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plant genetic resources for food and agriculture - FAO

plant genetic resources for food and agriculture - FAO

THE STATE-OF-THE-ART:

THE STATE-OF-THE-ART: METHODOLOGIES AND TECHNOLOGIES FOR THE IDENTIFICATION, CONSERVATION AND USE OF PGRFA based on linkage disequilibrium (non-random association between alleles at linked loci) without the necessity for creating structured segregating mapping populations. By mapping nearby SNPs it is therefore possible to ascertain the genome locations of genes associated with a trait without cloning the genes. Causal SNPs identified through high density association maps are usually subsequently confirmed through functional assays. There are three main advantages of association mapping over linkage analysis: increased mapping resolution, reduced research time and greater allele number. 42 The deployment of these strategies has been restricted primarily to crop improvement institutions which have also developed the capacity to produce sequence information for their target crops. National PGR conservation and utilization programmes are increasingly enhancing expertise and general capacity in plant biotechnology as documented in the country reports published as part of this SoWPGR-2. 43 International and other national efforts at capacity and infrastructure building have contributed to this emerging trend. However, full deployment of advanced breeding strategies, bioinformatics and genomics capabilities has not taken place in developing countries and even in many developed countries, they are only possible through collaboration with other national or international genomics projects. The challenge within a breeding programme would be the devising of appropriate strategies for the many different scenarios that call for the integration of molecular biology techniques in PGRFA 44 . For instance while, marker-assisted backcrossing might require a few markers for genotyping hundreds of samples (backcross progenies) for a particular simply inherited trait as would the screening for introgressed elements or GMO constructs, genetic characterization or fingerprinting on the other hand would require hundreds to thousands of markers in order to be effective. In general, a genomics research service centre would be required for programmes characterized by extensive marker diversity, high throughput and large sample sizes. This requirement for high start-up investment costs probably explains the preponderance of MAS applications in large multinational breeding companies to the exclusion of the publicly funded entities. Genetic transformation Methods based on recombinant DNA, i.e. molecules containing DNA sequences, derived from more than one source, are used to create novel genetic variations. In crop improvement, this has involved the incorporation of exogenous DNA or RNA sequences, using either biolistics or vectors, into the genome of the recipient organism which as a result expresses novel and agronomically useful traits. The new variants are referred to as genetically modified organisms or GMOs. Transgenic crops were first grown on a commercial scale in the mid-1990s about the time of the publication of the first SoW report. Since then, the commercially grown GMOs have been four commodity crops, namely, maize, soybean, canola and cotton). By 2008, these collectively accounted for over 99.5 percent of transgenic crop production (James, 2008 45 ). Interestingly also, only two transformation events, i.e. herbicide tolerance and insect resistance or their combinations were expressed in these crops. This implies therefore that more than 25 years after the first successful production of transgenic plants, the scope of the utility of genetic transformation as a routine crop improvement strategy remains limited in spite of the obvious potentials of this technology. The drawbacks include the lack of efficient genotypeindependent regeneration systems for most crops and probably most limiting of all factors is the associated IPR restrictions. When GMOs have remained the exclusive preserve of private sector breeding enterprises in developed countries it has restricted (with patents) several components of the research and development efforts in the lead up to production of the transgenic crops. The interesting emerging trends - that could ultimately precipitate the review of the place of IPR protections in PGRFA - are that GMO crops are currently grown in developing countries as exemplified in the cultivation of transgenic soybean in South America and the cultivation of transgenic cotton in both India and China (James, 2008; Glover 2007, 46 2008 47 ). As more developing countries acquire the requisite capacity for dealing with the statutory regulations governing the cultivation of GMOs, especially in line with biosafety regulations as enunciated in the 295

