Identification of Quantitative Trait Loci Determining Vegetative Growth Traits in Coffea Canephor

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

Terminal-repeat retrotransposons with GAG domain in plant genomes : a new testimony on the complex world of transposable elements

A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes

Dihaploid Coffea arabica genome sequencing and assembly.

Coffea arabica which accounts for 70% of world coffee production is an allotetraploid with a genome size of approximately 1.3 Gb and is derived from the hybridization of C. canephora (710 Mb) and C. eugenioides (670 Mb). To elucidate the evolutionary history of C. arabica, and generate critical information for breeding programs, a sequencing project is underway to finalize a reference genome using a dihaploid line and a set of Menu Abstract: Dihaploid Coffea arabica Genome Sequencing and Assembly (Plant and Animal Genome XXIII Conference) https://pag.confex.com/pag/xxiii/webprogram/Paper16983.html [25/02/2015 15:00:12] 30 C. arabica accessions

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

<p>Abstract</p> <p>Background</p> <p>The fermented dried seeds of <it>Theobroma cacao </it>(cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust <it>T. cacao </it>cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected.</p> <p>Results</p> <p>Here, we describe the construction of a BAC-based integrated genetic-physical map of the <it>T. cacao </it>cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of <it>T. cacao </it>is 374.6 Mbp. A comparative analysis with <it>A. thaliana, V. vinifera</it>, and <it>P. trichocarpa </it>suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two <it>T. cacao </it>cultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed.</p> <p>Conclusions</p> <p>The results presented in this study are a stand-alone resource for functional exploitation and enhancement of <it>Theobroma cacao </it>but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the <it>T. cacao </it>genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.</p

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Made available in DSpace on 2018-07-12T01:02:16Z (GMT). No. of bitstreams: 1 Science2014Denoeud11814.pdf: 1559498 bytes, checksum: 6f5cdb42fd6c137acb3220e6d823a1f9 (MD5) Previous issue date: 2015-01-22bitstream/item/116215/1/Science-2014-Denoeud-1181-4.pd

Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae)

Phenylalanine ammonia lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway producing phenolics, widespread constituents of plant foods and beverages, including chlorogenic acids, polyphenols found at remarkably high levels in the coffee bean and long recognized as powerful antioxidants. To date, whereas PAL is generally encoded by a small gene family, only one gene has been characterized in Coffea canephora (CcPAL1), an economically important species of cultivated coffee. In this study, a molecular- and bioinformatic-based search for CcPAL1 paralogues resulted successfully in identifying two additional genes, CcPAL2 and CcPAL3, presenting similar genomic structures and encoding proteins with close sequences. Genetic mapping helped position each gene in three different coffee linkage groups, CcPAL2 in particular, located in a coffee genome linkage group (F) which is syntenic to a region of Tomato Chromosome 9 containing a PAL gene. These results, combined with a phylogenetic study, strongly suggest that CcPAL2 may be the ancestral gene of C. canephora. A quantitative gene expression analysis was also conducted in coffee tissues, showing that all genes are transcriptionally active, but they present distinct expression levels and patterns. We discovered that CcPAL2 transcripts appeared predominantly in flower, fruit pericarp and vegetative/lignifying tissues like roots and branches, whereas CcPAL1 and CcPAL3 were highly expressed in immature fruit. This is the first comprehensive study dedicated to PAL gene family characterization in coffee, allowing us to advance functional studies which are indispensable to learning to decipher what role this family plays in channeling the metabolism of coffee phenylpropanoids

Genomics, molecular genetics and the food industry

The production of foods for an increasingly informed and selective consumer requires the coordinated activities ofthe various branches of the food chain in order to provide convenient, wholesome, tasty, safe and affordable foods.Also, the size and complexity of the food sector ensures that no single player can control a single process from seedproduction, through farming and processing to a final product marketed in a retail outlet. Furthermore, the scientificadvances in genome research and their exploitation via biotechnology is leading to a technology driven revolutionthat will have advantages for the consumer and food industry alike. The segment of food processing aids, namelyindustrial enzymes which have been enhanced by the use of biotechnology, has proven invaluable in the productionof enzymes with greater purity and flexibility while ensuring a sustainable and cheap supply. Such enzymes producedin safe GRAS microorganisms are available today and are being used in the production of foods. A second rapidlyevolving segment that is already having an impact on our foods may be found in the new genetically modified crops.While the most notorious examples today were developed by the seed companies for the agro-industry directed at thefarming sector for cost saving production of the main agronomical products like soya and maize, its benefits are alsobeing seen in the reduced use of herbicides and pesticides which will have long term benefits for the environment.Technology-driven advances for the food processing industry and the consumer are being developed and may bedivided into two separate sectors that will be presented in greater detail:1. The application of genome research and biotechnology to the breeding and development of improved plants. Thismay be as an aid for the cataloging of industrially important plant varieties, the rapid identification of key qualitytraits for enhanced classical breeding programs, or the genetic modification of important plants for improvedprocessing properties or health characteristics.2. The development of advanced microorganisms for food fermentations with improved flavor production, health ortechnological characteristics. Both yeasts and bacteria have been developed that fulfill these requirements, but areas yet not used in the production of foods