields. In addition, observed characters among population were also actually found highly varies from 159% in out-turn in population B to 28,333% in number of productive branch among population A. Low heritability （h2） that generally found in quantitative traits due to polygenic control was present in our studies in almost all characters observed. Therefore, selection for actual high yielding through conventional breeding will not efficient, and more convincing the power of selection using molecular markers to assist for cumulate additive effects in a single genotypes that resulted of high yielding in the future.

Mapping of Quantitative Trait Loci （QTLs） Controlling Cherry and Green Bean Characters in the Robusta Coffee （Coffea canephora Pierre）

In coffee breeding practice, two quantitative traits, namely cherry and green bean characters are the important phenotypic selection index. The synchronous of cherry maturation, size, weight and shape of green bean are desirable traits for the future breeding. In order to increase the breeding efficiency, a set of quantitative trait loci （QTLs） analysis controlling these traits was carried out. The QTL analysis was performanced in cross pollinated population of Coffea canephora using single nucleotide polymorphisms （SNPs） and simple sequence repeats （SSRs） markers. Totally 12 QTLs determined desirable cherry and green bean traits were identified on 9 linkage groups （LG）, where these QTLs mapped forming clusters in 11 different chromosomal regions. The desirable traits which can be detected by their QTLs are synchronous of cherry maturation （LG B and LG G）, cherry size （LG A, LG F and LG G）, bean shape （LG B, LG D and LG J）, bean weight （LG H）, bean size （LG A and LG E） and cherry-bean size （LG K） The gene action of these QTLs was dominance or an interaction of alleles （epistasis between alleles at the studied locus） effect. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in C. canephora breeding.

Impact of Teak （Tectona grandis Linn.） Thinning Out and Peacock-plume [Paraserianthes falcataria L. （1. Nielsen）] Harvesting on Mineral Cycle, Pod Rot Incidence, Changing of Cocoa Yield, and Land Productivity in Indonesia

In 2009, Indonesia was included in a group of the ten biggest countries emitting greenhouse gases, and forest sector contributes 85%. This forest exploitation should be stopped, and by this research the industrial wood species with special planting pattern was used as cocoa shade trees. The experiment was conducted in East Java, Indonesia, altitude 45 m above sea level using four planting patterns, i.e. （A） cocoa-Tectona grandis Linn. 3 m x 6 m, （B） cocoa-T, grandis 6 m x 4.2 m ~ 4.2 m （triangle）, （C） cocoa-Paraserianthesfalcataria L. （I. Nielsen） 3 m ~ 6 m, and （D） cocoa-Leucaena sp. 3 m ~ 6 m （control）. Cocoa was planted in 3 m ~ 3 m distance; between rows of teak and Paraserianthes was planted. Cassia surithensis of 3 m distance in the row, as reserve shade trees. At 6 year old, Paraserianthes was harvested, and at 7 year old, teak trees were thinned out 50% population for A and 66.7% for B treatments. The result showed that cocoa agroforestry by using timber trees in regular planting pattern and accurate spacing did not decrease cocoa yield but improved land productivity. Paraserianthes harvesting produced 0.71 m3 timber and the price was US$38.0-US $40.0 per tree, while teak thinning out produced 0.07 m3 wood per tree and it cost was US$5 per tree. From 108 Paraserianthes trees harvested, 81 cocoa trees were affected, 11.9% were seriously damage, 6.85% were medium damage, and 5.36% were light damage. On the other hand, teak spacing did not cause serious damage on cocoa trees. Biomass of harvested Paraserianthes and teak supplied back to soil 543 g and 250 g per tree respectively for equalities to total urea, SP 36, KC1, Kieserite and Dolomite. Paraserianthes harvest and teak thinning out made microclimate to be warmer, humidity to be lower, so pod rot incidence become lower and pod yield was improved, namely 71% and 27.25% for Paraserianthes plot and teak plot, respectively. Harvesting of Paraserianthes produced benefit/cost plot of 43.63, and teak thinning out of 3.60. The revenue obtained from timber sales easily offset the costs of damage of the cocoa crop. It is concluded that by using accurate planting pattern, cocoa area could produce industrial timber without sacrifying cocoa production and exactly improve land productivity.

