Genomics and Genetic Engineering Aryadeep Roychoudhury Editor

Rice Research for Quality Improvement: Genomics and Genetic Engineering Aryadeep Roychoudhury Editor

Rice Research for Quality Improvement: Genomics and Genetic Engineering Volume 2: Nutrient Biofortification and Herbicide and Biotic Stress Resistance in Rice Editor Aryadeep Roychoudhury Department of Biotechnology St. Xavier’s College (Autonomous) Kolkata, West Bengal, India

ISBN 978-981-15-5336-3 ISBN 978-981-15-5337-0 (eBook) https://doi.org/10.1007/978-981-15-5337-0

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This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Foreword

The signiﬁcant yield loss of rice in response to abiotic stress and development of resilient smart rice crop has been described and documented in Volume I of the series Rice Research for Quality Improvement: Genomics and Genetic Engineering. Vol- ume II of the series highlights broadly the biotic stress, herbicide resistance, and bioengineered biofortiﬁcation in rice.

Biotic Stress Resistance

Rice is constantly exposed to interaction with various organisms and subject to important diseases. An annual loss between 120 and 200 million tons of grain due to insects, diseases, and weeds in rice fields in tropical Asia is well documented. Biotic factors that damage paddy crop are virus, bacteria, fungi, nematodes, and insect pests. Many morphological, anatomical, physiological, and biochemical factors have been reported to be associated with resistance, each controlled by different sets of genes. Molecular breeding is used for development of resistant varieties by changes in the genetic background of promising lines through the introduction of a new resistance gene. Plant breeders’ and geneticists’ attempts to produce new varieties that better tolerate pathogen attack have not resulted in any satisfactory cultivar, particularly sheath blight-resistant rice. Consequently, there exists a high demand for novel efficient genomics and biotechnological methods for controlling plant diseases, as well as for producing plants of interest with increased resistance to biotic stress. The ability to maintain or increase rice production in a cost-effective manner will rely on developing varieties that can be productive in response to a variety of abiotic or biotic stresses. Overexpression of genes or RNA interference (RNAi) to knockout the expressions of genes proves helpful to understand the biological functions of genes and encoded proteins. Additional research in this field has been focused on a number of areas including siRNA, microRNAs, hairpin RNA, and promoter methylation.

v vi Foreword

Herbicide-Tolerant Rice

Weedy rice (Oryza sativa), a conspecific weed of cultivated rice, is also a global threat to rice production. Classified as the same species as cultivated rice, it is highly competitive, is difficult to control without damaging cultivated rice, and can often cause total crop failure. The competition of cultivated rice with weedy rice can lead to yield losses from less than 5% to 60%. Hence, there is a growing need for generating herbicide-resistant rice particularly with the advantage of using direct seeded rice (DSR) due to labor shortage and use of efficient mechanized rice cultivation.

Biofortification

The polished rice devoid of micronutrients may satisfy hunger, but there is a deeper problem of “hidden hunger” which is only fulfilled by nutritionally enriched food. Having a balanced diet is a far-fetched dream for the underprivileged people of the world. A carbohydrate-rich diet including rice, wheat, or maize (the major staple food) is consumed worldwide and mainly contributes to solving the problem of hunger; however, malnutrition still persists in the world. “Hidden hunger” is caused when the body is deprived of essential micronutrients. Nutrient deficiency or malnutrition has affected at least 2 billion people (or 1 out of 3), mostly in Africa, South Asia, and Latin America. Micronutrient deficiency is a silent epidemic condition—it slowly weakens the immune system, stunts physical and intellectual growth, and even causes death. Among micronutrient deficiencies, iron deficiency or iron deficiency anemia (IDA), zinc deficiency, and vitamin A deficiency (VAD) are wide- spread and cause serious consequences. More than 24,000 people globally die daily owing to “hidden hunger” and malnutrition. To combat these deficiencies, fortifica- tion of food with different biological and chemical supplements and the alterations of the food processing system are essential. Biofortified (including bioengineered) staple food crop is a sustainable alternative that can be highly beneficial for people who have limited access to varied dietary resources. Genetically modified (GM) rice, particularly pro-vitamin A rice engineered with three genes driven by endosperm- specific promoters, expressing in endosperm known as “Golden Rice,” and similarly engineered high iron rice with ferritin gene, may meet to fight against “hidden hunger.”

