Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance

BMC Genomics BioMed Central Research article Open Access Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance Javier Terol1, Ana Conesa1, Jose M Colmenero1, Manuel Cercos1, Francisco Tadeo1, Javier Agustí1, Enriqueta Alós1, Fernando Andres1, Guillermo Soler1, Javier Brumos1, Domingo J Iglesias1, Stefan Götz2, Francisco Legaz1, Xavier Argout3, Brigitte Courtois3, Patrick Ollitrault4, Carole Dossat5, Patrick Wincker5, Raphael Morillon4 and Manuel Talon*1 Address: 1Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain, 2BET-ITACA, Universidad Politécnica de Valencia, Camino de Vera, s/n 46022 Valencia, Spain, 3CIRAD AMIS, UMR PIA – Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France, 4Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry, France and 5CIRAD FLHOR, UPR "Amélioration génétique d'espèces à multiplication végétative", Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France Email: Javier Terol - ; Ana Conesa - ; Jose M Colmenero - ; Manuel Cercos - ; Francisco Tadeo - ; Javier Agustí - ; Enriqueta Alós - ; Fernando Andres - ; Guillermo Soler - ; Javier Brumos - ; Domingo J Iglesias - ; Stefan Götz - ; Francisco Legaz - ; Xavier Argout - ; Brigitte Courtois - ; Patrick Ollitrault - ; Carole Dossat - ; Patrick Wincker - ; Raphael Morillon - ; Manuel Talon* - * Corresponding author Published: 25 January 2007 BMC Genomics 2007, 8:31 doi:10.1186/1471-2164-8-31 Received: 19 July 2006 Accepted: 25 January 2007 This article is available from: http://www.biomedcentral.com/1471-2164/8/31 © 2007 Terol et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. Results: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis × Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of ~13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains Page 1 of 22 (page number not for citation purposes) BMC Genomics 2007, 8:31 http://www.biomedcentral.com/1471-2164/8/31 Conclusion: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays. Background Citrus fruits are the first fruit crop in international trade in terms of economic value (FAO, 2004). Citrus fruits are typically grown in 140 countries located in tropical and subtropical areas with "Mediterranean" type climates, often facing severe abiotic stresses such as salinity, drought and iron chlorosis. Citrus species also suffer from different diseases and pests that considerably affect tree growth and fruit crop. The survival of the citrus industry is today critically dependent on genetically superior cultivars. However, citrus improvement through traditional techniques is unfortunately very difficult due to the unusual combination of biological characteristics of Citrus species, their low genetic diversity and the long-term nature of tree breeding. Thus, Citrus show many biological characteristics such as gametophytic self- and crossincompatibility, apomixy, juvenility, heterozygosis, dormancy, and surprising root/shoot interactions, that strongly hamper Citrus breeding. On the other hand, genetic and allelic diversity in Citrus cultivars is very scarce. The global linkage disequilibrium in the cultivated citrus that probably originated from three major taxa, may be the result of an initial allopatric evolution and further limitation for predominant apomixy [1]. The fact that only mutational and/or epigenetic events are apparently involved in the diversification of secondary species, combined with human selection, have strongly reduced global genetic diversity, restricting opportunity for genetic advance. Genomics has provided new tools for crop improvement, helping to identify and select candidate genes responsible of agronomic characters of interest, and allowing the development of fast methods to incorporate these characters into crop plants. After the completion of the Arabidopsis genome sequence [2] and the publication of sequences of indica [3] and japonica [4] rice, plant researchers have been able to scan these genomes to identify and compare genes of interest. The completion of the poplar genome sequence [5] will supply a model for tree life forms. EST sequencing projects have facilitated appropriate strategies for gene discovery [6], molecular markers identification [7,8], and (...truncated)