Table Of Content

Genomics, Proteomics, and Biotechnology High-throughput molecular technologies (“omics”) can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways thereby allowing the discovery of biomarkers. Notably, the omics technologies along with computational methods, bioprospecting, and artificial intelligence will continue to lead to better understanding of biological mechanisms that are responsible for physical attributes, or phenotypes. Research breakthroughs obtained through these technologies can be used to enhance productivity of food animals, meet the increasing demand for animal-sourced foods, enhance high-quality nutrient availability, ensure nutrient safety, mitigate the effects of climate variability, and result in new technologies that provide continued improvement in food security worldwide. Such breakthroughs are an urgent necessity because over the past 50 years, there has been an unprecedented increase in the world’s population, which will reach ten billion by the year 2050. Innovative and technological advancements that enhance all aspects of food production will arise from basic, fundamental research. Besides food, animal by-products have found many applications in the fields of pharmaceuticals, cosmetics, and household and industrial products. Hence, the need to ameliorate the productivity, reproductivity, growth performance, and disease resistance in animals has created a worldwide interest in gaining a deeper understanding of animal biology, biotechnology and genomics, and proteomics. The present volume thoroughly discusses the omics studies in domestic and non-domestic animals and their role in mitigation of various challenges ahead. The volume thus focuses on i. Omics (genomics, proteomics, transcriptomics, metabolonomics) technologies in identifying, characterizing biodiversity ii. Role of molecular techniques for improvement of domestic and non-domestic organisms iii. Animal and alternative model systems (using stem cells, tissue engineering, cell free systems, 3D platforms etc.) for studying life phenomena iv. Genetically modified organisms as factories for the products Translating Animal Science Research Series Editor RC Sobti, Department of Biotechnology, Panjab University, Chandigarh, India Biodiversity: Threats and Conservation RC Sobti Environmental Studies and Climate Change RC Sobti, S.K. Malhotra, Kamal Jaiswal, and Sanjeev Puri Genomics, Proteomics, and Biotechnology RC Sobti, Manishi Mukesh, and Aastha Sobti For more information, visit webpage: www.routledge.com/Translating-Animal-Science-Research/ book-series/TASR?pd=published,forthcoming&pg=1&pp=12&so=pub&view=list?pd=published, forthcoming&pg=1&pp=12&so=pub&view=list Genomics, Proteomics, and Biotechnology Edited by RC Sobti, Manishi Mukesh, and Aastha Sobti Cover image credit: ©Shutterstock First edition published 2023 by CRC Press 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487–2742 and by CRC Press 2 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN CRC Press is an imprint of Taylor & Francis Group, LLC © 2023 selection and editorial matter, RC Sobti, Manishi Mukesh, and Aastha Sobit; individual chapters, the contributors Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, access www.copyright.com or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978–750–8400. 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 of Congress Cataloging-in-Publication Data Names: Sobti, R. C., editor. | Mukesh, Manishi, editor. | Sobti, Aastha, editor. Title: Genomics, proteomics and biotechnology / edited by RC Sobti, Manishi Mukesh and Aastha Sobti. Other titles: Translating animal science research (Series) Description: First edition. | Boca Raton, FL : CRC Press, 2023. | Series: Translating animal science research | Includes bibliographical references and index. Identifiers: LCCN 2022023880 (print) | LCCN 2022023881 (ebook) | ISBN 9781032116334 (hardback) | ISBN 9781032116341 (paperback) | ISBN 9781003220831 (ebook) Subjects: MESH: Genomics | Proteomics | Genetic Techniques—veterinary | Genetic Engineering—veterinary | Biomedical Technology—methods Classification: LCC QH447 (print) | LCC QH447 (ebook) | NLM QU 460 | DDC 572.8/629—dc23/eng/20220912 LC record available at https://lccn.loc.gov/2022023880 LC ebook record available at https://lccn.loc.gov/2022023881 ISBN: 978-1-032-11633-4 (hbk) ISBN: 978-1-032-11634-1 (pbk) ISBN: 978-1-003-22083-1 (ebk) DOI: 10.1201/9781003220831 Typeset in Times New Roman by Apex