A wake-up call with coffee Dani Zamir Science 345, 1124 (2014); DOI: 10.1126/science.1258941
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Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. Copyright 2014 by the American Association for the Advancement of Science; all rights reserved. The title Science is a registered trademark of AAAS.
Downloaded from www.sciencemag.org on September 4, 2014
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INSIGHTS | P E R S P E C T I V E S
The worldwide production of Arabica coffee relies on a small number of cultivars with very little genomic and phenotypic diversity between them, relative to those available in Africa, the center of origin. The key for ensuring that coffee can survive as an affordable crop lies in the genetic variation found in African species. This variation will help to mitigate the effects of unstable By Dani Zamir climate and plant diseases, as well as modify the wealth of healthhe captain of the starship related chemicals present in the Voyager from one of the coffee seeds (6) (e.g., naturally delatter-day Star Trek televicaffeinated Arabica coffee) (7). sion series expressed the A recent survey of coffee gesentiments of many by netic resources in Ethiopia found stating: “Coffee, the finan alarming rate of genetic eroest organic suspension ever desion of the gene pool due to deforvised.” On page 1181, Denoeud et estation coupled with inadequate al. present a draft genome of the conservation efforts. According diploid Coffea canephora (1), one to the Biological Diversity Conof the two founder species of the vention (8), the benefits derived tetraploid crop Coffea arabica. from discoveries made on the Coffee, the plant bearing the irbasis of biodiversity must be Smell the cofee. Cofea canephora joins many other crop species and varieties resistible bean that delivers the equitably shared with the counwith a draft genome sequence. most widely consumed psychotry of origin. The complexity of active drug in the world—caffeine—joins ing of repositories for data generated from monitoring beneficial traits introduced a long list of crop species that have been the many phenotypic studies that are being from endemic species often leads to situasequenced using ever-improving genomic conducted on sequenced plant varieties (3). tions where countries refuse to make their hardware and assembly software (2). HighWhat’s worse is that in most cases folgenetic resources accessible. Perhaps the quality genome assemblies facilitate the lowing publication of crop biology papers, draft coffee genome presented by Denoeud resequencing of many cultivated varieties, molecular data are released without the et al. can be used to provide an unequivolandraces (local ecotypes), and sometimes corresponding potentially commercially cal means to monitor, via SNP diversity, the wild, crop-related species. The challenge valuable phenotypic data. For example, in utilization of genetic resources after they now is to translate these decoded genomes rice (Oryza sativa), which feeds roughly leave their country of origin. The substaninto new and improved tools for plant half the world population, 3000 variants tial value of the coffee production chain breeding; there is a need for a better balfrom 89 countries were sequenced revealis accrued by highly profitable companies ance of research priorities, with greater eming 18.9 million single-nucleotide polymorthat transport, roast, blend, and sell the cofphasis on crop phenotypes. phisms (SNPs) (4). But what good are 3000 fee; these are typically located in rich, cofLinking genotypes to phenotypes is curgenomes if the associated phenotypic data, fee-importing countries. The danger to the rently a game with few rules, particularly and sometimes seed stocks, are kept procoffee crop (5) should provide an incentive when traits are challenging to describe or prietary? A wake-up call is needed for scifor all stakeholders to initiate international measure because of their continuous distrientists, granting agencies, journal editors, collaborations in genomic-assisted breedbution in populations—for example, mean and referees: What we eat are phenotypes, ing projects and germ plasm conservation yield or yield stability. One reason for the and seriously addressing global food secuwith poor, coffee-exporting countries. This slower progress in the arena of crop prority demands that, at least in the domain proposal is compatible with the fact that ductivity phenotyping is that scientists in of crop plants, phenotypic data should be coffee is the most popular plant associacademic institutions are less inclined to shared between scientists in the same manated with genomics, because every genome be passionate about observable or simply ner as for sequences (3). meeting has coffee breaks that are needed measured traits than about results from Coffee, which is admired for its aroma, to