APPENDIX 3 Cartagena Protocol on Biosafety, concerted efforts will need to be targeted at building capacity to navigate the IPR restrictions that effectively impeded the exploration of the full potentials of transgenesis in PGRFA. Moving forward, it is surmised that research efforts on the other hand will target the refining of plant regeneration systems and, quite importantly, expanding the scope of agronomic traits that can be improved using genetic transformation. So far, the stacking of several transformation events and getting them to express phenotypes in one recipient organism has remained impractical. Removing the technological barriers will be key to taking advantage of genetic transformation to address polygenic traits, especially those related to climate change and variations such as drought and salinity. Removing this bottleneck will also be important for gene pyramiding. A3.7 Bioinformatics One consequence of the relative ease for generating molecular genetic data has been the need for ever increasing capacity for electronic data storage, analysis and retrieval systems. Currently, the data storage requirements are estimated in petabytes, about three orders of magnitude greater than what was commonly in use in 1995. A trend in cost reductions for bioinformatics facilities is that costly mainframe computer installations for bioinformatics work have been mainly replaced at genomics centres by computer server farms comprised of off-theshelf, ordinary PCs or servers harnessed together to provide equal or greater computing capacity at lower cost and with built-in Central Processing Unit (CPU) redundancy. These units are conditioned to ensure greater reliability even with individual unit failures. Access to such storage and analysis systems is increasingly made available by the incorporation of internet servers within the system. It is the combination of creative software engineering, open-source operating systems and database software, the advent of the ubiquitous access to, and use of, the Internet and both private and public investment that have led to the availability of reliable tools to manage genomics laboratories and hence the 296 THE SECOND REPORT ON THE STATE OF THE WORLD’S PGRFA capacity to store, analyse, distribute and interpret the massive datasets generated from sequencing projects and molecular biology based activities. New algorithms and statistics are continually necessary to study relationships among data sets. Maps are the most common formats for presenting genetic information and developing software for producing and displaying maps has remained one of the most active fields of research and development in molecular biology. Advances in bioinformatics will continue to be necessary to facilitate the analysis of genomic data and the integration of genomics information with data from the related fields of transcriptomics, proteomics, metabolomics and phenomics. Collaborative genome projects have led to the creation of databases that store data centrally but are accessible globally. Integral to such efforts are collections of genomic resources whose inventories and access are components of the genome database. Funding for such projects has been largely within the public sector (nationally and internationally). A3.8 Policy, organizational and legal considerations The major international instrument impacting PGR conservation and use since 1995 was the ITPGRFA which was adopted in 2001 and came into force in 2004. 48 This agreement, aimed at improving upon the Convention on Biological Diversity, obligates parties to the Treaty to develop legislation and regulations to fulfill its mandates to facilitate conservation, exchange and use of the genetic resources covered by the ITPGRFA. The development of a specialized funding mechanism for the ITPGRFA subsequently took place and the GCDT was created in 2004. Currently, the GCDT is raising an endowment and additional funding for upgrading national germplasm collection facilities, building capacity and strengthening information systems. Special focus has been on the collaborative development of regional and global crop conservation strategies. 49 A major development in the exchange of PGRFA since the first SoW report has been the SMTA that provides the Contracting Parties

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    The Second Report on THE STATE OF T

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    I hope and trust that the informati

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    2.4 Global challenges to in situ co

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    5.5 Changes since the first State o

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    Appendix 2 Major germplasm collecti

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    3.2 Holders of the six largest ex s

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    The CGRFA requested that the SoWPGR

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    Chapter 7 - Access to plant genetic

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    Executive summary �his report des

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    documentation and characterization

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    Given the high level of interdepend

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    Chapter 1 The state of diversity CH

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    CHAPTER 1 1.2.1 Changes in the stat

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    TABLE 1.2 Comparison between the co

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    CHAPTER 1 in national agricultural

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    FIGURE 1.1 Global priority genetic

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    12 CHAPTER 1 AFRICA • Benin Molec

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    14 CHAPTER 1 NEAR EAST effective at

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    CHAPTER 1 comparisons, or use the i

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    18 CHAPTER 1 FIGURE 1.3 Interdepend

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    TABLE 1.4 (continued) Indicators of

