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Boosting the Big Data of Plant with Digital Identifiers BOOSTING THE BIG DATA OF PLANT WITH DIGITAL IDENTIFIERS Boosting The Big Data of Plant With Digital Identifiers Muhamad Sabran Puji Lestari Dani Satyawan Toto Hadiarto Mastur Rerenstradika Tizar Terryana Boosting The Big Data of Plant With Digital Identifiers @2020 IAARD PRESS Edisi 1 (Edition 1) : 2020 Hak cipta dilindungi Undang-undang (All rights reserved) @IAARD PRESS. Katalog dalam terbitan (KDT) BOOSTING the big data of plant with digital identifiers / editors, Muhamad Sabran ... [dkk.].—– Jakarta : IAARD Press, 2020. xxx, 451 hlm (451 pages); 21 cm. ISBN: 978-602-344-282-9 662.756 1. Plant genetic resources 2. Big Data 3. Digital Identifiers I. Sabran, Muhamad Editors: Muhamad Sabran Puji Lestari Dani Satyawan Toto Hadiarto Mastur Rerenstradika Tizar Terryana Perancang cover dan tata letak (Cover and layout designer) : Tim Kreatif IAARD Press (Creative Team of IAARD Press) Penerbit (Publisher) IAARD PRESS Badan Penelitian dan Pengembangan Pertanian (Indonesian Agency for Agricultural Research and Development) Jl, Ragunan No 29, Pasar Minggu, Jakarta 12540 Email: [email protected] Anggota IKAPI No: 445/DKI/2012 PREFACE ignificant research findings have been achieved in the area of information technologies concerning with the utilization S of plant genetic resources (PGR). Many progresses of big data produced from biological computation, omics and relevant management of the PGR have been reported. Despite the numerous contributions, there still exists a lack of representative information of the resulted big data of PGR along with digital object identifiers (DOI). This book contains several articles with various topics. Some articles have been presented at the conference on “Boosting Big Data of Plants with Digital Identifiers” held in Bali, Indonesia, June 11-13, 2019, and some others are purposively written for this book. The main articles are on the use of DOI as permanent unique identifier on PGR; however, some papers presented at the conference also include papers on Intellectual Property Rights (IPR) related to PGR and gene bank management. To give the reader a broad overview on the big data of plant, two articles on the fourth agriculture revolution and Global Information System (GLIS) on PGR are introduced in chapter 1. Chapter 2 reviewed the rights, conservation and use of PGR. The purpose of this book and the conference is to introduce to the scientific community, in particular agricultural scientist, the use of DOI as permanent unique identifier for plant genetic resources for food and agriculture (PGRFA); since agricultural scientist is one of the primary beneficiaries of the use of DOI on PGRFA. The assignation of DOI on PGR will trigger improvement in crops information system and facilitate the appropriate and quality-controlled sharing of information of the v PGRFA data. The adoption of unique identifier will further empower genomic and phenomic researches, functional gene discovery and increase the efficiency and effectivity of plant breeding program, which, ultimately increase the capacity to adapt to the climate change and food security. We wish to thank the secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) for funding the conference and the preparation of this book and the Director General of the Indonesian Agency of Agriculture Research and Development (IAARD) for publishing the book through the IAARD press and the Director of Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) for funding the final printing and multiplication of the book. Bogor, April 2020 Editors vi vii TABLE OF CONTENTS PREFACE ................................................................................................ v TABLE OF CONTENTS ..................................................................... viii ACKNOWLEDGEMENTS ................................................................. xii CONTRIBUTORS ................................................................................ xiv PROLOGUE: BOOSTING BIG DATA OF PLANTS WITH DIGITAL IDENTIFIER ................................................................... xxviii CHAPTER 1. THE FOURTH INDUSTRIAL REVOLUTION AND GLOBAL INFORMATION SYSTEM ON PLANT GENETIC RESOURCES FOR FOOD AND AGRICULTURE .............................. 1 The Fourth Industrial Revolution and Embracing The Latest Technologies to Support Crop Production Systems and Sustainable Agriculture ......................................................................... 3 Global Information System on Plant Genetic Resources for Food and Agriculture: The Use of Digital Identifier.................................. 16 CHAPTER 2. RIGHTS, CONSERVATION AND USES OF PLANT GENETIC RESOURCES ....................................................................... 