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Rice: Chemistry and Technology
Azioni libro
Inizia a leggereLunghezza: 1,375 pagine
- Editore:
- Elsevier Science
- Pubblicato:
- Nov 5, 2018
- ISBN:
- 9780128115091
- Formato:
- Libro
Descrizione
Rice Chemistry and Technology, Fourth Edition, is a new, fully revised update on the very popular previous edition published by the AACC International Press. The book covers rice growth, development, breeding, grain structure, phylogenetics, rice starch, proteins and lipids. Additional sections cover rice as a food product, health aspects, and quality analysis from a cooking and sensory science perspective. Final chapters discuss advances in the technology of rice, with extensive coverage of post-harvest technology, biotechnology and genomic research for rice grain quality.
With a new, internationally recognized editor, this new edition will be of interest to academics researching all aspects of rice, from breeding, to usage. The book is essential reading for those tasked with the development of new products.
Identifies the nutrition and health benefits of rice Covers the growing and harvesting of rice crops Includes the use of rice and byproducts beyond food staple Explains rice chemistries, including sections on starch, protein and lipids Contains contributions from a world leading editorial team who bring together experts from across the field Contains six new chapters focusing on rice qualityInformazioni sul libro
Rice: Chemistry and Technology
Lunghezza: 1,375 pagine
Descrizione
Rice Chemistry and Technology, Fourth Edition, is a new, fully revised update on the very popular previous edition published by the AACC International Press. The book covers rice growth, development, breeding, grain structure, phylogenetics, rice starch, proteins and lipids. Additional sections cover rice as a food product, health aspects, and quality analysis from a cooking and sensory science perspective. Final chapters discuss advances in the technology of rice, with extensive coverage of post-harvest technology, biotechnology and genomic research for rice grain quality.
With a new, internationally recognized editor, this new edition will be of interest to academics researching all aspects of rice, from breeding, to usage. The book is essential reading for those tasked with the development of new products.
Identifies the nutrition and health benefits of rice Covers the growing and harvesting of rice crops Includes the use of rice and byproducts beyond food staple Explains rice chemistries, including sections on starch, protein and lipids Contains contributions from a world leading editorial team who bring together experts from across the field Contains six new chapters focusing on rice quality- Editore:
- Elsevier Science
- Pubblicato:
- Nov 5, 2018
- ISBN:
- 9780128115091
- Formato:
- Libro
Correlati a Rice
Anteprima del libro
Rice
Rice
Chemistry and Technology
Fourth Edition
Editor
Jinsong Bao
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
Table of Contents
Cover image
Title page
Copyright
List of contributors
Preface to the fourth edition
Preface to the third edition
Preface to the second edition
Preface to the first edition
1. Origin, taxonomy, and phylogenetics of rice
1. Natural genetic variation in rice
2. Taxonomy and phylogenetics of rice
3. Domestication of cultivated rice
2. Gross structure and composition of the rice grain
1. Structure of the rice grain
2. Gross composition of grain parts and milling fractions
3. Changes during rice grain filling
3. Rice starch
1. Constituents of rice starch
2. The structural levels of starch
3. Starch functional properties
4. Starch biosynthesis
5. Future challenges
4. Rice proteins and essential amino acids
1. Seed storage proteins
2. Essential amino acids
3. Conclusion
5. Rice lipids and rice bran oil
1. Classification, structure, and content of rice lipids
2. Environmental and other factors affecting rice lipid composition
3. Genetic basis of rice lipids
4. Relationships between rice lipids and grain quality
5. Rice bran oil
6. Health benefits of RBO
7. Future prospects
6. Rice minerals and heavy metal(oid)s
1. Content of elements in rice grains
2. Natural variation for grain element content
3. Transgenic approaches for altering grain element content
4. Currently released cultivars
5. Concluding statement
7. Rice vitamins
1. Vitamin A
2. Vitamin B1
3. Vitamin B2
4. Vitamin B3
5. Vitamin B5
6. Vitamin B6
7. Vitamin B7
8. Vitamin B9
9. Vitamin B12
10. Vitamin C
11. Vitamin D
12. Vitamin E
13. Vitamin K
14. Conclusions and future prospects
8. Rice phenolics and other natural products
1. Phenolics
2. Genetics of phenolics
3. Other natural products
4. Future challenges
5. Conclusions
9. Rice end-use quality analysis
1. Physical properties
2. Functional properties
3. Biochemical properties
4. General techniques
5. Future research
10. Rice milling quality
1. Laboratory assessment of milling quality
2. Criteria for milling quality
3. Factors affecting milling quality
4. Genetics of milling quality
5. Breeding of milling quality
6. Future challenges
11. Rice appearance quality
1. Definition, classification, and diversity of rice appearance quality
2. Grain shape and rice yield
3. Effects of grain chalkiness on rice milling and eating quality
4. Genetic bases of rice grain shape
5. Genetic bases of rice grain chalkiness
6. Genetic improvement of rice appearance quality
7. Major issues and prospects in studies on rice appearance quality
12. Rice cooking and sensory quality
1. Consumer demand and sensory evaluation
2. Understanding cooking behavior and cooking quality
3. Future challenges
13. Impact of climate change on rice grain quality
1. Experimental approaches for investigating rice response to climate change
2. Milling quality
3. Appearance quality
4. Cooking and eating quality
5. Protein and its components
6. Concentration and bioavailability of elements
7. Future perspectives
14. Biotechnology for rice grain quality improvement
1. Omics technologies
2. Marker-assisted selection
3. Transgenic breeding
4. Genome editing technology
5. Future trends
15. Postharvest technology: Rice drying
1. Fundamental principles of rice drying
2. Grain bin fans
3. Rice drying systems
4. Recent developments in alternative drying technologies for rice
5. Impacts of drying on milled rice quality
16. Postharvest technology: Rice storage and cooling conservation
1. Terminology and processes definition
2. Rice storage systems
3. Aging of rice during storage
4. Effects of storage on the sensory and physicochemical properties of rice
5. Conclusions
17. Rice noodles
1. Noodles in Asian diet
2. Raw material characterization
3. Processing of rice noodles
4. Trends in product development
18. Rice in brewing
1. Rice in sake production
2. Rice in Huangjiu production
19. Utilization of rice hull and straw
1. Characteristics
2. Adsorbents
3. Biofuels
4. Other uses
5. Future challenges
Index
Copyright
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List of contributors
Griffiths G. Atungulu, Department of Food Science, University of Arkansas Division of Agriculture, Fayetteville, AR, United States
Jinsong Bao, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
Christine J. Bergman, Food Science and Nutrition, Food & Beverage and Event Management Department, University of Nevada Las Vegas, Las Vegas, NV, United States
Aurélien Briffaz
Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Université d’Avignon, Université de La Réunion, Montpellier, France
CIRAD/QualiSud, Cotonou, Bénin
Lilia S. Collado, Institute of Food Science and Technology, College of Agriculture and Food Science, University of the Philippine Los Banos, College, Laguna, Philippines
Karabi Datta, Lab of Translational Research on Transgenic Crops, Dept. of Botany, University of Calcutta, Kolkata, India
Swapan K. Datta, Lab of Translational Research on Transgenic Crops, Dept. of Botany, University of Calcutta, Kolkata, India
Subhrajyoti Ghosh, Lab of Translational Research on Transgenic Crops, Dept. of Botany, University of Calcutta, Kolkata, India
Yuqing He, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
Yu-Fong Huang, Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Republic of China
Xuehui Huang, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
Sachiko Iizuka, National Research Institute of Brewing, Higashihiroshima, Japan
Bienvenido O. Juliano, Philippine Rice Research Institute Los Baños, Laguna, Philippines