Male Sterility

Male sterility has been tested as a specific mechanism to contain gene outflow in various crops; the transgene of choice is transformed into the male sterile (female) inbred to form a hybrid and is much discussed as a containment method. A great deal of male sterility is cytoplasmic and inherited on the chondriome (mitochondrial genome). This will be difficult to perform as chondriome engineering is yet Foreword vii unknown. The ability of cytoplasmic male sterility to preclude transgene flow through pollen (using non-transgenic pollinators) seems helpful to decrease the risk of viable pollen flow, as tested under field conditions.

Rice Aroma

Fragrance in rice grain is the most attractive trait that fetches a premium price in the market. Continuously increasing demand for fragrant rice in global market has gained the special attention of rice breeders and forced them to consider rice grain aroma among major objectives for commercially improved rice varieties. Since aromatic varieties are very rare, these may be considered among the most precious treasures of India and can also be considered as national asset and pride. The fragrance of rice plays an important role in affecting the market value and consumers’ preference. Recent advancements in plant science and availability of high-density linkage maps and fully sequenced rice genome have provided better opportunities for plant scientists to look inside the secrets of aroma in rice. Hence, maintenance of aroma in rice is a signiﬁcant feature and is a vital objective for breeding rice cultivars for their commercial importance for the global market.

Flowering, Nitrogen Assimilation, and Particularly Grain Yield

Grain yield is related to the development of reproductive organs/tissues. A large number of genes are involved in the panicle development, fertilization, and seed development, including increased seed size. Analysis of gene clusters and network- ing would unravel the organ development and its linkage with encoded proteins and regulatory elements. Unﬁlled grains of most rice cultivars remained a challenging issue to be solved. ADP-glucose pyrophosphorylase (ADPPP) is referred to as limiting resource for starch biosynthesis and transport to grain. However, much more study is required to analyze this phenomenon and to ﬁnd the coordination of nitrogen assimilation in the growing rice plants and particularly in the reproductive organs, and its effective function to drive the ADPPP. The authors have summarized some of the key issues in this volume.

Policy Making and Biosafety on Transgenic Rice

Overall, Volume 2 of this book has 34 chapters, encompassing all the above aspects. The first ten chapters focus mainly on rice resistance to pathogen infection and herbicides. The next few chapters highlight development of male sterile rice lines, understanding the genetic basis of flowering response in rice, improving water and nitrogen use efficiency, and dissecting the genetic basis of aroma production in rice. A major section of this volume is devoted to the biofortification approaches to enhance several nutrients in rice, and a large number of chapters have been viii Foreword incorporated in this regard. There are a number of well-documented reviews worldwide which reveal that GM rice with inserted genes does not have any additional risk compared to traditionally developed improved rice. GM rice or GM crops so far commercialized do not have any special safety concerns. The public in some countries particularly in Europe is still skeptical regarding the consumption of GM food, and wide acceptance of such crops is only possible through adequate field trials and removal of public misconceptions. A chapter covering this aspect has therefore been included at the end. The only well-accepted hybrid Bt rice was developed at IRRI by the group of Dr. S.K. Datta and field-evaluated in China (Nature Biotech- nology, 2000: 18:1101–1104) with the collaboration of Dr. Qifa Zhang and eventu- ally marketed and consumed in China. Such examples of successful story in GM rice with improved traits are necessary for the consumers and economic benefits of the farmers and overall growth of agri-industry. All the chapters on the abovementioned subjects are well written by the eminent authors and reviewed by the experts and finally edited by Dr. Aryadeep Roychoudhury, a well-known rice scientist. This book would be a valuable asset for the library, students, teachers, and scholars of different fields and particularly in rice research.

