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PLANT ECOGENOMICS PLANT ECOGENOMICS Edited by Peerzada Arshid Shabir, PhD Peerzada Yasir Yousuf, PhD Khalid Rehman Hakeem, PhD First edition published 2023 Apple Academic Press Inc. CRC Press 1265 Goldenrod Circle, NE, 6000 Broken Sound Parkway NW, Palm Bay, FL 32905 USA Suite 300, Boca Raton, FL 33487-2742 USA 760 Laurentian Drive, Unit 19, 4 Park Square, Milton Park, Burlington, ON L7N 0A4, CANADA Abingdon, Oxon, OX14 4RN UK © 2023 by Apple Academic Press, Inc. Apple Academic Press exclusively co-publishes with CRC Press, an imprint of Taylor & Francis Group, LLC Reasonable efforts have been made to publish reliable data and information, but the authors, editors, and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. 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For works that are not available on CCC please contact [email protected] Trademark notice: Product or corporate names may be trademarks or registered trademarks and are used only for identification and explanation without intent to infringe. Library and Archives Canada Cataloguing in Publication Title: Plant ecogenomics / edited by Peerzada Arshid Shabir, PhD, Peerzada Yasir Yousuf, PhD, Khalid Rehman Hakeem, PhD. Names: Shabir, Peerzada Arshid, editor. | Yousuf, Peerzada Yasir, editor. | Hakeem, Khalid Rehman, editor. Description: First edition. | Includes bibliographical references and index. Identifiers: Canadiana (print) 20220255733 | Canadiana (ebook) 20220255776 | ISBN 9781774910184 (hardcover) | ISBN 9781774910191 (softcover) | ISBN 9781003282006 (ebook) Subjects: LCSH: Plant genetics. | LCSH: Plant ecology. | LCSH: Metagenomics. Classification: LCC QK981 .P53 2023 | DDC 581.3/5—dc23 Library of Congress Cataloging‑in‑Publication Data Names: Shabir, Peerzada Arshid, editor. | Yousuf, Peerzada Yasir, editor. | Hakeem, Khalid Rehman, editor. Title: Plant ecogenomics / edited by Peerzada Arshid Shabir, Peerzada Yasir Yousuf, Khalid Rehman Hakeem Description: First edition | Palm Bay, FL, USA : Apple Academic Press, 2023. | Includes bibliographical references and index. | Summary: “Plant Ecogenomics offers a valuable introduction to plant ecology from a genomics point of view. The editors present a thorough foundation and summary of modern approaches, methodologies, research goals, and evidence of plant ecology in the modern genomic era. They also present important updated information on the most recent knowledge of the different aspects of plant populations. The volume begins with a general overview of the various approaches to unravelling the genetic basis underlying fundamental responses of plants to their natural environments. It also describes in detail the concepts, aims, and approaches of plant ecological genomics along with the genomic tools embraced by ecologists for mining various ecological problems. Recent advances and breakthroughs made in molecular markers along with their applications in plant ecogenomic studies are shared, and specific applications, techniques, and tools are described as well, such advanced molecular techniques, next-generation sequencing, eDNA metabarcoding, among others. The authors look at community and ecosystem responses in the form of phylogenetic systematics and the theory and methodology for inferring phylogenetic trees or cladograms, including parsimony, Bayesian, and maximum likelihood methods. The employability of QTL analysis and reverse genetics in plant ecogenomics is discussed. Other topics include the role of eco-genomics in conservation and management, models to study the population structure along with the genetic basis of speciation and adaptation in plants, and more. The volume looks at how genetic variability is assessed with the help of various available tools and how effective they are in the conservation of important plant species. Inbreeding and genetic load and the role of ecogenomics in landscape genetic restoration are covered as well. This volume offers a rich store of information on the interdisciplinary field of ecological genomics that will be valuable for molecular biologists, ecologists, as well as for researchers, scientists, and faculty and students in related areas”-- Provided by publisher. Identifiers: LCCN 2022025310 (print) | LCCN 2022025311 (ebook) | ISBN 9781774910184 (hardback) | ISBN 9781774910191 (paperback) | ISBN 9781003282006 (ebook) Subjects: LCSH: Plant genetics. | Plant ecology. | Metagenomics. Classification: LCC QK981 .P48 2023 (print) | LCC QK981 (ebook) | DDC 