Update TRENDS in Plant Science decade has mobilized a partnership of private and public research groups to focus on the development of new technologies to support T cacao genetic improvement http www ars grin gov ars SoAtlantic Miami ngr cacao genetics meeting summary pdf with a degree of coordination by the International Group for Genetic Improvement of Cocoa INGENIC which promotes the exchange of information and international collaboration on topics related to cocoa genetics This initiative comes at a time of unprecedented new genomic tools that dramatically increase the genetic knowledge to inform breeding strategies and to accelerate notoriously slow tree breeding programs Over the next decade T cacao is likely to become a model of an essentially wild crop being transformed through genome based breeding It will be interesting to see whether these new tools can provide the basis simultaneously to address the improvement of cocoa productivity while maintaining the quality characteristics of the bean that are crucial for chocolate production References 1 Dillinger T L et al 2000 Foods of the gods cure for humanity A cultural history of the medicinal and ritual uses of chocolate J Nutr 130 2057S 2072S 2 Kris Etherton P M and Keen C L 2002 Evidence that the antioxidant flavonoids in tea and cocoa are beneficial for cardiovascular health Curr Opin Lipidology 13 41 49 3 Eskes B 2001 Introductory notes Proceedings of the International Workshop on New Technologies for Cocoa Breeding Kota Kinabalu Malaysia INGENIC London UK pp 8 11 4 Lockwood R 2003 Who needs clothing INGENIC Newsl 8 2 5 Vol 8 No 12 December 2003 563 5 Lanaud C et al 1995 A genetic linkage map of Theobroma cacao L Theor Appl Genet 91 987 993 6 Risterucci A M et al 2000 A high density linkage map of Theobroma cacao L Theor Appl Genet 101 948 955 7 Cheesman E E 1944 Notes on the nomencature classification and possible relationships of cocoa populations Trop Agri 21 144 159 8 Cuatracasas J 1964 Cacao and its allies a taxonomic revision of the genus Theobroma Contrib US Herb 35 379 614 9 De la Cruz M et al 1995 Origins of cacao cultivation Nature 375 542 543 10 Motamayor J C et al 2002 Cacao domestication I the origin of the cacao cultivated by the Mayas Heredity 89 380 386 11 Crouzillat D et al 2000 Quantitative trait loci analysis in Theobroma cacao using molecular markers inheritance of polygenetic resistance to Phytophthora palmivora in two related cacao populations Euphytica 114 25 36 12 Flament M H et al 2001 Genetic mapping of resistance factors to Phytopthora palmivora in cocoa Genome 44 79 85 13 Queiroz V T et al 2003 Identification of a major QTL in cocoa Theobroma cacao L associated with resistance to witches broom disease Plant Breed 122 268 272 14 Lanaud C et al 2001 Implications of new insight into the genetic structure of Theobroma cacao L for breeding strategies Proceedings of the International Workshop on New Technologies for Cocoa Breeding Kota Kinabalu Malaysia INGENIC London UK pp 89 107 15 Saunders J A et al 2001 USDA DNA fingerprinting program for identification of Theobroma cacao accessions Proceedings of the International Workshop on New Technologies for Cocoa Breeding Kota Kinabalu Malaysia INGENIC London UK pp 108 114 16 Jones P G et al 2002 Gene discovery and microarray analysis of cacao Theobroma cacao L varieties Planta 216 255 264 1360 1385 see front matter q 2003 Elsevier Ltd All rights reserved doi 10 1016 j tplants 2003 10 004 Why are there so many carbohydrate active enzyme related genes in plants Pedro M Coutinho Mark Stam Eric Blanc and Bernard Henrissat Architecture et Fonction des Macromole cules Biologiques UMR 6098 Centre National de la Recherche Scientifique Universite s Aix Marseille I and II 31 Chemin Joseph Aiguier 13402 Marseille cedex 20 France Plants contain far more carbohydrate active enzymeencoding genes than any other organism sequenced to date The extremely large number of glycosidase and glycosyltransferase related genes in plant genomes can be explained by the complex structure of the plant cell wall by ancient genome duplication and by recent local duplications but also by the recent emergence of novel and unrelated protein functions based on widely available pre existing scaffolds In plants carbohydrates in the form of glycosides are central to many biological pathways from cell wall structure to energy signalling and defence Glycosides are made from activated sugars by glycosyltransferases Corresponding author Bernard Henrissat bernard henrissat afmb cnrs mrs fr http plants trends com and are degraded by glycoside hydrolases glycosidases Genes encoding glycosidases and glycosyltransferases in all organisms all data available from the CarbohydrateActive enZymes server at http afmb cnrs mrs fr CAZY are currently analysed and listed based on the classifications of glycosidases 1 and glycosyltransferases 2 in sequence and structure based families Now that the genomes of many organisms have been completely sequenced it is possible to analyse the content of genomes from a global glycobiological perspective Content of genomes in carbohydrate active enzyme related genes One of the intriguing features of the analysis of the sequenced genomes is that for bacteria and for eukaryotes there appears to be a global correlation between the number of glycosidase and glycosyltransferase related genes and the Update 564 TRENDS in Plant Science total number of genes in the organism Figure 1 The archaea do not show such a correlation and it is likely that many if not all of their glycosidases have been acquired by horizontal transfer i e by transfer of genetic material between organisms other than by descent Figure 1 shows that Arabidopsis is a clear outlier with almost 800 glycosidase and glycosyltransferase related genes comprising 3 3 of its genes 3 By comparison the human genome has only 350 glycosidase and glycosyltransferase related genes Number of GH and GT related genes Origins of the multiplicity of carbohydrate active enzyme related genes in plants A survey of the sequences deposited in GenBank shows that the rice genome is likely to show a similar bias So why do plants have so many glycosidase and glycosyltransferase related genes There are several complementary explanations to this the most obvious being that many different glycosidases and glycosyltransferases are probably required for the biosynthesis and degradation of the complex polysaccharides of the plant cell wall