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Status of Perennial Tree Germplasm Resources in India and Their Utilization in the Context of Global Genome Sequencing Efforts

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Status of Perennial Tree Germplasm Resources in India and Their Utilization in the Context of Global Genome Sequencing Efforts Status of Perennial Tree Germplasm Resources in India and their Utilization in the Context of Global Genome Sequencing Efforts Kunasekaran Rajarajan, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, Puran Chandra, Sangram Bhanudas Chavan, Lal Chand, Veena Gupta, Ravinder Singh Dhillon, Chhavi Sirohi, Fatima Shirin, Sengodan Saravanan, Kundapura R Ravishankar, Murugan Sankaran, Harsh Mehta, Govindarajan Venkatesh, Archana Verma, Rajwat K Kalia, Modhumita Ghosh Dasgupta, Ramasamy Yasodha, Harish Singh Ginwal, Rupesh Deshmukh, Surendra Kumar Malik, Suryanarayan Bhaskar, Altafhusain Nadaf, Devashree Nayak, Shiv Kumar Dhyani, Prasad Suresh Hendre, Javed Rizvi Status of Perennial Tree Germplasm Resources in India and their Utilization in the Context of Global Genome Sequencing Efforts Kunasekaran Rajarajan, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, Puran Chandra, Sangram Bhanudas Chavan, Lal Chand, Veena Gupta, Ravinder Singh Dhillon, Chhavi Sirohi, Fatima Shirin, Sengodan Saravanan, Kundapura R Ravishankar, Murugan Sankaran, Harsh Mehta, Govindarajan Venkatesh, Archana Verma, Rajwat K Kalia, Modhumita Ghosh Dasgupta, Ramasamy Yasodha, Harish Singh Ginwal, Rupesh Deshmukh, Surendra Kumar Malik, Suryanarayan Bhaskar, Altafhusain Nadaf, Devashree Nayak, Shiv Kumar Dhyani, Prasad Suresh Hendre, Javed Rizvi LIMITED CIRCULATION Correct citation: Rajarajan K, Bharati A, Anuragi H, Handa AK, Gaikwad K, Singh NK, Mohapatra KP, Chandra P, Chavan SB, Chand L, Gupta V, Dhillon RS, Sirohi C, Shirin F, Saravanan S, Ravishankar KV, Sankaran M, Mehta H, Venkatesh G, Verma A, Kalia RK, Dasgupta MG, Yasodha R, Ginwal HS, Deshmukh R, Malik SK, Bhaskar S, Nadaf A, Nayak D, Dhyani SK, Hendre PS, Rizvi J. 2020. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. Working Paper number 311. World Agroforestry, Nairobi, Kenya. DOI http://dx.doi.org/10.5716/WP2020050.PDF The titles of the Working Paper Series are intended to disseminate provisional results of agroforestry research and practices and to stimulate feedback from the scientific community. Other World Agroforestry publication series include Technical Manuals, Occasional Papers and the Trees for Change Series. Published by World Agroforestry South Asia Regional Programme, C-Block, 1st Floor, NASC Complex, Dev Prakash Shastri Marg, Pusa Campus New Delhi – 110012 | India T: +91-11-25847885, 25847886 Email: [email protected] Website: www.worldagroforestry.org ICAR-Central Agroforestry Research Institute (CAFRI), Jhansi, Uttar Pradesh 284003, India Website: www.cafri.res.in © ICRAF & CAFRI, 2020 Working Paper No. 311 ii The views expressed in this publication are those of the contributor(s) and not necessarily those of the World Agroforestry (ICRAF) or ICAR-CAFRI. Articles appearing in this publication may be quoted or reproduced without charge, provided the source is acknowledged. ICRAF and ICAR-CAFRI encourage fair use of the material in this publication for non-commercial purposes with proper acknowledgment. The use of trade names in this publication does not imply endorsement of, or discrimination against, any product by ICAR-CAFRI and ICRAF. The geographic designations used here are not an expression of any opinion whatsoever on the part of ICAR-CAFRI and ICRAF concerning the legal delimitations and boundaries of towns and cities. iii ABOUT THE AUTHORS Dr. K. Rajarajan, Alka Bharati, H. Anuragi, Dr. A. K. Handa, S. B. Chavan, Lal Chand are scientists at the ICAR-Central Agroforestry Research Institute (CAFRI), Jhansi, Uttar Pradesh; Dr. Kishor Gaikwad Principal Scientist and Dr. N. K. Singh, Director at the ICAR-National Institute for Plant Biotechnology (NIPB), New Delhi; Dr. K. P. Mohapatra Principal Scientist, and Dr. Puran Chandra Scientist at the ICAR - Research Complex for North Eastern Hill Region, Umiam, Meghalaya; Dr. Veena Gupta Principal Scientist & Head, Division of Conservation at the National Bureau of Plant Genetic Resources (NBPGR) ICAR, New Delhi; Dr. R. S. Dhillon and Chhavi Sirohi are scientists at the Chaudhary Charan Singh Haryana Agricultural University, Hisar; Dr. Fatima Shirin and Dr. S. Saravanan are Principal Scientists at the Tropical Forest Research Institute, ICFRE Jabalpur; Dr. K.V. Ravishankar and Dr. M. Sankaran are Principal Scientists at ICAR’s Indian Institute for Horticulture Research (IIHR), Bengaluru; Dr. H. Mehta is a Principal Scientist and Head Division of Plant Sciences at ICAR’s Indian Institute of Soil & Water Conservation, Dehradun; Dr. G. Venkatesh is a scientist at the ICAR’s Central Research Institute for Dryland