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 # Springer Nature Singapore Pte Ltd. 2020 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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 mal- nutrition 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 defi- ciency 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 world- wide which