Coffee Agroforestry with Some Timber Shade Trees： Study on Carbon Stock, Mineral Cycle, and Yield

Coffee cultivation by using shade trees is simple of agroforestry, this system could get better ecosystem service and sustainable agricultural. The aims of this research are to study the possibility of some species of industrial woods as shade trees of Coffea canephora. The research was conducted in Jember, Indonesia （45 m asl., D rainfall type according to Schmidt and Ferguson）, and arranged in split plot design. The main plots were （A） coffee-T, grandis （3 m × 2.5 m ×12 m）, （B） coffee-P, falcataria single row （2.5 m ×6 m）, （C） coffee-P, falcataria double rows （3 m× 2.5 m × 12 m）, （D） coffee-P, falcataria vat. Solomon （3 m× 2.5 m × 12 m）, （E） coffee-M, azedarach （3 m ×5 m ×22.5 m）, （F） coffee-H, macrophyllus （3 m ×5 m ×12.5 m）, and （G） coffee-Leucaena sp. （3 m × 2.5 m） as control. The sub plots were coffee clones, i.e., BP 534, BP 409, BP 936, dan BP 939. Among those timber trees, Leucaena was planted as the alternative shade trees. The result showed that in comparison with control, all of coffee agroforestry system improved carbon sequestration. Total C-stock on （B） was highest, i.e., 1,007 percent to control while the lowest one was （A） 317.44% to control. During one year observation, litter weight of H. macrophyllus was heaviest followed by T. grandis. The lightest litter was obtained from M. azedarach. Based on its mineral contents, litters of T. grandis potentially supplied back nutrients that equaled to total Urea, SP-36, KC1, Dolomite, and Kieserite as much as 574.14 g; P. falcataria 287.57 g, P. falcataria var. Solomon 453.59 g, M. azedarach 450.84 g, H. macrophyllus 877.56 g, and Leucaena 445.12 g per tree per year. Because of heavily fallen leaves of M. azedarach during dry season and conversely too dense shading of H. macrophyllus, bean yield at 4 and 5 years old by using both species were consistently lower than that under T. grandis, P. falcataria and control. At those ages, effect of clone on cherry yield was still not consistent but there was a tendency that BP 939 was most productive, while BP 534 was the less. Its outturn was not influenced by agroforestry system but by clones. The agroforestry pattern influence physical bean characters, more dense of shading, more single bean and empty bean. That bean abnormality also genetically, on BP 939 percentage of round and empty bean was highest while on BP 936 was lowest. It was concluded that coffee agroforestry improve ecology service, but M. azedarach and H. macrophyllus were not appropriate to be used as coffee shade trees. P. falcataria is recommended as an alternative shade tree beside Leucaena sp.

Effect of Genetic and Altitude Differences on Stomata Characters as Resistance Indicators to Vascular Streak-Dieback （VSD） in COCOA （Theobroma cacao L.）

Preliminary research results indicated that the stomata is one important trait that can be used as an indicator of resistance to vascular streak dieback （VSD） disease. The influence of genotype and environment on the stomatal characters is expected to provide information for specificlocations （habitats） suitable for planting cocoa in particular to avoid VSD attack. The research was conducted at KendengLembu, PTPNXII, East Java. Experimental design used a splitplot design testing： location （altitude） and genotype factors. The location factors, distinguished on the basis of the altitude, were labelled highlands and lowlands. The genotype factors consisted of three clones with different levels of resistance to VSD diseases： PA 191 （tolerant）, BL 703 and GC 29 （susceptible）. The cocoa clones observed were top grafted onto locally available rootstock seedling and planted in 2006-2007. The maintenance of the plants was conducted in accordance with the standards of cocoa cultivation in the PTPN XII. Parameters measured were leaf stomata traits at different positions of the leaf （tip, middle and base）. Characters observed were the number of stomata, opening width of stomata, and diameter of the stomata. The results of the research showed that PA 191 in the lowlands had the lowest number, diameter and opening width of stomata. In contrast, GC 29 in the lowlands showed the highest number of stomata PA 191 and BL 703 in the highlands had a number, diameter and openings width of stomata that was relatively low compared with GC 29. However, the characters of the stomata （number, diameter and openings width of stomata） of the three genotypes in the highland showed a smaller value in each case than in the lowlands. The severity level of VSD attack was greater in the lowlands than in the highlands and PA 191 showed the lowest level of VSD attack at both altitudes.