J. Karcher, FrigorTec GmbH, Hummelau, Amtzell, Germany
Taiji Kawakatsu, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
R.E. Kolb, FrigorTec GmbH, Hummelau, Amtzell, Germany
Shang-Lien Lo, Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Republic of China
Zhan-Hui Lu, Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
Christian Mestres
CIRAD/QualiSud, F–34398, Montpellier, France
Qualisud, Univ Montpellier, CIRAD, Montpellier SupAgro, Université d’Avignon, Université de La Réunion, Montpellier, France
Z. Mohammadi Shad, Department of Food Science, University of Arkansas Division of Agriculture, Fayetteville, AR, United States
Gareth J. Norton, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
Masaki Okuda, National Research Institute of Brewing, Higashihiroshima, Japan
Sammy Sadaka, Department of Biological and Agricultural Engineering, University of Arkansas Division of Agriculture, University Avenue, Little Rock, AR, United States
Yafang Shao, China National Rice Research Institute, Hangzhou, China
Fumio Takaiwa, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
Chuan Tong, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
Arvin Paul P. Tuaño
Institute of Human Nutrition and Food, College of Human Ecology, University of the Philippines Los Baños, Laguna, Philippines
Department of Chemistry, College of Humanities and Sciences, De La Salle Health Sciences Institute, Dasmariñas, Philippines
Former Supervising Science Research Specialist, Philippine Rice Research Institute Los Baños, Laguna, Philippines
Dominique Valentin, INRA, UMR 1324 Centre des Sciences du Gout et de l’Alimentation, Universite de Bourgogne, UMR Centre des Sciences du Gout et de l’Alimentation, Dijon, France
Yunxia Wang, College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
Dong Wang, Jiangnan University, Wuxi, China
Xin Wei, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
Yan Xu, Jiangnan University, Wuxi, China
Lianxin Yang, Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
Peng Yun, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
Hao Zhou, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
Preface to the fourth edition
Rice (Oryza sativa L.) is recognized not only as a food security crop that feeds over half the global population but also as a source of essential and unique nutritional and functional properties vital for our health and well-being. Rice grain quality improvement remains a central objective of rice breeding programs worldwide. Rice quality is a primary determinant of its market price and consumer acceptance. For these reasons, scientific and technological advances in the field of rice grain quality need to be regularly summarized and updated in an easily accessible and authoritative form.
This fourth edition of Rice: Chemistry and Technology updates the previous three monographs, with emphasis on three features in rice grain quality research. The first feature reflects a new emphasis on nutritional value and health benefits of rice. Each compositional component of the rice grain, major and minor, has been described in its own individual chapter. The second feature is the advancement of understanding of the rice grain chemistry through integration with knowledge from the fields of genetics and molecular biology. In addition to new insights into varietal differences, genetics of chemical components and their regulation at the molecular level during seed development have now been well characterized. Finally, the third feature, biotechnology as a new tool, has been comprehensively and well applied in rice grain quality research, providing the impetus for further improvement of rice grain quality.
As a multiauthored work, each chapter of this monograph has been written by one or more experts on the subject. Although extensive and up-to-date references are included in each chapter, a single monograph cannot exhaustively cover all historical references and themes in the field. Readers are encouraged to continue to refer to the previous editions of this work, which cover other themes and the older literature in more detail.
I would like to thank all the contributors for their time and talent in writing the chapters. I dedicate this monograph to the Godfather of Rice Chemistry, Dr. Bienvenido O. Juliano, who passed away in February 2018, soon after he submitted chapter 2 for this edition. Finally, I would like to thank my wife, Yan Hong, and my son, Ziran Bao, for their patience and understanding during the preparation of the monograph.
Jinsong Bao
Preface to the third edition
Rice has taken center stage this last decade, not only as an important provider of nourishment for the world's population but as a grain now recognized as having many unique nutritional and functional attributes with potential to be captured in a multitude of value-added food and nonfood applications. Basic, up-to-date knowledge of rice chemistry and technology is needed to guide the research that will develop new applications and lead rice into the coming decades.
The third edition of Rice: Chemistry and Technology updates the 1985 monograph, with emphasis on current developments. The book presents, in a single work, comprehensive overviews covering topics ranging from the rice plant and varieties to rice structure and composition and the functionality of its components. Postharvest processing technologies for drying, storage, and milling and those for making traditional and new value-added products are discussed in detail. New nutritional findings are presented.
A multiauthored work, each chapter of the monograph has been written by one or more authorities on the subject. The authors have styled their chapters as overviews, with extensive bibliographies directing the reader to the primary literature. This monograph is intended to be an addition to your collection and not a replacement for the second edition, which covers the older literature in more detail.
I wish to thank the authors for their time and talent in writing the chapters. The authors and I acknowledge and dedicate this monograph to the godfather of the rice world, Bienvenido O. Juliano, whose contributions to the field have guided our research. You paved the way for us, Ben, and we thank you.
Elaine T. Champagne
Preface to the second edition
Rice is the principal food cereal in tropical Asia, where 90% of the world's rice crop is grown and consumed. Significant progress in the chemistry and technology of rice in the last decade has prompted the Publications Committee of the American Association of Cereal Chemistry (AACC) to revise its Monograph No. 4, Rice: Chemistry and Technology, edited by Dave Houston and published in 1972.
The present monograph updates the 1972 monograph, with emphasis on developments in the 1970s and 1980s. Chapters on parboiling and milling emphasize the Asian situation, since the status in the United States and Europe is adequately discussed in published chapters. Extrusion-cooked rice foods and rice noodles are emphasized, as well as Japanese convenience foods. Rice straw is included because of the current interest in biomass utilization. All chapters on technology and processing were contributed by authorities on the subject.
Contributors were encouraged to emphasize varietal differences and possible topics for future research. As editor, I elected to write most of the chemistry chapters and those on by-products and residue, to minimize overlap and maximize coverage of the interfaces between the chemistry and structure of the rice grain and its technological properties. This monograph was mainly planned, written, and edited in 1983–84 during my sabbatical leave from the International Rice Research Institute (IRRI).
I wish to thank the contributors for their time and talent in writing the chapters; R. Don Sullins, then chairman of the AACC Publications Committee, for his assistance and support; M. S. Swaminathan, Director General of IRRI, for approving my leave; the Southeast Asian Research Center for Agriculture for providing me a visiting professorship and office space; the IRRI Department of Communications and Publications for graphics and photography; the IRRI library staff for rechecking literature citations; Daisy Herrero for typing the manuscripts; and my research colleagues in the Cereal Chemistry Department for reviewing my chapters. Finally, I wish to thank my wife, Linda, and my children for their patience and understanding during the preparation of the monograph.
