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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 Gossypium hirsutum, Glycine max, Hordeum vulgare, Lotus japonicus, Medicago truncatula, Sorghum bicolor, Solanum lycopersicum, Triticum aestivum, Vitis vinifera and Zea mays. 16 Another source of sequence information is the collections of expressed sequence tags (ESTs, produced by the sequencing of complimentary DNA or cDNA libraries) that are being generated for many crops. Maize, wheat, rice, barley, soybean and Arabidopsis have the largest collections of EST sequences for plants; over one million ESTs have been published for each of these plant species. 17 The development of new DNA sequencing technology 18 has been driven by both publicly and privately funded research and development activities in human genomics. Lagging behind, but benefiting greatly nonetheless from progress being made in human genomics, is the application of these technologies to plant research in general, and more specifically, to research relevant to crop improvement, plant evolution and PGR conservation. Steady advances are being made in both the hardware and software for genome sequencing 19 and it is envisaged that in the near future, whole genome sequencing will become so widely affordable as to be the genome characterization strategy of choice. To buttress this prognosis, the so-called next generation sequencing platforms (i.e. the newer methods that are not based on the Sanger method of 1997, namely, Roche’s 454 sequencer and Illumina’s SOLEXA sequencer, but are rather based on the more cost-effective and faster pyrosequencing technology), are continually gaining acceptance and hence larger shares of the sequencing market. A3.4 Assessing and analysing genetic diversity There are currently many strategies for assessing genetic diversity and structure of plant populations. Many were in use at the time when the first SoW report was published and are still valuable; these include pedigree analysis and replicated field experiments (to quantify heritable variations and their components). The molecular tools used for germplasm characterization and diversity studies in 1995 included, isozyme, RFLPs, Random Amplified Polymorphic DNA (RAPD), Simple Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers. With more widespread genome sequencing and generation of ESTs, SSR markers have become easier to generate and thus more widely used. Developments in high throughput marker screening systems, especially platforms that are amenable to automation and varying degrees of multiplexing, have also led to greater ease and increased efficiencies for using PCRbased markers including AFLPs. Quite importantly, the ability to discover SNPs, a marker type that is fast becoming the preferred option in high throughput systems, with ease in all parts of genomes is a direct result of significantly enhanced sequencing capacity. SSRs and the more recent SNPs are suitable for genotype fingerprinting. 20 SNPs offer the promise of higher map resolution, higher throughput, lower cost and a lower error rate compared with SSR markers. 21 An additional feature of markers such as SNPs and SSRs is the possibility to transfer them from the genotypes in which they are identified to related materials for which sequence information is not available, without the need to re-sequence 22 . Fingerprinting individuals for SNPs dispersed throughout a genome or a particular section of interest has become a very powerful way to characterize collections such as breeding materials (including segregating populations) and genebank accessions. 23 The utility of SNP-based genome characterization for crop improvement and genebank (in situ and ex situ materials) may be compromised in situations where sequence information is not available. In such cases, SNPs would not be an option; a high throughput microarray assay procedure, Diversity Array Technology (DArT), may be a suitable alternative. DArT technology discriminates between individuals based on polymorphisms from their simultaneous comparisons to a defined common genomic representation. It is a low-cost high-throughput system that requires minimal DNA per individual and at the same time provides comprehensive genome coverage even in organisms without any DNA sequence information. 24 Since the proof of concept with Rice in 2001, DArT has been employed for high throughput analyses in many genera including barley, Musa and Eucalyptus. 291

APPENDIX 3 For instance, DArT markers were as useful at revealing genetic relationships among 48 Musa accessions (derived from two wild species with different genome compositions) as other markers were, but with a lower cost and greater resolution and speed. 25 Qualitative traits (such as many disease resistances and stress tolerances) and quantitative traits (such as indices of yield and productivity) are typically the targets for improvement in plant breeding programmes and for characterization of genebank collections. Obtaining this information for collections of individuals is laborious and costly, involving screening in the presence of pathogens and stresses in replicated field experiments with adequate sample sizes. The utility of molecular markers that could serve as proxies for this type of laborious and expensive studies is obvious. Both natural and artificial selections are directed at genes. Though selection is a locus-specific force, it creates a pattern of variation involving few loci in specific regions of the genome. Variation in the traits governed by genes should therefore be a measure of the adaptive genetic diversity or adaptive potential of a population or breeding genepool. A majority of molecular markers only measure neutral genetic variation, i.e. variations in sections of the genome not involved with coding for genes or in the regulation of genes and hence, assumed not to be under natural selection pressure. These patterns of genetic variation are genome wide. Due to the fact that molecular methods are fast and relatively cheap, surveys of molecular marker variations are becoming widespread and attractive as means for evaluating genetic diversity across populations or genepools. There are even greater benefits when gene-based markers are used for analysis. A relevant advance in the past decade is that the relationships between adaptive genetic diversity and neutral genetic diversity are becoming much clearer. 26 Unfortunately, many neutral molecular markers are not usually indicative of the adaptive potential of populations or accessions they are used to characterize (for example, RFLPs, RAPDs, AFLPs and SSRs). 27 In some cases, they have been used inappropriately for this purpose with the assumption that neutral markers and quantitative adaptive variation are positively correlated. There are uses of neutral molecular markers 292 THE SECOND REPORT ON THE STATE OF THE WORLD’S PGRFA that are appropriately of value for conservation and use of genetic resources. When the patterns of genetic variation at many neutral molecular markers randomly scattered throughout a genome can be measured, they can be very useful for providing a measure of processes within ecosystems such as gene flow, genetic drift and migration or dispersal, which act on the entire genome; these are important for population biology, for monitoring progress in maintaining species in protected areas, or for testing the success of spatial connections between reserves. 28 With the many recent, reasoned enunciations of the distinctions between types of molecular markers and the appropriateness of their respective usages for conservation and utilization of genetic resources, it is expected that any report on the deployment of molecular markers should provide a rationale for the type of marker used with respect to the objective of the work. 29 An example of investigating the utility of specific marker types for specific uses was an analysis in barley of three types of markers (ESTderived SSRs, EST-derived SNPs and AFLPs) for use in diversity analyses in breeding, natural populations and genebank materials. No one marker type was best for all studied uses. 30 Given the ability to work with raw genomic sequence, the comprehensive pattern of DNA polymorphisms within a species can now be appreciated. Arabidopsis thaliana is the most thoroughly studied plant at this level since its genome was sequenced. There is an abundant natural variation for both neutral DNA markers and also for those loci that cause phenotypic changes. 31 Building on this model will be increasingly possible for crop species themselves as the genomic sequences become readily accessible. SNPs derived from ESTs were used successfully for cultivar identification in melon; this provides an example of the deployment of DNA-level polymorphism for genome characterization where few genomic tools exist other than ESTs and genetic maps based on early molecular markers. 32 As researchers take advantage of these innovations, it needs to be emphasized that strategies adopted for estimates of genetic diversity have to be suitable to the objectives for the conservation and use of the genetic resources. To illustrate, if the aim for assaying

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    Appendix 2 Major germplasm collecti

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    98 CHAPTER 4 including rice, maize

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    118 CHAPTER 4 16 Op cit. Endnote 8.

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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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    BAAFS Beijing Academy of Agricultur

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    CN Centre Néerlandais (Côte d’I

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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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