Growth of Verticillium tricorpusmA Saprophytic Fungus and Potential Entomopathogen of Cocoa Pod Borer as Affected by the Medium and Light

Cocoa pod borer （CPB） has endangered Indonesian cocoa. Use of entomopathogen in biocontrol of pests is considered to be environmentally friendly approach. Verticillium tricorpus has been reported to be a potential agent for controlling CPB. The aim of this research was to study the possibility in using alternative, easy and cheap media and also the role of intensity and quality of light for mass production of V. tricorpus. The experiments were laid out in split-plot design as factorial, where every combination treatment was replicated three times. Medium, in form of semi-synthetic and natural, was treated as the main plot, while light as sub-plot. Results of this study showed that for the growth and development of fungus V. tricorpus, the use of alternative natural media in form of a mixture of cocoa pod husk and maize was the best. Use of cocoa dextrose agar （CDA） as semi-synthetic medium was more suitable for the growth and development of V. tricorpus compared to potato dextrose agar （PDA）. The semi-synthetic and natural media consisted of cocoa husk and maize are suitable for cocoa production area in Indonesia, where mostly cocoa is planted in lowland area and mostly is also suitable for corn but not for potato growing. Growth of the fungus colony especially on CDA medium reached its optimum condition when using white light with the intensity of 1,000 lux. This study proved that the requirement for light quality was different between growth and development purposes. Development of V. tricorpus until the production of conidia in optimal condition was reached with the use of yellow light with the intensity of 1,000 lux.

Ability of Non Symbiotic Nitrogen-Fixing Bacteria Isolated from Coffee Plant Rhizosphere and Their Effects on Robusta Coffee Seedlings

Nitrogen is one of the most needed elements by coffee plants. Utilization of biological nitrogen fixation by non symbiotic bacteria offers alternative to reduce the N fertilizer usage. This study was focused to obtain aerobic non symbiotic nitrogen-fixing bacteria from coffee rhizosphere. The application of those bacteria was expected to enhance coffee seedling growth. Sixty four aerobic nitrogen-fixing bacterial isolates were isolated from coffee plants rhizosphere from Jember, East Java using several nitrogen free medium, such as Ashby, malate acid, and fahreus agar. The nitrogen fixation ability of the isolates was determined by measuring their ability in pellicle formation on semi solid medium and ammonium excretion on growth medium. Ab Kws.l, Asm E6s.3.a, Asm Bsl.1, and Asm E6s were the isolates which showed the best performance on nitrogen fixation with excreted ammonium concentration ranged from 129.6 up to 239.8 pM/mg dry weight cell. Acetylene reduction assay was used to detect nitrogenase activity. Ab Kws.1 was the isolate which had the highest nitrogenase activity （7.4 mmol N2 fixed/gram dry weight cell/hour）. Inoculation of the four best isolates onto Robusta coffee seedling positively enhanced the seedling growth in this green house experiment. Based on the results of Becton Dickinson＇s （BD） PhoenixTM Automated Microbiology System biochemical tests, Asm Bls.l isolates has similarities with Achromobacter sp., Asm E6s.l and Asm E6s.3.a had similarities with Stenotrophomonas maltophilia, while Ab Kws. 1 had similarities with Leifsonia aquatica.

The Ability of Phosphate Solubilizing Bacteria Isolated from Coffee Plant Rhizosphere and Their Effects on Robusta Coffee Seedlings

Phosphate solubilizing bacteria isolated from rhizosphere of coffee plants may play an important role in improving phosphate availability for the plants. However, one of the factors influencing the degree of phosphate solubilization by these bacteria is the ability of the microorganisms to utilize phosphate. The objective of this study was to determine the ability of phosphate solubilizing bacteria isolated from coffee plant rhizosphere and their effects on robusta coffee seedling growth. This research was carried out by taking soil samples from Andungsari （Bondowoso District） and Kaliwining （Jember District） coffee plantations, both located in East Java. Liquid medium of Pikovskaya was used for isolation of phosphate solubilizing bacteria from the soil samples. Results of this study showed that 12 phosphate solubilizing bacteria were obtained from this isolation, eight isolates from Andungsari and four isolates from Kaliwining. Selection of those bacteria isolates was based on the qualitative ability in phosphate solubilizing by measuring the clear zone surrounding the colonies and quantitatively by measuring the solubilized phosphate using spectrophotometer. The results showed that four isolates, in the order of PFpKW1, PFpC61, PFsC62a, and PFsB 11, had the highest qualitative ability in solubilizing phosphate, while for the highest quantitative ability the order was PFpKW 1, PFpC61, PFsC62a, and PFsB 11. In a green house study, inoculation of these selected isolates onto Robusta coffee seedlings positively enhanced the coffee seedling growth. Phenotypic test indicated that the four isolates are similar to the genus of Pseudomonas.