B.O.J.
Preface to the first edition
Rice, as one of the two major food cereals, provides—together with a comparable amount of wheat—a large proportion of the total nourishment of the world's population. However, reported research on rice chemistry and technology has lagged markedly behind that reported for wheat. Moreover, the available information on rice other than on its culture has remained largely scattered in contrast to that for wheat, which has been well collected and summarized.
The present monograph, the fourth in the monograph series sponsored by the American Association of Cereal Chemists, attempts to minimize this disparity. The book has two major aims: to collect and present for the first time in a single work an ordered, coherent, and informative series of reviews on rice chemistry and technology; and to provide an extensive bibliography that will permit direct access to the primary literature. This combination offers useful data to all connected with the handling, processing, or sale of rice and its by-products, as well as to any individual seeking information on rice composition or technology. A third, minor, aim is to use predominantly the metric system of measurement in accordance with its extensive scientific acceptance and the worldwide trend toward its general adoption.
As a multiauthored work, the monograph has the advantage that each chapter is presented by an authority on the subject—and some disadvantages that inevitably accompany this type of publication. The dedicated efforts of the authors have provided the values to be found in this volume; errors and omissions must be attributed to the editor, who welcomes all corrections and suggestions for improving any possible later edition.
Credit for initiating this work belongs to the Monograph Committee of the Association and to Past President Byron Miller and Executive Vice-President Raymond J. Tarleton, who put the plan into effect. My particular thanks go to Director of Publications Merrill J. Busch, and to Assistant Editor Carolyn M. Light and her able proofreading and typesetting coworkers, who diligently, patiently, and cooperatively handled the multitude of details in preparing this work for publication. I thank also my wife, Twylla, not only for her aid but especially for her sustained forbearance during preparation of the monograph.
D.F.H.
1
Origin, taxonomy, and phylogenetics of rice
Xin Wei, and Xuehui Huang College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
Abstract
Rice (Oryza sativa L.) is one of the most important staple crops, feeding almost half of the world population. It is cultivated worldwide with a concentration in Asia. Rice domestication has greatly influenced the history and civilization of humans. Despite the primacy of rice, when, where, and how rice was domesticated was debated for decades. With much effort and the development of genomics, a comprehensive domestication map of rice subspecies was built recently. In this chapter, we discuss recent genetic work that is related to the origin, taxonomy, and phylogenetics of rice, and we describe the genomic research into the domestication of indica and japonica. Characterization of domesticated rice genes will lay a solid foundation for molecular breeding in the future.
Keywords
Domestication; Genomics; Geographic origin; Oryza rufipogon; Phylogenetics; Rice; Taxonomy
Rice, generally referred to as Asian cultivated rice (Oryza sativa L.), is one of the most important staple crops, feeding almost half of the world population. It is widely cultivated around the world and mainly in Asia. Domesticated rice has played a central role in human nutrition and culture during the past 10,000 years. The domestication of rice is one of the most important technological innovations in Asian history, significantly supporting the formation of two of the four ancient civilizations. There is no doubt that rice is one of the most important influential crops in Asia. However, the origin and the domestication processes of cultivated rice have been debated for decades, which is inconsistent with the important position of rice. In this chapter, we discuss recent genetic and archaeological work that reveals the origin, taxonomy, and phylogenetics of rice, and we describe the genomic research into the domestication of subspecies of rice. The development of genomic methods provides a clear picture of the domestication of rice and will certainly benefit the rice functional genomics studies and molecular breeding in the future.
1. Natural genetic variation in rice
1.1. Geographic distribution of rice and its phenotypic diversity
Nowadays rice is widely planted in more than 120 countries across the world, from 35°S to 53°N, with a concentration in tropical and subtropical areas of Asia. From 2010 to 2014, the world harvest area of rice was 163 million hectares per year, led by India, China, Indonesia, Bangladesh, and Thailand with a combined 67% of total (FAO, 2014). The planting area of rice increased approximately 42% in the last 50 years and is still increasing gradually. The increased planting area was mainly in Southeast and South Asia (about 75%), led by India, Indonesia, Thailand, China, and Vietnam. China and India are the biggest rice production countries, which produced approximately 50% of the world's rice. Rice is mainly grown in the Yangtze River basin, southeast coastal area, and northeast area of China. The planting region of rice in northeast area increased quickly in the last decades. The Gangetic Plain and coastal areas are the major rice production areas in India.
More than 400,000 rice accessions have been collected in the public germplasm repositories. The large germplasm resources conservation center of rice includes the International Rice Research Institute (>100,000 rice accessions), National Crop Genebank of China (>80,000), National Plant Germplasm System of United States Department of Agriculture (USDA, >18,000), and National Bureau on Plant Genetic Resources of India (>60,000). These accessions show various phenotypes and many agronomic traits, such as heading date, plant height, seed shape, pericarp color, and grain weight. Take the seed color for example, it could be white, red, black, brown, purple, or green. Rice is classified into two subspecies by their grain shapes and texture: indica and japonica. Generally, indica is long grain, relatively less sticky, with less amylopectin, while japonica is short grain and more sticky. Besides seed shape and texture, indica and japonica show significant differences in plant height, leaf shape, leaf color, plant type, awn length, density of glume pubescence, germinating rate, cold tolerance, lodging resistance, disease resistance, seed shattering, tiller number, and many other agronomic traits. Compared to indica, the japonica varieties have shorter plant height, shaper leaf shape, light leaf color, strong cold tolerance, strong lodging resistance, are nonshattering, but have lower tiller number, slower germinating rate, are sensitive to rice blast, have long and dense glume pubescence and long awn in some varieties. Differences between nonsticky (indica) and sticky (japonica) rice are even documented in Chinese literature as early as AD 100 (Matsuo et al., 1997).
Indica varieties are concentrated in the mostly submerged region in South Asia and Southeast Asia, while japonica varieties are mainly grown in the fields with less water, such as northern latitudes of East Asia, upland areas of Southeast Asia, and high elevations in South Asia. The planting area of japonica is about 13 million hectares, less than 10% of the total. Most japonica is grown in China (about 60%), and over 80% of it is in Northeast China, East China, and Yunnan-Guizhou Plateau.
