Chikmagalūr, India
Chikmagalūr, India

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Denoeud F.,French Atomic Energy Commission | Denoeud F.,French National Center for Scientific Research | Denoeud F.,DeVry University | Carretero-Paulet L.,State University of New York at Buffalo | And 68 more authors.
Science | Year: 2014

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin. © 2014, American Association for the Advancement of Science. All rights reserved.


PubMed | University of Barcelona, Bioversity International, University of Ottawa, Indonesian Coffee and Cocoa Institute and 16 more.
Type: Journal Article | Journal: Science (New York, N.Y.) | Year: 2014

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.


Bharatha Nandhini R.M.,Madurai Kamaraj University | Rahul R.N.,Andhra University | Thilaga S.,Manonmaniam Sundaranar University | Rao N.S.P.,Central Coffee Research Institute | Ganesh D.,Madurai Kamaraj University
South African Journal of Botany | Year: 2013

Interspecific C. ×. R hybrid (Coffea congensis×. Coffea canephora) in India is cultivated as mixed population with male parent C. canephora as this species is an efficient pollen donor for enhanced yield. But distinction of C. ×. R hybrid from C. canephora in old plantation is difficult due to varying plant sizes of C. ×. R hybrid and often resembles with C. canephora. C. ×. R hybrid cultivated under different agroclimatic conditions show distinct vegetative growth pattern with varying yields. Thus development of DNA marker for identification of C. ×. R hybrid is important for clonal propagation and seed preparation from selective individuals. In this study, two DNA bar coding loci of chloroplast genome (rbcL and matK) of parents, F1 hybrid and its back cross progeny were partially sequenced to identify SNPs as DNA marker for distinction of C. ×. R hybrid from C. canephora. Seven SNPs in the matK gene sequence and three nucleotides in the rbcL gene sequence were identified as DNA markers for the genetic identity of C. congensis. These SNPs were found in F1 and advanced progenies of C. ×. R hybrid due to maternal inheritance. Large number of samples of C. ×. R hybrids with varying morphological features revealed no polymorphism among C. ×. R hybrid and C. congensis. Thus, the SNPs in C. congensis can be used as DNA markers for precise identification of C. ×. R hybrid for production of clones besides tagging the chloroplast inheritance in advanced progenies. © 2013 South African Association of Botanists.


Anand C.G.,Central Coffee Research Institute | Kumar P.,Central Coffee Research Institute | D'souza G.F.,Coffee Research Sub Research Station
Indian Journal of Plant Physiology | Year: 2014

Coffee is a stimulating beverage crop and finds second place after petroleum products in the world trade. There are many species of coffee but only two species, Coffea arabica and C. canephora popularly called as arabica and, robusta coffees are commercially cultivated. The pre-mature fruit drop of 6–10 % occurs during early stage of berry growth and development in June–July, which is a common phenomenon due to various reasons irrespective of the crop season. However, certain pre-disposing factors such as wet feet condition due to excess rain fall coupled with cool ambient temperature, high relative humidity, cloudy weather and inadequate drainage leading to soil saturation and water logging, improper handling of bushes facilitating the secondary infection of stalk rot and black rot increases the pre-mature fruit drop. In general, fruit drop in coffee is not common at maturity/ripening stage unless the winter period that coincides with ripening stage experience heavy rain fall and hail storms leading to splitting and dropping of ripened fruits. Physiological pre-mature fruit drop under ‘Wet feet’ conditions, is associated with reduction in endogenous levels of cytokinins coupled with high content of abscisic acid (ABA) and reduction in carbohydrate reserve and nutrients. The competition among the different-sized developing berries for carbohydrate reserves causes’ additional drop of pre-mature berries. Plants bearing high number of berries are also vulnerable for high percentage of fruit drop due to competition among the developing berries for carbohydrate reserves and nutrients. Systematic studies have revealed that physiological intervention by use of plant growth regulators, coupled with adoption of good agronomic practices, reduces pre-mature fruit drop and defoliation, and enhance cropping wood for subsequent year, resulting in increase in crop yield by 12–20 %. Here we have reviewed physiology aspects associated with pre-mature fruit drop, pre disposing factors for defoliation and pre-mature fruit drop, use of plant growth regulators to minimize the losses and role of recommended cultivation practices for realizing yield potential. © 2014, Indian Society for Plant Physiology.


Divakara S.T.,University of Mysore | Santosh P.,Central Coffee Research Institute | Aiyaz M.,University of Mysore | Venkata Ramana M.,Defence Food Research Laboratory | And 3 more authors.
Journal of the Science of Food and Agriculture | Year: 2014

BACKGROUND: Fusarium spp. are not only pathogenic to plants but are also known as toxin producers that negatively affect animal and human health. The identification of Fusarium spp. remains one of the most critical issues in fungal taxonomy. In this study, different strains of Fusarium spp. were isolated from sorghum seed samples and identified at the molecular level by tef-1α gene amplification. A multiplex polymerase chain reaction (mPCR) assay was developed to differentiate toxigenic and non-toxigenic Fusarium spp. by designing a primer for the Fum21 gene along with the Fum1 and Fum8 genes. A competitive direct enzyme-linked immunosorbent assay (CD-ELISA) was employed to assess the fumonisin-producing ability of Fusarium spp. Phylogenetic analyses were performed using partial sequences of tef-1α and inter-simple sequence repeat (ISSR) markers of different Fusarium spp. RESULTS: All 27 isolates of Fusarium spp. were positive for the tef-1α gene and revealed the presence of F. verticillioides, F. thapsina and F. cf. incarnatum-equiseti complex. The standardized mPCR assay distinguished toxigenic and non-toxigenic F. verticillioides. Further, mPCR fumonisin-positive F. verticillioides isolates were also positive by CD-ELISA. The tef-1α gene sequence was found to be useful in revealing intraspecific polymorphism to some extent. ISSR markers revealed a high level of polymorphism among different isolates of Fusarium spp., and the dendrogram of ISSR analyses grouped the 27 isolates into two major clusters. CONCLUSION: The present method provided rapid and reliable detection of fumonisin-producing Fusarium spp. The mPCR assay could be an alternative strategy to current conventional mycotoxin analytical techniques and a reliable tool for high-throughput monitoring of major mycotoxin-producing fungi during the processing steps of food and feed commodities. © 2013 Society of Chemical Industry.


Garcia C.A.,CIRAD - Agricultural Research for Development | Garcia C.A.,French Institute of Pondicherry | Bhagwat S.A.,University of Oxford | Ghazoul J.,ETH Zurich | And 6 more authors.
Conservation Biology | Year: 2010

The new approaches advocated by the conservation community to integrate conservation and livelihood development now explicitly address landscape mosaics composed of agricultural and forested land rather than only protected areas and largely intact forests. We refer specifically to a call by Harvey et al. (2008) to develop a new approach based on six strategies to integrate biodiversity conservation with sustainable livelihoods in Mesoamerican landscape mosaics. We examined the applicability of this proposal to the coffee agroforests of the Western Ghats, India. Of the six strategies, only one directly addresses livelihood conditions. Their approach has a clear emphasis on conservation and, as currently formulated risks repeating the failures of past integrated conservation and development projects. It fails to place the aspirations of farmers at the core of the agenda. Thus, although we acknowledge and share the broad vision and many of the ideas proposed by this approach, we urge more balanced priority setting by emphasizing people as much as biodiversity through a careful consideration of local livelihood needs and aspirations. ©2009 Society for Conservation Biology.

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