University of Calcutta Swapan K. Datta Kolkata, India

Swapan K. Datta, Ph.D., is currently holding the DBT Distinguished Biotechnol- ogy Research Professor position at the Department of Botany, University of Calcutta, where he also served as Rashbehari Ghosh Chair Professor. Dr. Datta received B.Sc. (Hons.) from Presidency College (1972), M.Sc. (1974) and Ph.D. (1980) from the University of Calcutta. Dr. Datta received DAAD fellowship while working at Visva-Bharati University (1985–1986) and worked in Germany with Prof. G. Wenzel on resistance genetics of wheat and barley. Dr. Datta was awarded the Friedrich Miescher Institute (FMI) Fellowship attached to CIBA-GEIGY at Basel, Switzerland (1987). He took the senior scientist position at Swiss Federal Institute of Technology (ETH), Zurich, Switzerland (1987–1993) and worked on Gene technology for crop improvement with Prof. Ingo Potrykus, being associated with International collaborators. Dr. Datta was awarded Rockefeller Foundation supported Senior Visiting Faculty at UC-Davis, USA (1989) before joining at International Rice Research Institute (IRRI), Manila, Philippines where he contributed signiﬁcantly to rice improvement with Dr. Gurdev Khush and with many International collaborators (1993–2005). Dr. Datta is a recipient of many national and international fellowships/awards including TATA Innovation Fellow- ship (2007–2009), CGIAR-best science research paper, and Paul Johnnes Brouhl Memorial Medal (2009). Attached with Professional afﬁliations: Elected Fellow of the Indian National Science Academy in 2014 (FNA), Elected Fellow of the Indian Academy of Science in 2017 (FASc), Elected Fellow of the National Academy of Agricultural Science in 2005 (FNAAS), Elected Fellow of National Academy of Foreword ix

Sciences in 2006 (FNASc), Elected Fellow of the World Academy of Science in 2014 (TWAS), Dr. Datta contributed signiﬁcantly to Rice research and traits improvement over 40 years of research in Agriculture and Plant Biology, particularly on genetic transformation system in rice, jute, and chickpea, which has been established with landmark crop improvement. He has published over 150 research papers appearing in reputed journals including Nature, Science, Nature Biotechnol- ogy, and Nature Genetics with the contributions from 38 Ph.D. students and post- doctoral fellows and a large number of international collaborations. Preface

Volume I of this book was mostly focused on the diverse environmental stresses encountered by rice plants and the means to tackle them using genomics approaches and genetic engineering to develop abiotic stress-tolerant rice. Environmental or climatic fluctuations, which are beyond control by humans undoubtedly appear to be the most severe challenge to any crop species like rice and hence deserve the most attention in terms of rice productivity. However, rice plant is also susceptible to infections by a host of pathogens like bacteria, fungus, insects, nematodes, and herbivores, as well as pathogen-induced wounding. Turning back the pages of history will show that the Bengal famine of 1943 was actually due to a disease called brown spot of rice caused by the fungus Helminthosporium oryzae, which ravaged fields of rice, leaving millions of people impoverished and to suffer or die from acute hunger. Blast disease, caused by the fungus Magnaporthe oryzae, and bacterial blight, provoked by the bacterium Xanthomonas oryzae pv. oryzae, repre- sent two of the most destructive diseases of rice. The dissection of several signaling molecules inducible by the pathogens as a result of host–pathogen interaction, along with whole genome transcriptome analyses, proteomic studies, posttranslational modifications, and microRNA analyses, provides platforms for finding out novel genes for targeting in infected rice plants through either overexpression or microRNA technology-dependent downregulation. Unlike abiotic stress which is essentially a multigenic trait, governed by simultaneous regulation of a gene cas- cade, biotic stress can more often be controlled by genetic engineering of a single gene, e.g., Xa21 overexpression generating rice lines resistant to bacterial blight. Apart from pathogen resistance, rice growers all over the world would largely benefit from development of herbicide-resistant rice cultivars which would eliminate weedy rice species and provide the possibility of selective control of “hard-to-kill” weeds evolving resistance to herbicides used in rice fields. Rice, as a food crop, is the major source of carbohydrates. The aleurone layer of dehusked rice grain, which is rich in micronutrients, is lost during polishing so that rice grains we consume lack vitamins, micronutrient cations, and antioxidants. Therefore, consumption of rice from the dietary point of view can mitigate hunger, but does not resolve the problem of ‘hidden hunger’. Hence, it is necessary to biofortify the nutrient content in polished rice grains through gene pyramiding by