1.2. IRGSP and OMAP
To meet the projected food demands of growing populations, the world rice production must increase by 30% over the next 20 years. The utilization of biotechnology and molecular breeding to increase the rice yield potential and yield stability is particularly important, in which a high quality reference rice genome sequence is much required. The International Rice Genome Sequencing Project (IRGSP), established in 1998, set the power of sequencing groups from 10 nations to draw a complete precise map of the rice genome (Nipponbare, a japonica cultivar). The IRGSP released a high-quality finished genome sequence of japonica rice in 2005. The rice genome is the first completely sequenced monocot plant genome and the second plant genome after Arabidopsis (a dicot). The highly accurate and public IRGSP sequence opened the door for functional characterization of the rice genome and permitted rice geneticists to identify the genes underlying complex agronomic traits. Based on the rice genome, understanding of the biological function of rice genes and the genetic improvement of rice production and quality has been greatly facilitated. Through comparative analyses, the domestication and evolution research of rice and other cereal crops was also largely promoted (Paterson et al., 2004; Salse et al., 2008; Wang et al., 2005; Yu et al., 2005). Benefiting from the high quality genome and other research for rice, such as the smallest genome of the major cereals, dense genetic maps and relative ease of genetic transformation, rice has been developed to be one of the model species for molecular and genetic research in plants.
The complete japonica rice genome that was released by IRGSP adopted the clone-by-clone approach (International Rice Genome Sequencing Project, 2005). Before that, draft genome sequences of indica (93-11) and japonica (Nipponbare) were acquired by a whole-genome shotgun method and released in 2002 (Goff et al., 2002; Yu et al., 2002). These draft maps of the rice genome sequences have laid a solid foundation for studying the differences among subspecies of rice.
Rice (O. sativa) belongs to the genus Oryza, which consists of two cultivated (O. sativa and O. glaberrima) and 22 wild species (Ge et al., 1999). Based on the karyotype and molecular analysis, Oryza is divided into four complexes, including O. sativa, O. officinalis, O. ridleyi, and O. meyeriana. Ten genome types (A, B, BC, C, CD, E, F, G, HJ, and HK) are recognized in the rice genus. Each genome type contains one to eight species. The two cultivated species and six wild relatives are classified as AA genome diploid species. The other 17 wild species are clustered into another nine genome types. Compared with cultivated rice, the wild rice species generally show a stronger tolerance to drought, salt, disease, and insect stresses as well as higher nutrient-absorption activity. The wild rice species can offer a largely valuable resource of superior genes to the genetic improvement of the cultivated rice. The Oryza Map Alignment Project (OMAP) began in 2005, aiming to better investigate the wild species of rice. The OMAP initially planned to sequence the genomes of African cultivated rice and 11 wild species by constructing bacterial artificial chromosome (BAC) libraries, constructing physical maps and aligning them to the IRGSP genome sequence (Wing et al., 2005). The ambitious goal of OMAP is to construct a genome research platform for evolution, domestication, polyploidy, development, and gene network of the genus Oryza and genetic improvement of rice.
1.3. Large-scale resequencing and genomic variation
Sanger dideoxy enzymatic DNA sequencing technology was developed in 1977, making automated and large-scale sequencing possible, which is widely used to obtain information on genes, genetic variation, and gene function for biological and medical research. It also played significant roles in the genome sequencing of humans, Drosophila, Arabidopsis, rice, and other important species. However, the exorbitant cost and laborious work limited the use of Sanger sequencing in the ultra-large-scale genome sequencing. Therefore, the high-throughput sequencing technology, also known as next-generation sequencing (NGS), began to be developed in the end of 1990s, and three mainstream NGS platforms, including Illumina/Solexa, Roche/454, and ABI/SOLiD sequencing were released from 2005 to 2006. These sequencing technologies greatly decreased the financial and time costs of DNA and RNA sequencing, and revolutionized genomics and molecular biology research. In the last decade, more than 200 animal and plant genomes were successfully sequenced by NGS. As a self-fertilizing diploid species with a small completed high-quality genome, the genomics and functional genomics studies of rice have been greatly enhanced by using NGS (Guo et al., 2014).
Combination of the completed high-quality rice genome and NGS technology brought us to a new era of whole genome resequencing. Whole genome-resequencing of rice means that the individuals are sequenced by NGS without genome assembly, but through short-read alignment. Genomic variations, including structure variation (SV), insertions/deletions (InDels), copy number variations (CNVs), and single nucleotide polymorphisms (SNPs), between the sequenced individuals and the reference genome, are assayed by aligning the short-sequence reads against the reference genome. It is used to identify genomic variation in key germplasm and recombinant populations. Based on the information from whole genome resequencing, rice researchers have characterized numerous genomic variations, identified many quantitative trait loci (QTLs) with high mapping resolution, and developed new molecular breeding systems.
One japonica elite cultivar, Koshihikari, was sequenced by NGS with 15.7× genome coverage in depth, and 67,051 SNPs were identified and used in the definition of the pedigree haplotypes of closely related japonica cultivars (Yamamoto et al., 2010). Forty accessions of cultivated rice and 10 accessions of wild rice (O. rufipogon and O. nivara) were resequenced. In total, 6,496,456 SNPs, 808,000 InDels, 94,700 SVs, and 1676 CNVs were identified (Xu et al., 2012). A large population of Chinese landraces (517 accessions) was resequenced with approximately one-fold coverage. By aligning to the rice reference genome, a total of 3,625,200 nonredundant SNPs were identified, resulting in an average of 9.32 SNPs per kb, with 167,514 SNPs located in the coding regions of 25,409 annotated genes. A high-density SNP map and haplotype map (HapMap) of the rice genome was constructed (Huang et al., 2010). Subsequently, the population was extended to a larger and more diverse sample—950 worldwide rice cultivars. In the genic regions, 4,109,366 nonsingleton SNPs and 191,476 nonredundant InDels ranging from 1 bp to 376 bp in size were identified (Huang et al., 2012b). The authors investigated the worldwide rice population structure and constructed a neighbor-joining tree involving five divergent groups: indica, aus, temperate japonica, tropical japonica, and intermediate, which were consistent with the five distinct groups detected by previous research (Garris et al., 2005). After that, 533 represented rice accessions were resequenced and combined with the 950 sequenced germplasms, in which a total of 6,551,358 high-quality SNPs with the minor allele of each SNP shared by at least five accessions were identified (Xie et al., 2015). The 3000 Rice Genomes Project released sequenced genomes of a core collection of 3000 rice accessions from 89 countries with an average sequencing depth of 14X, and about 20 million rice SNPs were identified (Alexandrov et al., 2015). Based on genome-wide SNP analysis, genomic changes associated with the breeding effect in the indica subspecies were identified. These whole genome resequencing studies revealed relationships among landraces and modern varieties of rice, and genetic diversity that can be used for breeding programs in rice.
1.4. Rice germplasm resources for breeding
A strong genetic bottleneck was generated during the domestication and modern breeding of rice. It was estimated that cultivated rice lost more than 75% of the genetic diversity found in the wild progenitors (Zhu et al., 2007). The superior genes or alleles that contribute to yield, disease resistance, and drought tolerance might be lost in the modern rice varieties because of the genetic drift through bottleneck effects. Future rice improvement needs the genetic variation from traditional varieties and related wild species to cope with the many biotic and abiotic stresses that challenge rice production around the world. However, the wild species are threatened with extinction as their habitats are destroyed by human disturbance and the traditional landraces are being lost as the farmers prefer high-yield commercial varieties. Thus, rice scientists make their efforts for the collection of rice germplasm resources worldwide. For instance, the International Rice Genebank of IRRI held more than 127,000 rice accessions and 4600 wild relatives in the beginning of 2017 (The International Rice Genebank: http://irri.org/our-work/research/genetic-diversity). These rice germplasm resources are indispensable genetic resources for further improvement of cultivated rice varieties. With the development of NGS, rice genome variation and regulatory genes of important agronomic traits (e.g., plant height, flowering time, grain yield, grain quality, and stress resistance) have been exploited. Genome-wide superior alleles that improve the rice yield and quality have been detected in the rice germplasm resources. The collected and conserved rice germplasm resources are the most important strategic resource for rice breeding.