36 Dynamic and Implication of Rights on Plant Genetic Resources... 38 Efficient and Effective Management and Use of Genetic Resource in Indonesia .......................................................................................... 54 Characterization of Butterfly Pea as a Model of Underutilized Crop Management in Indonesia ......................................................... 67 Sustainable Use of Cassava Genetic Resources in Tanzania Through Genetic Databases ................................................................ 83 viii Conservation and Exploration of Plant Genetic Resources in Vietnam ................................................................................................ 102 Present and Future Aspect of In Vitro Conservation Research in IAARD .................................................................................................. 114 Improvement of Rice Resistant to Important Rice Virus Diseases with the Benefit of Indonesian Local Varieties ............................... 131 CHAPTER 3. BIG DATA ON GENOMIC FOR CROP IMPROVEMENT................................................................................. 148 Agricultural Biotechnology Trends and the Digital Transformation of Plant Genetic Resources .................................... 150 Digital Sequence Information – Legal Questions for Patent, Copyright and Trade Secret Protection and Sharing of Genomic Sequencing Data ................................................................................. 171 NGS-Based Genomic Characterization of Agriculturally Important PGR to Support National Breeding Program ............... 184 Towards Building the Big Data of Shallot: Phenomic, Metabolomic and Genomic ............................................................... 206 CHAPTER 4. DIGITAL OBJECT IDENTIFIER FOR PLANT GENETIC RESOURCES MANAGEMENT ..................................... 218 Accelerating DOI Registration of PGRFAs from Asian and African Countries Through Integration-Toolkit Dissemination .. 221 Genomic Information as a Potential Descriptor of Genetic Resources ............................................................................................. 236 Current and Future of DOI Implementation in the Lao National Genebank ............................................................................................. 258 Digital Object Identifiers for Easy Access of Information and Exchange of Germplasm .................................................................... 266 ix Role of Digital Object Identifiers for Networking and Managing Data to Agriculture Biodiversity’s Future ....................................... 273 PhilRice GEMS Database: Its Upgrade and Impact ....................... 282 MARDI Agrobiodiversity Information System (AgrobIS) to Support Genetic Resources for Food and Agriculture (PGRFA) Conservation in Malaysia .................................................................. 295 The Implementation of Digital Object Identifier on Germplasms at the Genebank of CARDI ................................................................ 305 Significance of Digital Object Identifiers for Plant Genetic Resources Management and Utilization .......................................... 315 CHAPTER 5. DIGITAL OBJECT IDENTIFIER FOR RICE GERMPLASM ..................................................................................... 326 Digital Object Identifiers for Indonesia Rice Germplasm ............. 328 Diversity of DOI Registered Rice Landraces from Southeast Asia for Genetic Improvement .................................................................. 346 Digital Object Identifiers (DOI) for Local Rice Genetic Resources of Central Kalimantan ........................................................................ 364 The Four Yogyakarta’s Local Rice Superiority Registered by Digital Object Identifier ..................................................................... 378 DOI Implementation on Rice Germplasms of BRRI Genebank: Present and Future Aspects ............................................................... 398 Management of Local Rice Resources Assigned Their DOIs Originating from West Nusa Tenggara ........................................... 410 Status of Plant Genetic Resources Conservation and Digital Object Identifiers Registration for Rice Germplasm in Zambia ... 424 Rice Genetic Resource Management for Supporting Indonesia Agriculture in Industrial 4.0: Case Study in Indonesian Center for Rice Research ....................................................................................... 433 x EPILOGUE: FUTURE CHALLENGES IN THE MULTILATERAL SYSTEM ON ACCESS AND BENEFIT SHARING OF PLANT GENETIC RESOURCES
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