xi xii Preface overexpression of genes encoding multiple enzymes in a biosynthetic pathway for a particular metabolite. On the other hand, RNA interference-mediated approaches to lower down the level of anti-nutrients have also been adopted in certain cases to improve the nutrition level in rice grains. Such work definitely holds immense importance from the humanitarian point of view in achieving food security, since poor people of developing nations cannot afford to have supplemented diversified foods and hence solely rely on nutrient-enriched staple food crop to overcome malnutrition. Improvement of rice quality in terms of other physiological traits like flowering, water and nitrogen use efficiency, and male sterility also appears to be extremely important. Flowering is directly related to seed production and grain yield. Male sterility is a useful agronomic trait for producing F1 hybrids in self-pollinating crops like rice, which eliminates the tedious emasculation technique. These beneficial traits also involve elaborate genomics studies and breeding techniques or genetic engineering tools to come up with superior, value-added rice. Another desirable trait found in aromatic rice is the desirable fragrance, which is attributed to a host of volatile compounds, of which 2-acetyl-1-pyrroline is the predominant one. Efforts are being made to downregulate betaine aldehyde dehydrogenase 2 (BADH2) through RNA interference, so as to enhance aroma level in rice. Volume 2 of this book has 34 chapters which revolve around all the above aspects. The first ten chapters focus mainly on rice resistance to pathogen infection and herbicides. The next few chapters highlight development of male sterile rice lines, understanding the genetic basis of flowering response in rice, improving water and nitrogen use efficiency, and dissecting the genetic basis of aroma production in rice. A major section of this volume is devoted to the biofortification approaches to enhance several nutrients in rice, and a large number of chapters have been incorporated in this regard. Developing genetically modified (GM) rice also brings in the biosafety issues together with the commercialization and public acceptance of the transgenic crops. The public is still skeptical regarding the consumption of GM rice, and wide acceptance of such crops is only possible through adequate field trials and removal of public misconceptions. A chapter covering this aspect has therefore been included at the end. I strongly feel that this volume, like the earlier one, will be in great demand for the students, research scholars, teachers, and scientists working on diverse areas of rice improvement, at research institutes, universities, and colleges all over the world. It will also be helpful to the multinational companies involved in agricultural development or seed production. I am immensely grateful to all the contributors and academicians involved in rice research who have been highly instrumental in making this volume a success. I pay respect to all my teachers who taught me the basics of plant science and created my interest in the field of rice research. I acknowledge the support and encouragement of the Principal, St. Xavier’s College (Autonomous), Kolkata, where I am currently Preface xiii working. I thank all my family members for their continued support and patience in my academic pursuits. I appreciate the cooperation and support of Springer Nature, which largely helped me to handle this Herculean task of editorial work single- handedly. Finally, I surrender myself totally to Almighty God who has always instilled in me the strength and power to trudge this struggling path of life against all adversities.

Kolkata, West Bengal, India Aryadeep Roychoudhury Contents

Understanding the Mechanism of Host-Pathogen Interaction in Rice Through Genomics Approaches ...... 1 Yogita N. Sarki, Riwandahun Marwein, Sanjay Singh, Hariprasanna Dekaboruah, Dhanawantari L. Singha, and Channakeshavaiah Chikkaputtaiah Genetic Engineering and Genome Editing Strategies to Enhance Diseases Resistance of Rice Plants: A Review of Progress and Future Prospects ...... 35 Subhasis Karmakar, Kutubuddin A. Molla, and Johiruddin Molla Transgenic Rice Live Against Bacterial Blight ...... 61 Nilanjan Chakraborty, Anik Sarkar, and Krishnendu Acharya Genetic Engineering of Cultivated Rice for Viral Resistance ...... 79 Devarajan Thangadurai, Ravichandra Hospet, Jeyabalan Sangeetha, Stefﬁ Simmi Maxim, Saher Islam, Jasmin Habeeb, and Abdel Rahman Mohammad Said Al-Tawaha Genomics and Genetic Engineering for Polyamine-Mediated Tolerance of Rice Against Pathogen Infection ...... 93 Dew Biswas, Tania Ghatak (Chakraborty), Anuradha Mukherjee, Samapika Nandy, Devendra Kumar Pandey, and Abhijit Dey Genomics and Genetic Engineering of Rice for Resistance to Different Insect Pests ...... 107 Dhriti Kapoor, Mamta Pujari, and Mahendra Pratap Singh Genetic Engineering of Rice for Resistance to Insect Pests ...... 129 Akhtar Rasool, Fazal Akbar, Abdul Rehman, and Hina Jabeen Increasing Rice Grain Yield Under Biotic Stresses: Mutagenesis, Transgenics and Genomics Approaches ...... 149 Aamir Raina and Samiullah Khan Temporal and Spatial Dynamics of Microbial Communities in a Genetically Modiﬁed Rice Ecosystem ...... 179 Qasim Ali, Rashida Parveen, Ayesha Anwar, and Abdul Rehman xv xvi Contents