2. Taxonomy and phylogenetics of rice
2.1. Phylogenetics of wild rice (AA-group in Oryza genus)
The genus Oryza is classified into 10 genomes comprising 24 species (two cultivated and 22 wild). The two cultivated species and six wild relatives belonged to O. sativa complex are classified as AA genome diploid species, including Asian cultivated rice (O. sativa), African cultivated rice (O. glaberrima), common wild rice (O. rufipogon), annual wild rice (O. nivara), Barth's rice (O. barthii), longstamen rice (O. longistaminata), Australian wild rice (O. meridionalis), and South American wild rice (O. glumaepatula). The geographical distributions of these eight species are totally different: O. sativa is grown all around the world with a concentration in Asia, O. rufipogon and O. nivara mainly distribute in Asia, O. glaberrima is concentrated in West Africa, O. barthii and O. longistaminata are found in tropical Africa, O. meridionalis is in Australia, and O. glumaepatula is in South America. Generally, the O. sativa, O. glaberrima, O. nivara, O. barthii, and O. meridionalis are annual species whereas the others are perennial species. However, a perennial form O. meridionalis was found in Australia recently (Sotowa et al., 2013).
Based on the morphology, geographic distribution, and levels of partial sterility in F1 hybrid, O. rufipogon and O. nivara were supposed to be progenitor species of O. sativa while O. barthii might be the ancestor of O. glaberrima. Phylogenetic relationships of species in the genus Oryza have been well analyzed by molecular approaches, including chloroplast DNA (Chen et al., 1993; Dally and Second, 1990; Kumagai et al., 2010), nuclear restriction fragment length polymorphism (RFLP) (Wang et al., 1992), two microsatellites (Akagi et al., 1998), two nuclear genes and a chloroplast gene (Ge et al., 1999), multilocus in nuclear genome (Zhu et al., 2007), 53 nuclear genes and 16 intergenic regions (Zhu et al., 2014), and chloroplast genomes (Wambugu et al., 2015). These phylogenetic analyses supported the morphological and crossing results.
To lay the foundation for the comprehensive genome comparison and construct a convincing phylogenetic tree of the AA-genome Oryza species, the IRGSP, OMAP, and other genome sequencing projects were funded to provide high-quality genome research and generate a large array of publicly available genomic resources. Genome-sequencing of O. rufipogon, O. glaberrima, and O. longistaminata was completed by OMAP in 2012, 2014, and 2015, respectively (Huang et al., 2012c; Wang et al., 2014; Zhang et al., 2015), and the other genomes will be released in the near future. These genomes provide the opportunity to compare the genomes and elucidate the convincing phylogenetic relationships of all AA-group species. Based on 2305 one-to-one, single-copy orthologous genes from these genomes, the robust phylogeny of these species was constructed (Zhang et al., 2014). The evolutionary relationships are consistent with the calculated phylogeny of all AA-genome Oryza species in previous study (Zhu et al., 2014). Using the large gene set, the divergence times between AA and FF genomes was dated 35.3 million years (Myr). The divergence time between O. barthii and O. glaberrima is 0.26 Myr, and the divergence time between O. sativa and O. nivara is 1.2 Myr (Zhang et al., 2014).
2.2. Phylogenetics of Asian cultivated rice
As a predominantly autogamous species, gene flow of Asian cultivated rice is restricted. Because of fewer opportunities for cross-pollination, the phylogeny of rice may be affected by the natural distribution of the ancestral species, as well as domestication and artificial selection. As a result, the geographically or ecologically distinct groups of rice, indica and japonica subspecies, which are mainly grown in tropical Asia and temperate East Asia, respectively, are expected to show greater genetic differentiation than that in the outcrossing species. At all levels of analysis, including morphological, physiological, and molecular, the differences between the indica and japonica subspecies are quite significant (Oka and Morishima, 1982).
To define the phylogeny of Asian cultivated rice, molecular markers have been used in the phylogenetic analysis from three decades ago. Using 15 isozyme loci, 1688 traditional rices from Asian rice were classified into six groups. The two largest groups were regarded as indica and japonica, the two minor ones was regarded as aus and Basmati rice, and the satellite ones were restricted to some deepwater rices in Bangladesh and Northeast India (Glaszmann, 1987). After that, RFLP was used in the phylogenetic analysis of rice (Nakano et al., 1992; Zhang et al., 1992), and the differentiation of indica and japonica was detected. A sample of 234 accessions of rice was genotyped at 169 nuclear simple sequence repeats (SSRs) and two chloroplast loci, five divergent groups were detected, corresponding to indica, aus, aromatic, temperate japonica, and tropical japonica rice (Garris et al., 2005). A core collection of USDA world rice collections, including 1763 accessions representing all rice collections, was genotyped using 72 genome-wide SSR markers, and the results showed that the collection consisted of 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus, and 4% aromatic (Agrama et al., 2010). The drought-tolerant, early maturing aus, which is grown in Bangladesh during the summer season, is a minor group that has generally been considered to be indica ecotype. Aromatic, such as basmati from Pakistan, is highly praised for its fragrance and quality. Tropical japonica, also is named javanica initially, is grown in the high-elevation areas of Southeast Asia. Both aromatic and tropical japonica have a close relationship with temperate japonica. Later, microarrays were used in the population structure analysis of rice. The resequencing microarrays, which consist of 100 Mb of the unique fraction of the reference genome, were used to construct the phylogeny of 20 diverse varieties and landraces rice (McNally et al., 2009). In total, 160,000 nonredundant SNPs were detected. The phylogenetic tree revealed three distinct groups, with temperate japonica, tropical japonica, and aromatic closely allied in one group and the other groups correlating with aus and indica types. Another Affymetrix SNP array containing 44,100 SNPs was applied in the genotyping of a rice diversity panel consisting of 413 inbred accessions of O. sativa collected from 82 countries (Zhao et al., 2011). The five subpopulations indica, aus, temperate japonica, tropical japonica, and aromatic were clearly clustered based on the top four principal components analysis. These results were in agreement with previous SSR and SNP analysis (Agrama et al., 2010; Ali et al., 2011; Garris et al., 2005; Zhao et al., 2010).