Effect of Rootstocks on Growth, Yield and Bean Quality of Coffea canephora Clones

Coffee cultivation on dry area lately faces more often drought condition because of global warming effect. One effort to solve the problem is by using tolerant clones or varieties as the rootstocks. The aim of this research is to observe influence of BP 308, BP 409, and Exelsa as rootstocks, on growth, yield and bean quality of BP 409, BP 534, BP 936 and BP 939 clones as scions. The research was conducted in Temanggung district of Central Java, Indonesia, using randomized complete block design with 5 replications 10 plants per replication. The result showed that rootstock influenced stem height and number of branches, leaf relative water content （RWC） during dry season, but not stem diameter. BP 308 and BP 409 rootstocks supplied water more than Exelsa, it seem RWC scion on both rootstocks were higher （82.0%） than that of Exelsa （80.0%）. Exelsa rootstock cause scion grow more slowly, so bean yield was lower than on BP 308 and BP 409. Yield accumulation until 4 years old on Exelsa was 55% to BP 308, and 52.2% to BP 409 rootstock. Yield of BP 939/BP 308 and BP 409/BP 409 （scion/rootstock） tend to the highest. Rootstocks did not influence percentage of normal and abnormal beans and the outturns. Bean outturn was more influenced by clones. Exelsa rootstock improves caffeine content, body, astringent and bitterness characters of scion cherries, but decreases fragrance and aroma characters of scion yield. It is concluded that farther taxonomical relationship of rootstock, their influence on scion growth, yield and cup test characters are stronger.

Effects of Agricultural Practices on Soil Organic Nitrogen Fractions in an Inceptisol of a Cocoa Plantation

The effect of agricultural practices on soil organic nitrogen （N） fractions in a cocoa plantation has not been much revealed till now. Despite the fact that soil organic N has been long admitted for its importance to maintain soil fertility. Presented field experiment was conducted in Kaliwining Experimental Station, Indonesian Coffee and Cocoa Research Institute （ICCRI）, Jember, East Java, Indonesia, to investigate the effect of cocoa farm management, namely fertilization, weeding and soil tillage on the content of soil organic N fractions. The design of experiment was arranged in a split-split plot with two levels of weeding as main plots, two levels of soil tillage as subplot and three different fertilizer treatments as sub-sub plot. The analysis of soil N including total N and soil organic N fractions, namely, total hydrolized N, ammonium N, amino sugar N and amino acid N, were performed. The result showed that the effect of fertilization treatment was significant to the content of total N, ammonium N, amino sugar N and amino acid N. No-tillage treatment resulted in total N and amino sugar-N content increasing by 8% and 24%, respectively, over tillage treatment. Slashing treatment caused increase of the total N by 3% from herbicide treatment, whilst decrease of ammonium N and amino sugar N by 7% and 24%, respectively.

Investigation of Different Characters of Stomata on Three Cocoa Clones with Resistance Level Difference to VSD （Vascular Streak dieback） Disease

The development of the science of cytology and genetics, particularly on cell structure and function provided a breakthrough for breeders and allowed for early selection. Character of stomata density on some commodities was reported as important factor to determine the disease resistance. The research was done for getting information about the differences in the stomata characters influenced on the level of Vascular Streak dieback （VSD） resistance on cocoa. The research was conducted in the Laboratory of Genetics, Gadjah Mada University and leaves samples were conducted in Kendeng Lembu Gardens, PTPN XII. The research used a split plot design with three factors included the type of clones with different levels of VSD disease resistance （PA 191, BL 703 and GS 29）, leaf position （top, middle and base） and leaf age （young and old）. Stomata characters included number of stomata, stomata opening width, stomata wide and stomata diameter were observed. The results showed that the stomata characters in three cacao genotypes with different resistance levels indicated a difference in number of stomata, stomata size, stomata opening width, stomata wide and stomata diameter. Stomata number, stomata opening width and stomata diameter on PA 191 （resistance clone） were lower than the susceptible clones （BL 703 dan GS 29）. The lowest of number and diameter stomata on the base position on the old leaves tissues. Number of stomata, stomata opening width and stomata diameter were estimated role in mechanism of VSD resistance and that were expected could be used as criteria selection to VSD resistance.