581.3/5--dc23/eng/20220707 LC record available at https://lccn.loc.gov/2022025310 LC ebook record available at https://lccn.loc.gov/2022025311 ISBN: 978-1-77491-018-4 (hbk) ISBN: 978-1-77491-019-1 (pbk) ISBN: 978-1-00328-200-6 (ebk) About the Editors Peerzada Arshid Shabir, PhD, MSc, is a plant science professional with a specialization in plant reproductive ecology and is currently working as Assistant Professor of Botany in the Department of Higher Education, Jammu and Kashmir, India. Dr. Shabir received his PhD in the field of plant reproductive ecology and genetic diversity from the University of Kashmir, Srinagar. He has published several research articles and book chapters in reputed international journals and has also presented his work at various national and international conferences. He has also been a reviewer for many reputed international journals. His current research interests include the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation. He has ten years of research experience and is currently actively engaged in the teaching of undergraduate subjects like plant reproductive ecology, plant physiology, cell and molecular biology, and genetic engineering of plants. Dr. Shabir has also been conferred with junior and senior research fellowships by the Counsel of Scientific and Industrial Research, New Delhi. Peerzada Yasir Yousuf, PhD, is Assistant Professor of Botany in the Department of Higher Education, Government of Jammu and Kashmir, India. He has published several research articles and book chapters in globally reputed journals, including Frontiers in Plant Science, Genes, Plos One, Protoplasma, Plant Growth Regulation, Environmental Science and Pollution Research, etc. Dr. Yousuf has presented his work at several national and international conferences. He has also delivered extension lectures in different fields of plant sciences at various institutes. He is a lifetime member of several national and international organizations and is the recipient of several fellowships. Dr. Yousuf also serves as a reviewer and editorial board member of many research journals. He is actively engaged in the research fields of plant physiology and molecular ecology. He formerly worked at the Molecular Ecology Laboratory as a Senior Research Fellow in the Department of Botany Jamia Hamdard, New Delhi. Dr. Yousuf also taught environmental science as guest faculty in Jamia Hamdard in different faculties, including Faculty of Unani Medicine and vi About the Editors the Faculty of Information Technology. He has teaching experience of 11 years and research experience of eight years. Dr. Yousuf earned his BSc from the University of Kashmir and MSc and PhD degrees in Botany from Jamia Hamdard, New Delhi, respectively. During his PhD program, he worked on the biochemical and molecular aspects of stress tolerance in plants. He has qualified for many national competitive examinations like UGC-CSIR NET (AIR 39), ARS-NET, GATE (AIR 45), and JK-SET. In addition, he has completed many online certification courses in the various fields of biology from different nationally and internationally reputed institutes. He was selected for the SERB National Postdoctoral Fellowship (N-PDF) by the Department of Science and Technology, Government of India in 2016. Khalid Rehman Hakeem, PhD, is Professor at King Abdulaziz University, Jeddah, Saudi Arabia. After completing his doctorate (botany, specializa tion in plant eco-physiology and molecular biology) from Jamia Hamdard, New Delhi, India, he worked as a lecturer at the University of Kashmir, Srinagar, India, at Universiti Putra Malaysia, Selangor, Malaysia, where he was a Postdoctorate Fellow and Fellow Researcher (Associate Professor) for several years. Dr. Hakeem has more than 10 years of teaching and research experience in plant eco-physiology, biotechnology and molecular biology, medicinal plant research, plant-microbe-soil interactions, as well as in environmental studies. He is the recipient of several fellowships at both national and international levels. He has served as a visiting scientist at Jinan University, Guangzhou, China. Currently, he is involved with several international research projects with various government organiza tions. To date, Dr. Hakeem has authored and edited more than 60 books with international publishers. He also has to his credit more than 115 research publications in peer-reviewed international journals and 55 book chapters in edited volumes. At present, Dr. Hakeem serves as an editorial board member and reviewer for