With the development of NGS, whole-genome resequencing was used in the phylogenetic analysis of rice. Resequencing of 950 worldwide rice germplasms (Huang et al., 2012b) showed that the worldwide rice collection has five distinct groups: indica, aus, temperate japonica, tropical japonica, and intermediate. Among these subpopulations, indica and aus were within the indica subspecies, whereas temperate japonica and tropical japonica were clustered into the japonica subspecies. The tropical japonica and aus accessions were not found in the traditional Chinese landraces. Subsequently, another rice collection containing 533 accessions was sequenced. Combined with the 950 sequenced germplasms, a total of 6,551,358 high-quality SNPs were identified. The population structure analysis revealed six distinct groups: indica I, indica II, temperate japonica, tropical japonica, aus, and an intermediate group (Xie et al., 2015). Most Chinese indica (71%) was divided into indica I group. The indica II group contained most of the accessions from the IRRI (95%), many accessions from Southeast had parentage of IRRI varieties, and some elite varieties bred in China with an IRRI variety parent.
2.3. Differentiation between indica and japonica subspecies
Rice consists of two subspecies: indica and japonica. The distinction of the two subspecies has been documented in ancient Chinese books since the Han dynasty (Oka, 1988). Reproductive isolation, which is the most important standard to define the species or subspecies, is observed in the F1 of the indica and japonica cultivars (about 70% F1 sterility). Besides that, significant differentiation is found in morphological characteristics (Morishima and Oka, 1981), isozyme data (Glaszmann, 1987), DNA markers (Mackill, 1995; Ni et al., 2002; Zhang et al., 1992), and genomes (Feltus et al., 2004; Huang et al., 2008).
The IRGSP sequenced a japonica cultivar (Nipponbare) using a BAC-based strategy (International Rice Genome Sequencing Project, 2005), and the Beijing Genomics Institute used a shotgun approach to sequence an indica variety (Yu et al., 2002). The availability of genomes of the two rice subspecies offers the opportunity to compare the genomics. Based on the alignment of the draft genomes of indica and japonica, 408,898 DNA polymorphisms were discerned, including 384,341 SNPs and 24,557 single-base Indels (Feltus et al., 2004). On average, the polymorphism rate was 1.70 SNPs/kb and 0.11 Indel/kb. The distribution across the genome of the SNPs was not random, with 328 contigs that had high polymorphism rates and 237 contigs that had a low level of polymorphism. Comparative genomic analysis also detected 2041 transposon insertion polymorphisms (TIPs) between the two subspecies genomes (Huang et al., 2008). TIPs represented more than 50% of large insertions and deletions (>100 bp) in the rice genome and generated approximately 14% of the genomic DNA sequence.
Genome resequencing of the indica and japonica populations generated numerous genomic variations that can be applied in the investigation of differentiation between the two subspecies. More than 500 Chinese rice landraces with approximately one-fold-coverage genome sequencing (Huang et al., 2010) were studied. A total of 3,625,200 nonredundant SNPs were identified and used in the construction of phylogenetic relationships. On the basis of the neighbor-joining tree, 373 typical indica and 131 typical japonica landraces were identified. Sequence diversity (π) was estimated at 0.0024, 0.0016 and 0.0006 for all samples, indica and japonica, respectively, suggesting that the indica landraces have much higher genetic diversity than the japonica landraces. The population-differentiation statistic (Fst) between the indica and japonica landraces was estimated at 0.55, much higher than in human populations (Consortium, 2003) and a typical oilcrop, sesame (Wei et al., 2015). The high Fst value indicated a very strong population differentiation of indica and japonica. Further analysis of the highly differentiated SNPs revealed that 367,081 SNPs were nearly fixed and 127,729 SNPs were completely fixed. The completely fixed SNPs had a smaller proportion in the coding region. In total, 53 genes that had large-effect complete-differentiation SNPs were identified, which might be related in the differentiation of the two subspecies.
2.4. Rice taxonomy is changing in modern breeding
Previous phylogeny and population analysis revealed five main groups of rice: indica, aus, aromatic, temperate japonica, and tropical japonica rice (Garris et al., 2005; Huang et al., 2010, 2012b). Genome-wide SNPs further divided indica group into indica I and indica II groups (Xie et al., 2015). The phylogeny of rice strongly related to the distribution of different groups. Indica I is mainly from South China, indica II is from Southeast Asia, temperate japonica is grown in Northeast Asia, aus is grown in South Asia, while aromatic is distributed in South Asia and Middle Asia. The population structure of rice might result from the adaptation of climate and light conditions in different areas. Most traditional rice, or named landraces, could be clustered into the five groups. For instance, Huang et al. (2010) sequenced 517 Chinese landraces and analyzed the phylogeny based on all identified SNPs. The results showed that 97.5% (504 of 517) accessions could be clearly divided into indica or japonica and only 13 intermediate landraces were detected. Because of the distinct geographic distribution of the five rice groups, crosses of different groups rarely occurred. The intermediate landraces might result from occasional crossing between indica and japonica.
Modern breeding of rice, crossing of different rice cultivars and artificially selecting the outstanding progenies according to their phenotypes, began approximately 100 years ago. It has greatly improved the agronomic and economic characteristics of rice varieties, including yield, biotic and abiotic tolerance, eating quality, adaptability, and a number of other agronomic traits. Green Revolution, which largely improved the yield of rice varieties in the 1960s, successfully introduced the semi-dwarf traits into many modern-bred varieties. The breeding of the three-line system
of hybrid rice efficiently utilized heterosis of rice. Based on the hybrid breeding, superior traits from maintainer lines (indica I) and restorer lines (indica II) were combined in the hybrid rice and resulted in much higher (>20%) yield in 1970s–1980s. Meanwhile, the genome constitution of the ancestors of modern rice has been great changed by the modern breeding. According to the estimation of linkage disequilibrium from SNP alleles and determination of haplotype diversity from consecutive alleles, polymorphisms in the haplotype blocks were found to be reduced in several chromosomal regions and the haplotype blocks became less diverse over time as a result of the breeding process (Yonemaru et al., 2012). However, new polymorphisms were also generated across the genome during the breeding process. Additionally, Xie et al. (2015) identified that most Chinese rice landraces are divided into indica I, whereas the varieties bred by IRRI are clustered in indica II. The taxonomy of rice had been changed by modern breeding.
Because of the distinct distribution and partial reproductive isolation of indica and japonica, large gene flow between indica and japonica was rare in the landraces. However, high heterosis performance is observed from the hybrid of indica and japonica. Pioneer breeders have made great efforts to create high-yield hybrid rice and inbred rice varieties by crossing different lines of indica and japonica as well as performing successive selection. A large number of elite hybrid varieties, including 1439 indica-indica type, 38 japonica-japonica type, and 18 indica-japonica type, were resequenced and genome aligned (Huang et al., 2015b). The result revealed that the genomes of varieties generated from indica-japonica crosses were strikingly different from that of indica-indica- and japonica-japonica-type varieties.