reinvigorate the audiences and to prosophisticated high-throughput machines flavor, and the alkaloid stimulant caffeine, mote communication, conversation, and that profile many molecular or growthhas a number of attributes that make it parthe sharing of knowledge. ■ related traits. In addition, phenotyping of ticularly suitable for linking genomes and REFERENCES such integrative quantitative traits is much phenotypes for the purpose of sustaining 1. F. Denoeud et al., Science 345, 1181 (2014). more challenging to archive than the digital an industry that is struggling with climate 2. R. K. Varshney, R. Terauchi, S. R. McCouch, PLOS Biol. 12, cracking of four-base nucleic acid codes or change and pests (5). The center of coffee e1001883 (2014). 3. D. Zamir, PLOS Biol. 11, e1001595 (2013). 20 amino acid–based proteins. Unlike the diversity is in Africa. From there the bev4. 3,000 Rice Genomes Project, GigaScience 3, 7 (2014). well-established, publicly available reposierage spread throughout the world begin5. M. Gross, Curr. Biol. 24, R503 (2014). tories for DNA and proteins, there exists ning as early as 500 years ago. Nowadays, 6. J. P. Labouisse, B. Bellachew, S. Kotecha, B. Bertrand, Genet. Resour. Crop Evol. 55, 1079 (2008). no equivalent consensus on the structurthe top coffee-growing countries are Brazil, 7. M. B. Silvarolla, P. Mazzafera, L. C. Fazuoli, Nature 429, 826 Vietnam, Indonesia, Colombia, and Ethio(2004). pia—this last being the birthplace of the 8. S. McCouch et al., Nature 499, 23 (2013). Institute of Plant Sciences and Genetics, Faculty of crop plant and where more than 1 million Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel. E-mail: [email protected] 10.1126/science.1258941 households are engaged in growing coffee. BOTANY
A wake-up call with coffee Recording and archiving crop phenotype diversity needs to catch up with genomic data
1124
sciencemag.org SCIENCE
5 SEP TEMBER 2014 • VOL 345 ISSUE 6201
Published by AAAS
PHOTO: JOHN M. SCOTT/ISTOCKPHOTO
T
This copy is for your personal, non-commercial use only.
If you wish to distribute this article to others, you can order high-quality copies for your colleagues, clients, or customers by clicking here.
The following resources related to this article are available online at www.sciencemag.org (this information is current as of September 4, 2014 ): Updated information and services, including high-resolution figures, can be found in the online version of this article at: http://www.sciencemag.org/content/345/6201/1124.full.html A list of selected additional articles on the Science Web sites related to this article can be found at: http://www.sciencemag.org/content/345/6201/1124.full.html#related This article cites 8 articles, 1 of which can be accessed free: http://www.sciencemag.org/content/345/6201/1124.full.html#ref-list-1 This article appears in the following subject collections: Botany http://www.sciencemag.org/cgi/collection/botany Genetics http://www.sciencemag.org/cgi/collection/genetics
Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. Copyright 2014 by the American Association for the Advancement of Science; all rights reserved. The title Science is a registered trademark of AAAS.
Downloaded from www.sciencemag.org on September 4, 2014
Permission to republish or repurpose articles or portions of articles can be obtained by following the guidelines here.
INSIGHTS | P E R S P E C T I V E S
The worldwide production of Arabica coffee relies on a small number of cultivars with very little genomic and phenotypic diversity between them, relative to those available in Africa, the center of origin. The key for ensuring that coffee can survive as an affordable crop lies in the genetic variation found in African species. This variation will help to mitigate the effects of unstable By Dani Zamir climate and plant diseases, as well as modify the wealth of healthhe captain of the starship related chemicals present in the Voyager from one of the coffee seeds (6) (e.g., naturally delatter-day Star Trek televicaffeinated Arabica coffee) (7). sion series expressed the A recent survey of coffee gesentiments of many by netic resources in Ethiopia found stating: “Coffee, the finan alarming rate of genetic eroest organic suspension ever desion of the gene pool due to deforvised.” On page 1181, Denoeud et estation coupled with inadequate al. present a draft genome of the conservation efforts. According diploid Coffea canephora (1), one to the Biological Diversity Conof the two founder species of the vention (8), the benefits derived tetraploid crop Coffea arabica. from discoveries made on the Coffee, the plant bearing the irbasis of biodiversity must be Smell the cofee. Cofea canephora joins many other crop species and varieties resistible bean that delivers the equitably shared with the counwith a draft genome sequence. most widely consumed psychotry of origin. The complexity of active drug in