several high-impact international scien tific journals. He is included in the advisory board of Cambridge Scholars Publishing, UK. He is also a fellow of the Plantae Group of the American Society of Plant Biologists, member of the World Academy of Sciences, member of the International Society for Development and Sustainability, Japan, and member of the Asian Federation of Biotechnology, Korea. Contents Contributors ......................................................................................................... ix Abbreviations .....................................................................................................xiii Foreword ..............................................................................................................xv Preface .............................................................................................................. xvii 1. Ecogenomics: An Appraisal ....................................................................... 1 Bilal Ahmad Wani, Peerzada Yasir Yousuf, and Peerzada Arshid Shabir 2. Advancement in Molecular Tools of Plant Population Genetics........... 19 Divya Raj Prasad, Tarun Minocha, Bipin Maurya, and Peerzada Yasir Yousuf 3. Application of Next‑Generation Sequencing in Plant Molecular Ecology..................................................................................... 47 Harshit Kumar Soni and Aparna Singh 4. Approaches for Metabarcoding and Environmental DNA (eDNA) Assays in Plants .................................................................. 83 Mahak Majeed and Reiaz Ul Rehman 5. Role of Epigenetics in Ecogenomics ...................................................... 105 Shahjahan Rashid, Sumiah Wani, Farhana Wani, Adil Rashid Nath, and Aflaq Hamid 6. QTL Analysis and Reverse Genetics in Molecular Systematics .......... 123 Sumiah Wani, Shahjahan Rashid, Farhana Wani, and Aflaq Hamid 7. Dispersal, Gene Flow, and Population Structure .................................139 Naveed Ul Mushtaq, Seerat Saleem, Aadil Rasool, Wasifa Hafiz Shah, and Reiaz Ul Rehman 8. Ecological Genomics in Context with Plant Adaptations and Speciation ................................................................... 157 Sheikh Tajamul Islam, Basharat Ahmad Bhat, Inayatullah Tahir, and Tanvir Ul Hassan Dar viii Contents 9. Role of Ecogenomics in Conservation and Management .................... 175 Shahid Ul Islam, Zahid Ahmad Mangral, Lubna Tariq, Basharat Ahmad Bhat, Haider Mehraj, Sheikh Tajamul Islam, and Tanvir Ul Hassan Dar 10. Genetic Diversity as a Conservation Tool ............................................. 201 Fayaz Ahmad Dar, Inayatullah Tahir, and Reiaz Ul Rehman 11. Inbreeding and Genetic Load and Role of Ecogenomics in Landscape Genetic Restoration .............................................................215 Meenu Garg, Pragyanshree Nayak, Alok Kumar Singh, and Ashwini Kumar Ray 12. Plant Ecogenomics: Challenges and Opportunities ............................. 231 Bipin Maurya, Lakee Sharma, Sabitri Kumari, Nidhi Rai, and Shashi Pandey-Rai Index ................................................................................................................. 249 Contributors Basharat Ahmad Bhat Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India Fayaz Ahmad Dar Department of Bioresources, Amar Singh College Campus, Cluster University, Srinagar 190008, Jammu and Kashmir, India; E-mail: [email protected] Tanvir Ul Hassan Dar Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India; E-mail: [email protected] Meenu Garg Department of Microbiology, Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, 110096 Delhi, India Aflaq Hamid Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Science and Technology, Shalimar Srinagar, Kashmir, India; E-mail: [email protected] Khalid Rehman Hakeem Department of Biological Sciences, Faculty of Science, KAU, Jeddah, Saudi Arabia; E-mail: [email protected] Shahid ul Islam Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India Sheikh Tajamul Islam Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India Sabitri Kumari Laboratory of Morphogenesis, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India Mahak Majeed Department of Bioresources, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, India Zahid Ahmad Mangral Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India Bipin Maurya Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; E-mail: [email protected] Laboratory of Morphogenesis, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India