Genetic bottleneck, which results from domestication and modern breeding, is detected to be severe in rice. More than 75% of the genetic diversity in wild rice was lost (Zhu et al., 2007). Some favorite genes or alleles that constituted the wild rice genome and contributed to strong biotic and abiotic tolerance cannot be found in current rice varieties. Numerous genes or alleles that are involved in the tolerance of cold, flood, drought, and salt stresses in wild rice have been identified (Ma et al., 2016; Mishra et al., 2016; Niroula et al., 2012; Singh et al., 2015). Meanwhile, numerous genes contributing to the resistance of rice blast, bacterial blight, bacterial leaf streak, and brown planthopper also were detected in wild rice (Du et al., 2009; Gu et al., 2005; Qu et al., 2006; Song et al., 1995; Wang et al., 2015). Breeders have successfully introduced these superior genes or alleles from wild rice into cultivated rice and significantly improved the tolerance of abiotic stresses and resistance of the biotic stresses of modern rice varieties. The Xa21 gene, the first important functional gene identified from wild rice (O. longistaminata) and which showed highly resistance of rice blast disease, had been widely used in marker-assisted rice breeding (Luo et al., 2012). The brown planthopper resistance gene, Bph14, was the first cloned insect resistance gene. It is isolated from O. officinalis, and also was introduced into bred varieties (Li et al., 2006b). Introducing these genes from wild rice not only enhanced the phenotypic performance of new bred cultivars but also dynamically changed the genomic component of modern varieties and produced a profound effect on the rice taxonomy.
2.5. Hybrid rice from indica-japonica crosses
Hybrid rice is bred from two significant different parents with heterosis in yield. The first hybrid rice variety was created by three-line hybrid system and released in the 1970s in China. The Chinese breeders successfully transferred the male sterility gene from wild rice to generate the cytoplasmic genetic male-sterile line. The male-sterile line was reproduced by crossing with the maintainer line, and the hybrid rice was produced by the combination of restorer line and male-sterile line. Using this technology system, the first generation of hybrid rice varieties produced 15%–20% higher yields than inbred rice varieties of the same growth duration. The annual harvest areas of hybrid rice in China has increased from 0.14 million hm² to about 15 million hm² in the last four decades, accounting for about 50% of the total rice planting areas. The exploitation of hybrid rice has met the increased demand for rice in China and Southeast Asia.
Although scientists realized that exploitation of indica/japonica heterosis can heighten the level of hybrid rice yield, few indica-japonica hybrid rice varieties have been bred. In the collection of ∼1500 hybrid rice varieties (Huang et al., 2015), the group of indica-japonica crosses has a higher level of heterozygosity (45.1%) than that of indica-indica crosses (21.8%) and japonica-japonica crosses (15.8%). By calculating the genetic effects of heterozygous alleles on heterosis, the results showed that effective pyramiding of rare superior alleles with positive dominance in hybrids led the higher yield. Thus, the heterotic phenomenon that the hybrids from indica-japonica crosses out yield other hybrids in different environments might result from the introduction of superior alleles between indica and japonica. With the discovery of low-frequency favorite alleles in indica and japonica, better performance of indica-japonica hybrid rice can be expected in the future.
3. Domestication of cultivated rice
3.1. Domestication traits and related genes
Domestication is usually referred to as a sustained multigenerational process of conscious selective breeding in which humans convert wild animals and plants into predictable livestock and crops. It has contributed to one of the greatest revolutions in human history—the transition from gathering foods from the wild to producing them in farms. Charles Darwin had recognized that the domestication mainly happened in some desirable traits of the domestic species (Darwin, 1868). The domestication of animals mostly occurred in the genes that controlled behavior, while the domestication of plants significantly influenced the genes related to ripening or shattering, plant architecture, timing of germination, seed size, and adaptation. Unlike the improvement traits of domestic plants, the domestication traits are generally fixed in the initial domestication and appear in all individuals and populations. Cultivated rice significantly differs from its wild ancestor, O. rufipogon, in the morphology and environment adaptation. The most noticeable domestication traits of cultivated rice are lack of seed shattering, erect growth, annual habit and loss of seed dormancy. Other domestication traits of rice consist of seed coat color, flowering time, plant height, seed length, seed width, awn length, and eating quality. A large number of genes that are related to these domestication traits have been identified.
Loss of seed-shattering habit is considered to be the most critical event in rice domestication. One layer between pedicel and spikelet at the base of rice seed is observed in wild rice and some indica varieties, resulting in a stronger seed-shattering phenotype. Based on the linkage mapping, two independent research groups identified two genes, sh4 and qSH1, that caused loss of seed shattering in all rice and japonica rice, respectively (Konishi et al., 2006; Li et al., 2006a). The sh4 was detected from the recombination population derived between indica and O. nivara, explaining 69% variation on the reduction of grain shattering in cultivated rice (Li et al., 2006a). Similarly, qSH1 was detected from the Kasalath (a typical aus cultivar) and Nipponbare (a temperate japonica cultivar) population, explaining 68.6% of the total variation in the population. Further analysis showed that the nonshattering sh4 allele had a single origin and was fixed in all rice cultivars by artificial selection during the domestication of rice (Zhang et al., 2009). Selection on the nonshattering qSH1 allele mainly distributed in japonica and was rare in indica. The results are consistent with the fact that japonica varieties have a greater hard-to-shatter level than indica varieties.
Another significant domestication event of rice is the transition from the prostrate growth of wild rice to the erect growth of cultivated rice. The PROG1 gene that encodes a single Cys2-His2 zinc-finger protein and controls tiller angle and number of tillers of rice was identified from the ancestral wild rice O. rufipogon (Jin et al., 2008; Tan et al., 2008). The mutant allele, prog1, in cultivated rice led to smaller tiller angle, greater tiller number, and erect growth. Sequence comparison of indica and japonica variations revealed that all erect growth rice varieties had the same SNPs and Indels, implying that the favored prog1 allele might have been singly originated and strongly selected during rice domestication (Tan et al., 2008).
Other important domesticated genes that were related to the domestication traits include but not limited to Rc (Sweeney et al., 2006), Bh4 (Zhu et al., 2011), Waxy (Olsen and Purugganan, 2002; Qiao et al., 2012; Wang et al., 1995), TAC1 (Jiang et al., 2012; Yu et al., 2007), qSW5/GW5 (Shomura et al., 2008; Weng et al., 2008), Sdr4 (Sugimoto et al., 2010), Sd1 (Asano et al., 2011; Sasaki et al., 2002), OsLG1 (Ishii et al., 2013; Zhu et al., 2013), An-1 (Luo et al., 2013), LABA1 (Gu et al., 2015; Hua et al., 2015), and GAD1 (Jin et al., 2016). Unlike the domesticated alleles of sh4 and prog1 genes that were fixed in all cultivated rice, domestication of these genes exist in a large range of variations in rice. Rc, which encodes a basic helix–loop–helix transcription factor, conditioned the rice seed coat color change from red to white pericarp (Sweeney et al., 2006). The domesticated rc allele, which had a 14 bp deletion, has not been selected in all cultivated rice accessions. Similar to the qSH1 gene, domestication of TAC1 (plant architecture related), OsLG1 (panicle architecture related), and qGW5 (seed width related) were mainly domesticated in japonica (Huang et al., 2009; Ishii et al., 2013; Konishi et al., 2006; Shomura et al., 2008; Yu et al., 2007). Selection of the photoperiod genes, such as Hd1, Ehd1, Hd3a, Ghd7, Ghd8, and DTH2, extends the distribution of rice from tropical and subtropical area to temperate area, resulting in rice changing from a regional plant to a worldwide plant (Takahashi et al., 2009; Wei et al., 2010; Wu et al., 2013; Xue et al., 2008).