Genetic Engineering for Developing Herbicide Resistance in Rice Crops ...... 209 Jeyabalan Sangeetha, Abdel Rahman Mohammad Said Al-Tawaha, Devarajan Thangadurai, Nusrat Jahan, Saher Islam, Lalitha Sundaram, Iraj Nosratti, Jadhav Mulji Alabhai, Suresh Arakera, Santhakumari Rajendran, Ravichandra Hospet, and Nithyapriya Subramaniyam An Insight into the Factors Regulating Flowering in Rice: From Genetics to Epigenetics ...... 233 Supratim Basu Breeding and Bioengineering of Male Sterility in Rice ...... 249 K. N. Poornima, S. J. Satheesh Naik, and Abhishek Bohra Male Sterility System for Hybrid Rice Breeding and Seed Production . . . 269 Nimisha Amist and N. B. Singh Advancement in Tracking Down Nitrogen Use Efficiency in Rice: Molecular Breeding and Genomics Insight ...... 291 Supratim Basu and Brian Jenkins Improving Water Use Efficiency and Nitrogen Use Efficiency in Rice Through Breeding and Genomics Approaches ...... 307 Abdel Rahman Mohammad Said Al-Tawaha, Satybhan Singh, Virendra Singh, Uzma Kafeel, Mohd Irfan Naikoo, Aradhna Kumari, Imran, Amanullah, Abdel Razzaq Al-Tawaha, Ali M. Qaisi, Samia Khanum, Devarajan Thangadurai, Jeyabalan Sangeetha, Saher Islam, Hassan Etesami, N. Kerkoub, A. Amrani, Z. Labidi, H. Maaref, H. Nasri, Swapnil Ganesh Sanmukh, and Eduard Torrents Serra Rice Breeding and Genomics Approaches for Improving Water and Nitrogen Use Efficiency ...... 339 M. Abu Syed, M. Ashraful Alam, Akbar Hossain, M. Rafiqul Islam, Hindu Vemuri, and Nasrin Jahan Aromatic Rice: Biochemical and Molecular Basis of Aroma Production and Stress Response ...... 373 Puja Ghosh and Aryadeep Roychoudhury Genomics and Genetic Engineering of Rice Elucidating Cross Talk Between Stress Signaling and Nutrition Enhancement via Regulation of Antioxidant, Osmolyte, and Metabolite Levels ...... 409 Faiçal Brini, Inès Yakoubi, and Walid Saibi Contents xvii