the world—caffeine—joins ing of repositories for data generated from monitoring beneficial traits introduced a long list of crop species that have been the many phenotypic studies that are being from endemic species often leads to situasequenced using ever-improving genomic conducted on sequenced plant varieties (3). tions where countries refuse to make their hardware and assembly software (2). HighWhat’s worse is that in most cases folgenetic resources accessible. Perhaps the quality genome assemblies facilitate the lowing publication of crop biology papers, draft coffee genome presented by Denoeud resequencing of many cultivated varieties, molecular data are released without the et al. can be used to provide an unequivolandraces (local ecotypes), and sometimes corresponding potentially commercially cal means to monitor, via SNP diversity, the wild, crop-related species. The challenge valuable phenotypic data. For example, in utilization of genetic resources after they now is to translate these decoded genomes rice (Oryza sativa), which feeds roughly leave their country of origin. The substaninto new and improved tools for plant half the world population, 3000 variants tial value of the coffee production chain breeding; there is a need for a better balfrom 89 countries were sequenced revealis accrued by highly profitable companies ance of research priorities, with greater eming 18.9 million single-nucleotide polymorthat transport, roast, blend, and sell the cofphasis on crop phenotypes. phisms (SNPs) (4). But what good are 3000 fee; these are typically located in rich, cofLinking genotypes to phenotypes is curgenomes if the associated phenotypic data, fee-importing countries. The danger to the rently a game with few rules, particularly and sometimes seed stocks, are kept procoffee crop (5) should provide an incentive when traits are challenging to describe or prietary? A wake-up call is needed for scifor all stakeholders to initiate international measure because of their continuous distrientists, granting agencies, journal editors, collaborations in genomic-assisted breedbution in populations—for example, mean and referees: What we eat are phenotypes, ing projects and germ plasm conservation yield or yield stability. One reason for the and seriously addressing global food secuwith poor, coffee-exporting countries. This slower progress in the arena of crop prority demands that, at least in the domain proposal is compatible with the fact that ductivity phenotyping is that scientists in of crop plants, phenotypic data should be coffee is the most popular plant associacademic institutions are less inclined to shared between scientists in the same manated with genomics, because every genome be passionate about observable or simply ner as for sequences (3). meeting has coffee breaks that are needed measured traits than about results from Coffee, which is admired for its aroma, to reinvigorate the audiences and to prosophisticated high-throughput machines flavor, and the alkaloid stimulant caffeine, mote communication, conversation, and that profile many molecular or growthhas a number of attributes that make it parthe sharing of knowledge. ■ related traits. In addition, phenotyping of ticularly suitable for linking genomes and REFERENCES such integrative quantitative traits is much phenotypes for the purpose of sustaining 1. F. Denoeud et al., Science 345, 1181 (2014). more challenging to archive than the digital an industry that is struggling with climate 2. R. K. Varshney, R. Terauchi, S. R. McCouch, PLOS Biol. 12, cracking of four-base nucleic acid codes or change and pests (5). The center of coffee e1001883 (2014). 3. D. Zamir, PLOS Biol. 11, e1001595 (2013). 20 amino acid–based proteins. Unlike the diversity is in Africa. From there the bev4. 3,000 Rice Genomes Project, GigaScience 3, 7 (2014). well-established, publicly available reposierage spread throughout the world begin5. M. Gross, Curr. Biol. 24, R503 (2014). tories for DNA and proteins, there exists ning as early as 500 years ago. Nowadays, 6. J. P. Labouisse, B. Bellachew, S. Kotecha, B. Bertrand, Genet. Resour. Crop Evol. 55, 1079 (2008). no equivalent consensus on the structurthe top coffee-growing countries are Brazil, 7. M. B. Silvarolla, P. Mazzafera, L. C. Fazuoli, Nature 429, 826 Vietnam, Indonesia, Colombia, and Ethio(2004). pia—this last being the birthplace of the 8. S. McCouch et al., Nature 499, 23 (2013). Institute of Plant Sciences and Genetics, Faculty of crop plant and where more than 1 million Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel. E-mail: [email protected] 10.1126/science.1258941 households are engaged in growing coffee. BOTANY
A wake-up call with coffee Recording and archiving crop phenotype diversity needs to catch up with genomic data
1124
sciencemag.org SCIENCE
5 SEP TEMBER 2014 • VOL 345 ISSUE 6201
Published by AAAS
PHOTO: JOHN M. SCOTT/ISTOCKPHOTO
T
