Table Of ContentPLANT ECOGENOMICS
PLANT ECOGENOMICS
Edited by
Peerzada Arshid Shabir, PhD
Peerzada Yasir Yousuf, PhD
Khalid Rehman Hakeem, PhD
First edition published 2023
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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