Genetically Modified Rice Stacked with Antioxidants for Nutrient Enhancement and Stress Tolerance ...... 433 Qasim Ali, Muhammad Shabaan, Sana Ashraf, Abdul Rehman, and Hafiz Naeem Asghar Breeding and QTL Mapping for γ-Oryzanol and Nutrition Content in Rice ...... 469 Anirban Roy and Somnath Bhattacharyya Genetic Enhancement of Nutritional Traits in Rice Grains Through Marker-Assisted Selection and Quantitative Trait Loci ...... 493 Devarajan Thangadurai, Mojtaba Kordrostami, Saher Islam, Jeyabalan Sangeetha, Abdel Rahman Mohammad Said Al-Tawaha, and Souhat Jabeen Breeding Approaches to Generate Biofortified Rice for Nutritional Enhancement ...... 509 Abdul Rehman, Hafiza Iqra Almas, Komal Mazhar, Fazal Akbar, Qasim Ali, Muhammad Tehseen Azhar, and Xiongming Du Improvement of Nutritional Quality of Rice Seed Through Classical Breeding and Advance Genetic Engineering ...... 541 Subhankar Mondal, Dipak Gayen, and Subhasis Karmakar Genetic Engineering of Rice to Fortify Micronutrients ...... 563 Aryadeep Roychoudhury and Rituparna Bhowmik Golden Rice: Genetic Engineering, Promises, Present Status and Future Prospects ...... 581 Amna, Sadia Qamar, Aadil Yousuf Tantray, Sheikh Shanawaz Bashir, Abbu Zaid, and Shabir H. Wani Biofortification of Rice with Iron and Zinc: Progress and Prospects .... 605 Usman Zulfiqar, Muhammad Maqsood, and Saddam Hussain Biofortification of Iron, Zinc and Selenium in Rice for Better Quality . . . 629 Mumtaz Khan, Qudrat Ullah Khan, Rafia Younas, Salma Shaheen, Rehan Ahmad, Naqib Ullah Khan, Mona H. Soliman, Muhammad Rizwan, and Shafaqat Ali Micronutrient Biofortification in Rice for Better Quality ...... 639 Imran, Amanullah, Abdel Rahman Mohammad Said Al-Tawaha, Abdel Razzaq Al Tawaha, Ali M. Qaisi, Devarajan Thangadurai, Jeyabalan Sangeetha, Saher Islam, Yousef M. Abu-Zaitoon, Wafa’a A. Al-Taisan, Alla Aleksanyan, and Ezz Al-Dein Al-Ramamneh Rice Genetic Engineering for Increased Amino Acid and Vitamin Contents ...... 655 Devarajan Thangadurai, C. Soundar Raju, Jeyabalan Sangeetha, Ravichandra Hospet, and Ramachandra Pandhari xviii Contents

Biofortification of Iron, Zinc, and Selenium in Rice for Better Quality . . . 669 M. Ashraful Alam, Hindu Vemuri, Akbar Hossain, M. Abu Syed, M. Khorshed Alam, and M. Rafiqul Islam Quantitative Trait Loci for Rice Grain Quality Improvement ...... 687 Saket Chandra, Aditya Banerjee, and Aryadeep Roychoudhury Improvement of Rice Quality via Biofortification of Selenium, Iron, and Zinc and Its Starring Role in Human Health ...... 699 Imran, Amanullah, Tariq Mahmood, Muhammad Sajid, Abdel Rahman Altawaha, Abdel Razzaq Al-Tawaha, and Ali M. Qaisi Improvement of Rice Quality via Biofortification of Micronutrients .... 715 Mohammad Hasanzadeh and Nahid Hazrati Involvement of Policymakers, Public Acceptance, and Commercialization of Nutritionally Enhanced and Genetically Modified Rice ...... 749 Surekha Challa, Nageswara Rao Reddy Neelapu, Titash Dutta, and Malay Ranjan Mishra About the Editor

Aryadeep Roychoudhury is working as Assistant Pro- fessor at the Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India. He received his B.Sc. (Hons.) in Botany from Presidency College, Kolkata, and M.Sc. in Biophysics and Molecular Biology, University of Calcutta, West Bengal, India. He did his Ph.D. from Bose Institute, Kolkata, under Jadavpur University, Kolkata. His Ph.D. thesis was mostly based on characterization of different salt- inducible genes in rice. Following his Ph.D. work, he joined as Research Associate (Postdoctorate) at the Uni- versity of Calcutta, continuing with rice as model system. Dr. Roychoudhury is currently handling several government-funded projects on abiotic stress responses in rice and supervising ﬁve (05) Ph.D. students as Princi- pal Investigator. To date, he has published over 110 articles in peer-reviewed journals and chapters in books of international and national repute. He is a regular reviewer of articles in high-impact, international journals, life member of different scientiﬁcassociationsand societies, and the recipient of the Young Scientist Award 2019, conferred upon him by International Foun- dation for Environment and Ecology, at the University of Allahabad, Prayagraj, Uttar Pradesh.

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