CoVantage, LLC Content Editor Biographies ...........................................................................................................................vii List of Contributors ..........................................................................................................................ix Chapter 1 Genomics, Transcriptomics and Proteomics for Computational Biology ...................1 Abhishek Sharma and Ashok Kumar Chapter 2 Genomics: The Rise of Sequencing Technology .......................................................13 Archana Chauhan, Ahmad Ali and Phuntsog Dolma Chapter 3 Role of Omics Technologies in Animal Science ....................................................... 41 Monika Sodhi, Nampher Masharing, Vishal Sharma, RC Sobti and Manishi Mukesh Chapter 4 Analysis of Gene Expression at mRNA Level: Technological Evolution .................65 Anju Kumari, Harjot Kaur, Ravinder Kumar and Vijay Kumar Chapter 5 Concept of Cre-Lox Recombination System .............................................................79 Ravneet Kaur Chapter 6 Applications of Tag-SNPs in Quantitative Trait Loci (QTL) Identification ..............89 CS Mukhopadhyay and Bhawanpreet Kaur Chapter 7 Flow Cytometry and Its Applications ...................................................................... 101 Himanshu Tillu, Rekha R. Gour and Hemant Agrawal Chapter 8 CRISPR/Cas Gene Editing System in the Silkworm, Bombyx mori .......................117 Venkatesh R Kumar, Devika Srivastava and Rajendra Mundkur Chapter 9 Metagenomic Approaches for Harnessing Microbial Enzymes and Bioactive Molecules ................................................................................................. 137 Ankita Srivastava, Akanksha Vishwakarma, Vinay Kumar and Digvijay Verma Chapter 10 Metagenomic Insights of Human Oral Microbiome ................................................ 155 Sonu Bhatia, Vivek Tiwari, Neetu Sharma, Abhinashi Singh Sodhi and Navneet Batra Chapter 11 Role and Application of CRISPR-Cas System in Genetic Disorders ...................... 177 Ravi Kr. Gupta, Shilpi Yadav, Ruchi Sankhwar and Abhishek Kumar v vi Content Chapter 12 Prospects of Genomics Tools in Conservation of Farm Animal Breeds ................. 191 SK Niranjan and Manishi Mukesh Chapter 13 Genomic Evaluation of Dairy Sires: The Process, Challenges, and Prospects .................................................................................................................. 199 Supriya Chhotaray and Vikas Vohra Chapter 14 Advancement in Reproductive Biotechnologies in Livestock ................................. 215 Dharmendra Kumar, Meeti Punetha, Seema Dua, Pradeep Kumar and PS Yadav Chapter 15 Proteomics-Based Advancements in Research toward Sustainable Production of Dairy Livestock ................................................................................. 231 Sudarshan Kumar, K Mohanty, JK Kauhsik, M Mukesh and Nikunj Tyagi Chapter 16 Buffalo Cloning: Multiplying India’s Black Gold .................................................... 239 Naresh L Selokar, Manoj Kumar Singh, Dharmendra Kumar, Rakesh Sharma, Manmohan Singh Chauhan and Prem Singh Yadav Chapter 17 Applications of Biotechnological Techniques in Mitigating Environmental Concerns .........................................................................................249 RC Sobti, Apurav Sharma and Sanjeev Kumar Soni Chapter 18 Anti-Biofouling of Heterogeneous Surfaces: A Green Approach Using Microbial Enzymes .................................................................................................. 313 Praveen Rishi, Arashdeep Kaur, Ritika Sahi, Harmanpreet Kaur and Sanjeev Kumar Soni Chapter 19 Biofertilizers for Sustainable Agriculture: Current Trends and Future Perspective ............................................................................................................... 331 Sanjeev Kumar Soni, Ritika Manhas, Yudhvir Jakhar, Apurav Sharma and Raman Soni Chapter 20 Microbiofuels: The Sustainable Energy Source for the Future ...............................357 Sanjeev Kumar Soni, Nisha Phour Dhull, Raman Soni and Apurav Sharma Chapter 21 Biomedical Applications of Fungal Enzymes ......................................................... 