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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 a number of populations of a species for diversity - as measured by a neutral molecular marker - is to accord higher priority for conservation to the most diverse populations with the assumption that this will also conserve the greatest adaptive genetic diversity, the researcher may decide that relatively few populations might be needed to capture the greatest amount of the neutral genetic diversity. A possible pitfall in this scenario is that if, for instance, the other populations were abandoned to the exclusion of the few diverse populations, significant amounts of adaptive genetic diversity, which is not distributed uniformly among all populations, would thus be lost. This would then be contrary to the originally stated objective for the assessment of genetic diversity. 33 Molecular markers are also increasingly been used in more downstream applications. For instance, in addition to serving as tools for conserving and using genetic resources, markers have been used successfully to investigate the genetic impacts of traditional farmer practices which are often poorly documented. A case study involving yams in Benin showed that the traditional practice by farmers of selecting spontaneous wild yams from areas surrounding farms and cultivating them resulted in the creation of new varieties with new genetic combinations. These new variants arose as a direct result of sexual reproduction between wild and cultivated yams as the alleles could be traced to the progenitors. The markers used in this study were SSRs. It was therefore deduced that the mix of a cycle of sexual reproduction followed by the traditional vegetative propagation (using tubers) leads to the large-scale cultivation of the best genotypes while facilitating the introgression of potential diversity that could be useful for future adaptation. 34 A3.5 Conservation technologies and strategies An aspect of the use and conservation of PGRFA that has remained largely without significant advances since the first SoW Report is the orthodox seed storage conditions. Current recommendations for temperature and humidity are still the same as those developed before the first SoW report. Since then, however, the country reports that are part of this SoWPGR-2 and the crop-specific conservation strategy developed by the GCDT, call attention to the concerns for backlogs in accession testing and regeneration. For instance, it has been reported that viability testing results have indicated the need for regeneration after shorter periods of storage than were currently the norm. It is possible that, as one researcher has shown, humidity is the more critical of the two storage factors, and that seeds are exposed to higher humidity levels in the seed packaging materials than are optimal with resulting losses of viability. 35 Given the room for potential enhancements in efficiencies in seed storage, it is probably time to apply the innovative tools of biology to decipher the seemingly complex interactions in the seed storage container types, temperature and humidity regimen matrices. 36 In the past 12 years, there have been progressively increasing reports of the assessments of the utility of molecular markers as reliable tools for managing conserved diversity in genebanks. One example of this kind of study was the use of AFLP markers to assess the extent of within-accession genetic diversity for the self-fertilizing species, lettuce, at the Centre for Genetic Resources (CGN), in the Netherlands. Two plants each with a total of 1390 accessions, (comprising six cultivar types) were screened by the array of available markers. Overall, there was a very low average probability (about one percent) that the two plants of an accession would differ. However, this probability differed among the cultivar types. The types composed of accessions that are primarily modern cultivars had probabilities of difference between the two plants of about 0.5 percent, while the two types composed of accessions which are mainly landraces had probabilities greater than one. This information would be useful in determining whether and how the observed level of diversity for each accession should be maintained in future generations of the accession. 37 The utility of molecular markers in contributing to decisions in strategies for managing conserved diversity has also been demonstrated amply with field collections. Fingerprinting techniques have been used to determine identity and redundancy in large field collections. For example, at the ICGT in 293

APPENDIX 3 Trinidad and Tobago, over 2 000 crop accessions are maintained as a field collection, with each accession being represented by as many as 16 individual trees, with an overall average of six trees per accession. Multi-locus SSR fingerprinting was successfully used to resolve ambiguities arising from mislabelling of plants, a critical problem in such extensive operations. 38 An emerging trend, for the past 12 years has been the maintenance of DNA banks of PGRFA. There have been reported cases of DNA libraries of germplasm accessions, mapping populations, breeding materials, etc. that are retrieved at will for use in subjecting the materials to molecular assays. This practice is bound to become more pervasive as the costs for molecular assays and the requisite facilities become cheaper in turn rendering this technology option more accessible to practitioners in this field. It is indicative of this trend that more formal repositories for plant DNA have been established under the auspices of botanic gardens (with examples including the RGB Kew DNA Bank or the DNA bank at the Berlin Botanic Garden and Botanical Museum) or as stand-alone entities (e.g. the Australian Plant DNA Bank and the National Institute of Agrobiological Sciences [NIAS] DNA Bank, Japan). In addition to the usual data management platforms for classical germplasm accessions, an associated bioinformatics facility is required for a DNA bank in order to accommodate the management of molecular data such as sequence and marker information for each accession. DNA banks could also serve as sources of genetic information from endangered taxa without the need for additional germplasm prospection. 39 A3.6 Breeding methodologies Upfront, it is worthy to emphasize that the use of genomic tools in the different facets of PGRFA management has not reduced the importance of phenotypic characterization of breeding materials, mapping populations and natural populations, or genebank accessions. On the contrary, thorough and accurate phenotyping remains as important as it has ever been and is key to the utility of molecular data as markers have value only as long as they are accurately linked to phenotypes. 294 THE SECOND REPORT ON THE STATE OF THE WORLD’S PGRFA Early efforts to develop large numbers of molecular markers, high-density genetic maps and appropriately structured mapping populations have now begun to enhance the efficiency of the genetic improvement of many crop species. The results from numerous mapping studies provide greatly improved estimates for the number of loci, allelic effects and gene action controlling traits of interest. 40 There have been several major advances in the incorporation of molecular techniques in crop breeding strategies since the publication of the first SoW report. These advances have led to the paradigm of molecular breeding, the collective term that encompasses marker assisted selection and recombinant DNA technologies as crop improvement strategies. MAS This refers to the novel crop improvement strategy of using molecular markers (genome landmarks) to aid decision making in the screening of breeding materials. This paradigm shift has been greatly facilitated by high-throughput methods for identifying and using molecular markers on a large scale, including information technology infrastructure, and by interdisciplinary approaches that make phenotyping and trait characterizations possible across several environments. Firm verifications of the co-segregation of the trait of interest with one of the many possible types of DNA markers precede the use of the marker to select for the trait in breeding materials. MAS is becoming a valuable tool for many different crops with its utility expected to greatly increase as molecular biology assays become more cost efficient. 41 Marker development has been greatly facilitated by improvements in the genome locations of gene alleles that control traits. The advances in the construction of molecular genetic linkage maps, in building physical maps and more recently, association mapping, contribute to continually populate the repertoire of useful molecular markers for crop improvement. Association mapping, also known as linkage disequilibrium (LD) mapping or association analysis and the most novel of the mapping methods, is a population-based survey used to link sequence polymorphisms (usually SNPs) to phenotypic variations

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    The Second Report on THE STATE OF T

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    Appendix 2 Major germplasm collecti

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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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    Chapter 1 The state of diversity CH

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    FIGURE 1.1 Global priority genetic

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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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    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 EX SITU CONSERVATION 3

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    THE STATE OF EX SITU CONSERVATION 1

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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 biosafety monitoring and

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    CHAPTER 4 improvement. While the fi

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    CHAPTER 4 A number of countries 36

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    118 CHAPTER 4 16 Op cit. Endnote 8.

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    CHAPTER 5 Box 5.2 India’s Protect

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    146 CHAPTER 6 PGRN has continued to

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    Chapter 7 Access to Plant Genetic R

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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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    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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