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    CHAPTER 1 even national, germplasm

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    24 CHAPTER 1 9 Hammer, K. 2003. A p

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    26 CHAPTER 1 X. & Li, Z. 2006. Gene

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    THE STATE OF IN SITU MANAGEMENT 2.1

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    THE STATE OF IN SITU MANAGEMENT (ba

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    THE STATE OF IN SITU MANAGEMENT the

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    THE STATE OF IN SITU MANAGEMENT Max

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    THE STATE OF EX SITU CONSERVATION 3

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    THE STATE OF EX SITU CONSERVATION F

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    THE STATE OF EX SITU CONSERVATION A

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    THE STATE OF EX SITU CONSERVATION A

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    THE STATE OF EX SITU CONSERVATION C

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    THE STATE OF EX SITU CONSERVATION N

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    THE STATE OF EX SITU CONSERVATION t

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    THE STATE OF EX SITU CONSERVATION 1

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    Chapter 4 The state of use CHAPTER

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    96 CHAPTER 4 very similar (approxim

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    98 CHAPTER 4 including rice, maize

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    CHAPTER 4 In the United States of A

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    CHAPTER 4 biosafety monitoring and

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    CHAPTER 4 improvement. While the fi

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    CHAPTER 4 exchange of material and

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    CHAPTER 4 seed legislation to meet

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    CHAPTER 4 A number of countries 36

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    CHAPTER 4 Different plants are rich

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    CHAPTER 4 breeding activities over

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    118 CHAPTER 4 16 Op cit. Endnote 8.

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    Chapter 5 The state of national pro

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    CHAPTER 5 national system based on

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    CHAPTER 5 involvement vary from the

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    CHAPTER 5 of Bolivia, for example,

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    CHAPTER 5 In some countries includi

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    CHAPTER 5 Africa, Burkina Faso, Cam

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    CHAPTER 5 Box 5.2 India’s Protect

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    CHAPTER 5 the adoption of national

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    138 CHAPTER 5 10 Available at: http

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    Chapter 6 The state of regional and

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    CHAPTER 6 a) those that focus on co

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    146 CHAPTER 6 PGRN has continued to

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    CHAPTER 6 • the Regional Cooperat

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    CHAPTER 6 and African countries for

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    CHAPTER 6 few years, the CGIAR Syst

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    CHAPTER 6 Varieties. Central Americ

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    CHAPTER 6 the first SoW report was

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    160 CHAPTER 6 12 Available at: www.

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    Chapter 7 Access to Plant Genetic R

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    CHAPTER 7 Box 7.1 Benefit-sharing u

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    CHAPTER 7 laws, regulations and con

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    170 CHAPTER 7 THE SECOND REPORT ON

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    CHAPTER 7 has been adapted to incor

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    CHAPTER 7 changes after the initial

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    CHAPTER 7 regional workshops on Far

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    THE CONTRIBUTION OF PGRFA TO FOOD S

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    LIST OF COUNTRIES THAT PROVIDED INF

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    LIST OF COUNTRIES THAT PROVIDED INF

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    Annex 2 Regional distribution of co

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    EUROPE 214 ANNEX 2 ASIA AND THE PAC

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    STATUS BY COUNTRY OF NATIONAL LEGIS

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    MAJOR GERMPLASM COLLECTIONS BY CROP

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    346 APPENDIX 4 217 Op cit. Endnote

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    348 APPENDIX 4 291 Op cit. Endnote

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    350 APPENDIX 4 366 Ibid. Endnote 35

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    BAAFS Beijing Academy of Agricultur

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    CN Centre Néerlandais (Côte d’I

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    DTRUFC División of Tropical Resear

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    HRIGRU Horticultural Research Inter

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    INIA CARI Centro Regional de Invest

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    IVM Institute of Grape and Wine «M

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    NISM National Information Sharing M

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    REHOVOT Department of Field and Veg

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    SRI Sugar Crop Research Institute,

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    WCMC World Conservation Monitoring

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