381 Deepak K Rahi, Sonu Rahi, Maninderjeet Kaur and Ekta Chaudhary Index ..............................................................................................................................................399 Editor Biographies Ranbir Chander Sobti, former Vice-Chancellor at Panjab University in Chandigarh and at Babasaheb Bhimrao Ambedkar University (Central University) in Lucknow, is a scientist, an able administrator, and dynamic institution builder. He has published more than 300 papers in journals of national and international repute, such as Mutation Research, Carcinogenesis, Achieves of Toxicology, Cancer Genetics and Cytogenetics, Molecular Cell Biochemistry, and PLOS I to name a few. He has also published more than 50 books with international publishers such as Springer, Academic Press, CRC, Elsevier, and others. He is a Fellow of the Third World Academy of Sciences, National Academy of Sciences India, Indian National Science Academy, National Academy of Medical Sciences, National Academy of Agricultural Sciences, Canadian Academy of Cardiovascular Diseases, and others. He was the general president of Indian Science Congress for the 102nd session held at the University of Jammu in 2013. Dr. Sobti is the recipient of many prestigious awards, like the INSA Young Scientist Medal, UGC Career Award, Punjab Rattan Award, JC Bose Oration and Sriram Oration Awards, and of Life Time Achievement Awards of the Punjab Academy of Sciences, Zoological Society of India, and the Environment Academy of India, besides many other medals and awards at national and international levels. Manishi Mukesh is Principal Scientist (Professor) at ICAR-National Bureau of Animal Genetic Resources in Karnal (India), and engaged in the characterization and conservation of indigenous livestock breeds. He has more than 25 years of experience as a research scientist in the area of cattle and buffalo genomics. He has been engaged in assessing the genome diversity of various cattle breeds of India using neutral and functional markers. He has recently co-authored Advances in Animal Biotechnology (Springer). Dr. Mukesh has been awarded the ICAR National Fellow position twice for two terms since May 2011 by Indian Council of Agricultural Research for his contribution in the area of animal sciences. He is also the recipient of the Dr PG Nair Memorial award, the Dr BS Chauhan Gold Medal, and an Eminent Scientist award from different national agencies. Aastha Sobti has a master’s degree in clinical dentistry and oro-facial surgery (UK) and works in the field of head and neck cancers using her intellect and her background in oral and maxillofacial surgery to bring reforms that are required in the present multifarious surgical and research areas. She has teaching and research experience of about seven years and has published a number of papers in reputed journals. She has been awarded a number of prizes and medals for her exceptional work. She has attended and presented papers in international conferences in Croatia, Brazil, Canada, USA, Japan, Switzerland, and other countries. vii Contributors Hemant Agrawal Phuntsog Dolma Flowcytometry Solutions Pvt Ltd Department of Zoology Jaipur, India Panjab University, Sector 14 Chandigarh, India Ahmad Ali Department of Zoology Seema Dua Panjab University, Sector 14 ICAR-Central Institute for Research on Chandigarh, India Buffaloes Hisar, Haryana, India Navneet Batra Department of Biotechnology Ravi Kr. Gupta Goswami Ganesh Dutta Sanatan Dharma Department of Environmental Microbiology College, Sector 32 Babasaheb Bhimrao Ambedkar University Chandigarh, India Yudhvir Jakhar Sonu Bhatia Department of Microbiology Department of Biotechnology Panjab University Goswami Ganesh Dutta Sanatan Dharma Chandigarh, India College, Sector 32 Chandigarh, India Arashdeep Kaur Department of Microbiology Ekta Chaudhary Panjab University Department of Microbiology Chandigarh, India Panjab University Chandigarh, India Bhawanpreet Kaur College of Animal Biotechnology Archana Chauhan Guru Angad Dev Veterinary and Animal Department of Zoology Sciences University Panjab University, Sector 14 Ludhiana, Punjab, India Chandigarh, India Harjot Kaur Manmohan Singh Chauhan Department of Zoology ICAR-Central Institute for Research on Panjab University Buffaloes Chandigarh, India Hisar, Haryana, India Maninderjeet Kaur Supriya Chhotaray Department of Microbiology Animal Genetics and Breeding Division Panjab University ICAR-National Dairy Research Institute Chandigarh, India Karnal, Haryana, India Ravneet Kaur Nisha Phour Dhull Department of Zoology Department of Microbiology Post Graduate Government College Panjab University Chandigarh, India Chandigarh, India ix