Identification of Quantitative Trait Loci （QTLs） Determining Flowering in the Robusta Coffee （Coffea canephora Pierre）

The quantitative trait loci （QTLs） analysis for flower traits were performed based on three crossing of Coffea canephora in Indonesia. This study successfully identified 19 QTLs related to flowering. These QTLs consisted of 1） three QTLs associated with green candle flowering time located at linkage groups of A and D; 2） one QTL associated to white candle flowering time located at linkage groups of B; 3） two QTLs associated to blossom flowering time located at linkage groups of B; 4） two QTLs associated to number of flowers located at linkage groups of G and H; 5） five QTLs associated to score of flowers quality located at linkage groups of A, C and D; 6） five QTLs associated to number of star flowers located at linkage groups of D, E, F and G. Due to some QTLs are overlapping on the same linkage group, thus, these 19 QTLs for flower traits might be considered as 15 different ones which distributed on 14 regions of the eight linkage groups. Although pleiotropic genes might be the most likely explanation for the collocation of these QTLs, the present data are not sufficient to distinguish between a pleiotropic gene and a cluster of different loci controlling several traits. These results can be a first step for molecular breeding on Robusta coffee mainly in order to improve potential suitable characteristics such as number of flowers and number of normal flowers as well as to reduce adverse characteristics such as number of star flowers.

Participatory Breeding on Arabica Coffee to Obtain Superior Local Varieties to Support Origin Specialty Coffee Product Development in Indonesia

A participatory breeding on Arabica coffee involving farmers and plant breeders to select superior local varieties has been conducted at Lintong highland （North Sumatra）, Gayo highland （Central Aceh, Northern Sumatra） and Kendenan Plateau （Enrekang, South Sulawesi）. The aim of using this method was to find out superior varieties of Arabica coffee having appropriate specific traits and adaptable to such locations and accelerating the process of variety adoption by local farmers. Selection process was initiated by the farmer（s） based on high yielding performance by using their native experiences. The next step was conducted by plant breeder in collaboration with coffee farmers and other relevant scientists to evaluate more detail of cup quality, resistance to leaf rust and/or parasitic nematode as well as yielding potential and agronomic traits at different farmer＇s sites for several years observations. Research finding showed that three selected varieties namely Sigarar Utang, Gayo 1 and Gayo 2 had already been released by Minister of Agriculture for commercial planting at North Sumatera and Gayo highland. They performed excellent cup profile with high yielding ability （more than 1 t/ha） and tolerant to leaf rust disease. Therefore, it could support origin specialty coffee product at Gayo and Lintong highlands. However, observation over of selected local variety at Kendenan Plateau namely Salongge variety performed lower yielding ability （below 1 t/ha） and less stable yield over years as well as more heterogenous population in their offsprings than that of existing released varieties planted at the same location. Therefore, it could not be released as local varieties which adapted to specific location.

Using information from images for plantation monitoring: A review of solutions for smallholders

Technologically empowering farmers/smallholders notably accelerates the knowledge transfer to monitor plantations in developing countries.Advanced,cost-effective technologies can rapidly increase the effectiveness of using expenses,labor,and time.There is no limit to using digital cameras for non-destructive measurements,such as nutrient monitoring,pests and diseases,yield monitoring,and other information related to individual plant conditions in the plantation area.This paper elaborates the fundamental concepts and best practices for future research on how to use image information from a single digital camera in decision support systems as a solution to monitoring plantations such as coffee,cocoa,and tree crops.This paper reviews the recent and potential research on plantation monitoring using a digital camera and other suitable integrated sensors.Moreover,we propose a protocol for use as a possible solution for smallholders to cope with the limitation in network/internet access infrastructure.Following this protocol,an integrated system for monitoring the farm activities of smallholders can be established.