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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 A3.1 Introduction The magnitude and structure of the genetic diversity of a population determine the ability of that population to adapt to its environment through natural selection. This is because when genetic diversity is low, the possible combinations of genes that can confer fitness, and hence, adaptation to variations in environmental conditions are reduced, decreasing the probability of successful individuals arising in the population. Thus, a population in nature (or managed in a protected area) needs to have adequate genetic diversity to sustain its continued existence in the face of the continually changing biotic and abiotic components of its ecosystem. A parallel scenario depicting natural populations takes place in crop improvement programmes with regard to available heritable variation within the germplasm. Breeders seek and recombine genetic variability in their breeding populations and screen for desired traits or characteristics that enable the crop to be successful in target environments or against targeted pests or pathogens. Breeders therefore need access to adequate genetic diversity for success in breeding programmes. Underlying these scenarios (variations in nature and in germplasm collections for breeding), superficially conceptualized as ‘diversity is good’ in nature and in crop improvement programmes, there are many complicated issues. A fundamental imperative is the need to distinguish phenotypic diversity (net result of the interaction between both heritable and nonheritable components of variation) from genetic (heritable) diversity. Other issues relate to strategies for finding genetic diversity, maintaining, measuring and monitoring it, as well as devising mechanisms for exploiting it most efficiently. The processes of both scenarios can be further complicated by the biology of the species which encompass its breeding system, whether it is annual or perennial, the ploidy levels, and its ecological tolerances. The extent to which these factors are understood therefore has an impact on the ability of researchers to develop breeding or conservation strategies for the species in question. There are also non-biological issues that can complicate management practices for both natural populations and breeding materials; these include organizational, policy, legal and economic issues. There are also issues of scale - ranging from national through regional to global - with respect to collaboration, incentives and efficiencies that facilitate conservation and use of genetic resources. The objective of this Appendix is to summarize primarily the status of scientific knowledge, practices and technologies pertaining to genetic diversity that have arisen since the first SoW report published in 1998 which had a similar summary presented in Annex 1. The status of the social enabling environment also will be addresses as its components impact directly on national capacities for the conservation and use of genetic resources. Annex 1 to the first SoW report clearly set out the importance of genetic diversity in the context of both the conservation and use of plant germplasm; the contrasts between qualitative and quantitative genetic variation and the different emphasis placed on these by curators and users of genetic resources; the means and techniques for conservation; the various breeding strategies and their roles and challenges with respect to breeding goals and finally, the legal and economic issues that can promote or deter conservation and use of genetic resources. This Appendix will not repeat that information but will focus on new developments since the publication of first SoW report. A3.2 Advances in knowledge of genetics relevant to PGRFA conservation and use The principal advances in the understanding and application of heredity in the management of PGRFA in the past 12 years emanate from the immense strides that have been made in molecular biology during the period especially with regard to genomics, the study of the totality of an individual’s genetic makeup (genome). With the ability to sequence whole genomes in a timely and cost-efficient manner, the period has been characterized by an ever increasing volume of publicly accessible DNA, gene and protein sequence information. This has been complemented by the incredible advancements in the scopes for 287

APPENDIX 3 both the generation and analysis of data to degrees that were unfathomable a couple of decades ago. This paradigm contrasts sharply with the significantly narrower scope of the understanding of heredity that had hitherto been possible using classical genetics in isolation. Genomics and the related fields of proteomics (the study of proteins), metabolomics (the study of metabolites) and the more recent phenomics (study of phenotypes in relation to genomics) have developed from the confluence of classical genetics, automated laboratory tools for generating molecular data, and methods of information management, especially bioinformatics. Advances in taxonomy and systematics, largely attributable to refined information arising from the use of molecular biology approaches in genome characterizations, have led to better understanding of the structure of genepools, relationships within and between taxonomic groupings and, in some cases, to the reversal of hitherto assigned taxonomic classifications. These novel fields of the biological sciences have direct implications for germplasm management (e.g. in the designation of core collections) and in determining the needs for further collections of genetic resources. Furthermore, molecular data, being environment-neutral, are particularly useful in devising crop improvement strategies including pre-breeding activities as they are particularly suited for trawling through the genepool for new sources of gene alleles. The contributions of genomics and the other – omics to basic biology have been equally profound as their judicious applications continue to lead to better understanding of metabolic processes, their key components and pathways. This allows researchers to ultimately achieve greater precision in the identification of genes and their alleles for use in crop improvement. Quite importantly also, molecular biology techniques are permitting better and more precise understanding of adaptation and evolution making it possible therefore to delineate reliably neutral genetic diversity from adaptive genetic diversity, and the role different markers can play in identifying and using genetic diversity. With the current pervasive ability to use appropriate molecular approaches to identify genome segments that discriminate between individuals (known as 288 THE SECOND REPORT ON THE STATE OF THE WORLD’S PGRFA molecular markers) and apply statistical algorithms to identify precisely the genome locations of these “landmarks”, molecular markers are now the tools of choice for both tracing the inheritance of target regions of genomes in plant breeding programmes (marker assisted selection) and for characterizing germplasm collections. The routine use of molecular tools in analysing germplasm collections in PGRFA management, will lead to enhanced efficiencies in the management of collections. Advantages would include greater ease in the identification and elimination of duplicates (or other levels of redundancies) in germplasm collections and at the same facilitate the creation of core collections. Another area of PGRFA management that has been profoundly impacted by the applications of molecular biology techniques is population genetics. This is on account of the widespread use of molecular data in the study of populations (diversity and structure). The heavy reliance on molecular data in population genetics has spawned the neologism, population genomics. It is becoming commonplace, for instance, to identify specific loci under natural selection and thus of adaptive importance merely by sampling at a population level . It has also become quite routine to track gene expression (based on transcript profiling; or transcriptomics), even at tissue levels, under different environmental influences (biotic and abiotic) and under a time series regimen. Such a strategy, in addition to permitting the identification of genes that modulate particular phenotypic expression, also leads to the elucidation of the functions of genes and their interactions with other genes. The refined understanding of genes and their functions and the tools being generated in this manner will prove invaluable as efforts are invested in crop improvement programmes to develop varieties that will thrive in spite of the extreme climatic conditions expected as consequences of global climate change and variations. One specific example of the striking contrast between what was considered possible in 1995 and what is possible now comes from Annex 1 of the first SoW report, where it was stated that the direct application of DNA sequencing was more useful in the identification of a gene or genes than for analysing a complete genotype. The conclusion at the time

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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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    FIGURE 1.1 Global priority genetic

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    CHAPTER 1 even national, germplasm

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    THE STATE OF EX SITU CONSERVATION 1

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    98 CHAPTER 4 including rice, maize

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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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    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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    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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    APPENDIX 4 FIGURE A4.5 Global yield

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    338 APPENDIX 4 are also conserved.

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    340 APPENDIX 4 WebPDF/Crop percent2

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    342 APPENDIX 4 90 Op cit. Endnote 2

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    344 APPENDIX 4 159 GCDT. 2007. Glob

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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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