Agriculture, Hyderabad; Dr. Archana Verma and Dr. Rajwat K. Kalia are scientists at the ICAR’s Central Arid Zone Research Institute, Jodhpur; Dr. S. K. Malik is Principal Scientist at ICAR’s Krishi Bhawan, while Dr. S. Bhaskar is an Assistant Director General (Agronomy, Agroforestry and Climate Change) at ICAR’s Natural Resource Management Division, Pusa, New Delhi; Dr. Modhumita Ghosh Dasgupta and Dr. R. Yasodha are scientists at the Institute of Forest Genetics & Tree Breeding, ICFRE, Coimbatore; Dr. H. S. Ginwal is a scientist at the Division of Genetics and Tree Improvement, Forest Research Institute Dehradun, ICFRE, Dehradun; iv Dr. Rupesh Deshmukh is a scientist at the National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Mohali; Dr. Altafhusain Nadaf is a Professor in the Department of Botany, Savitribai Phule Pune University, Pune; Devashree Nayak and Dr. S. K. Dhyani are scientists at the South Asia Regional Programme (SARP), World Agroforestry (ICRAF) based at New Delhi, India, while Dr. Javed Rizvi is the Director of SARP; Dr. Prasad S. Hendre is a genomics scientist at World Agroforestry (ICRAF) HQ, Nairobi, Kenya. Corresponding contributors Dr. A. K. Handa, Central Agroforestry Research Institute (CAFRI) ICAR, Jhansi email: [email protected]; Dr. S. K. Dhyani, World Agroforestry, ICRAF, New Delhi email: [email protected] The Organizations The Central Agroforestry Research Institute (CAFRI) is a national institute and India’s only dedicated research institution on agroforestry under the umbrella of the Indian Council of Agricultural Research (ICAR). It promotes and works on improving the quality of life of rural people through integration of perennials in agricultural landscapes for economic, environmental and social benefits. The Indian Council of Agricultural Research (ICAR) is the research wing of the Ministry of Agriculture & Farmers Welfare, Government of India. It harnesses the power of science and innovation for food security, food safety and farmer’s prosperity, as well as enhances the natural resource base to promote inclusive growth and sustainable development. World Agroforestry (ICRAF) is a centre of scientific excellence that harnesses the benefits of trees for people and the environment. Leveraging the world’s largest repository of agroforestry science and information, ICRAF develops knowledge practices, from farmers’ fields to the global v sphere, to ensure food security and environmental sustainability. ICRAF is the only institution that does globally significant agroforestry research in and for all of the developing tropics. The knowledge produced by ICRAF enables governments, development agencies and farmers to utilize the power of trees to make farming and livelihoods more environmentally, socially and economically sustainable at scale. ICRAF is a member of the CGIAR Consortium. Its headquarters are based in Nairobi, Kenya, with six regional and sub-regional offices located across Africa, Asia, and Latin America. The Consortium of International Agricultural Research Centres (CGIAR) integrates and coordinates the research of its 15 Member Centres to increase the effectiveness and relevance of their work, and to enhance the impact of research by setting common objectives and planning concerted action. vi TABLE OF CONTENTS ABOUT THE AUTHORS ....................................................................................................................... iv ACKNOWLEDGEMENTS ..................................................................................................................... x LIST OF ABBREVIATIONS AND ACRONYMS ..................................................................................... xi ABSTRACT ........................................................................................................................................ xvi 1. INTRODUCTION .............................................................................................................................. 1 2. GENOME SEQUENCING TECHNOLOGIES .................................................................................... 3 2.1. Capillary-based first-generation sequencing technologies ...................................................... 3 2.2. Second-generation sequencing (SGS) technologies ................................................................ 3 2.3. Third-generation sequencing (TGS) technologies .................................................................... 4 2.4. Chromatin conformation capture and sequencing ................................................................... 5 3. GLOBAL STATUS OF GENOME SEQUENCING OF WOODY PERENNIAL AND TREE SPECIES .. 5 4. APPLICATION OF GENOMIC-BASED TECHNOLOGIES FOR PERENNIAL WOODY AND TREE SPECIES ...........................................................................................................................................
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