3.2. Recent studies on domestication processes
Domestication process is one of the most fundamental questions of crop research. The domestication of many crops has been illuminated by genetic, biochemical, and molecular evidence, such as maize, wheat, and tomato. For rice, the most important crop, the domestication was not clearly demonstrated. It is generally accepted that cultivated rice was domesticated from the wild relative rice in Asia about 10,000 years ago. However, the four basic questions of rice domestication—the ancestor, geographic origin, domestication time, and the number of domestication times—all have been argued for a long time (Kovach et al., 2007; Sang and Ge, 2007a, 2007b; Sweeney and McCouch, 2007). The puzzle of rice domestication mainly related to the complex population structure of rice. Rice consists of two subspecies: indica and japonica. Recent genomic analysis revealed that the two subspecies could be further divided into five groups: indica, aus, temperate japonica, tropical japonica, and aromatic. The debates about the single or multiple domestication events and the geographic origin of rice are both closely related to indica and japonica—Were indica and japonica domesticated from one or two distinct populations of wild rice? Which subspecies was domesticated first? Where are the starting domestication areas of indica and japonica?
Two major hypotheses were proposed in rice domestication: the first one is that indica and japonica had a single origin in one area; the other is that the subspecies or five groups have multiple origins in geographically distinct regions from different wild ancestor populations. The single origin hypothesis was popular before the application of biochemistry and genetic markers in the rice domestication research. It suggested that O. sativa was domesticated from O. rufipogon or O. nivara directly and then diverged into two subspecies (Chang, 1976; Oka and Morishima, 1982), or indica was domesticated firstly and then japonica was derived from indica (Ting, 1957). The isozymes, RFLPs, SNPs, transposons analysis of natural populations showed that indica and japonica were domesticated from indica-like and japonica-like O. rufipogon (Cheng et al., 2003; Londo et al., 2006; Rakshit et al., 2007; Second, 1982; Sun et al., 2002; Wei et al., 2012).
With the development of NGS, genome sequences and genome-wide variations of wild and cultivated rice were used in the rice domestication study and enabled us to evaluate the hypotheses in the genomics level. Sixty-six accessions of indica, japonica, and O. rufipogon were resequenced with 1.5X genome coverage per accession. The genomic analysis supported a history of independent origin of indica and japonica from wild rice. However, some low-diversity regions in the genomes originated only once in one population and spread across all cultivars through introgression and human selection (He et al., 2011). Two O. rufipogon accessions were genome sequenced and the genomes were compared with that of cultivated rice. The results provided evidence of the independent domestication of japonica and indica with gene flow from japonica to indica (Yang et al., 2012). In total, 630 gene fragments on chromosomes 8, 10, and 12 from 40 cultivated rice and 17 wild relative accessions were sequenced. Using patterns of SNPs, 20 putative selective sweeps in cultivated rice were identified and a single domestication origin of rice was supported by the demographic modeling (Molina et al., 2011). Although similar strategies were used in the research of Molina et al. (2011) and He et al. (2011), two opposite conclusions were obtained. This result might relate to the small size of samples used in these studies. To make an accurate and comprehensive study of domestication, a large scale of samples from a broad distribution region was required. To investigate the population structure of Oryza rufipogon, 42 genome-wide sequence-tagged sites were used to survey 108 O. rufipogon accessions throughout the native range of the species. Two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II, were identified. Ruf-I showed genetic similarity with indica, whereas Ruf-II was not found to be closely related to cultivated rice varieties. The results support the hypothesis of a single origin of rice and that indica was domesticated firstly (Huang et al., 2012a). Subsequently, genome sequences of 446 geographically diverse accessions of the wild rice species O. rufipogon (including O. nivara), and from 1083 cultivated indica and japonica varieties, were generated and a comprehensive map of rice genome variation was constructed (Huang et al., 2012c). The O. rufipogon population was clustered into three groups: Or-I, Or-II, and Or-III by 5 million SNPs. In total, 55 selective sweeps that have occurred during domestication were identified. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that japonica was first domesticated from Or-III, and that indica was subsequently developed from crosses between japonica rice and wild rice in Or-I (also called O. nivara). One study (Civan et al., 2015) suggested a multiple-origin model hypothesizing japonica, indica, and aus having three separate origins with independent domestications (but was argued by Huang and Han, 2016). Recently, a new model that suggested that different rice subspecies had separate origins but only one domestication was constructed by comparing the genomes of wild and cultivated rice (Choi et al., 2017), consistent with the previous study (Huang et al., 2012c).
For the ancestor of O. sativa, both O. rufipogon and O. nivara were considered as the progenitors of rice (Grillo et al., 2009; Khush, 1997; Vaughan et al., 2008). O. rufipogon is perennial, photoperiod sensitive, and largely cross-fertilized; it is widely distributed from South China to North Australia. O. nivara is an annual wild relative of rice, which is mainly found in South and Southeast Asia (Zhou et al., 2008). It was derived from O. rufipogon about 0.16 million years ago associated with an ecological shift from a persistently wet to a seasonally dry habitat (Liu et al., 2015; Zheng and Ge, 2010). Chen et al. (1993) detected a deletion in chloroplast DNA in 137 cultivars and 117 strains of wild rice from various countries. The result revealed that indica and annual type of O. rufipogon (also named O. nivara) had the deletion while japonica and perennial type of O. rufipogon had the nondeletion, suggesting that indica might have a close relationship to O. nivara. The genomics research supported that O. nivara had a closer relationship to indica. Xu et al. (2012) resequenced 40 accessions of cultivated rice and 10 accessions of O. rufipogon and O. nivara. With the 6.5 million SNPs, phylogenetic analysis showed that indica and japonica had a close relationship to O. nivara and O. rufipogon, respectively. Huang et al. (2012c) also identified that indica came from the cross of japonica and Or-I (mainly O. nivara). Thus, the genomic results showed that O. nivara might be the main ancestor of indica, whereas japonica was domesticated only from O. rufipogon.
Based on these genome studies, a model that might be close to the truth of rice domestication was constructed (Fig. 1.1). Some mutations that related to shattering, tilling angle, and seed coat color were discovered in the O. rufipogon from South China and fixed in the ancient japonica. When the ancient japonica spread to South Asia, it was crossed with O. rufipogon in the local region. Thus, proto indica and proto aus that carried domesticated genes were developed, respectively. Finally, with long time artificial selections, indica, japonica, and aus varieties were generated and the domestication alleles were fixed in modern rice.
Figure 1.1 The domestication model of cultivated rice. The genomes of rice and wild rice are indicated by ovals in different colors. Red (light gray in print version): indica and Oryza rufipogon in South Asia. Blue (dark black in print version): japonica and O. rufipogon in South China. Purple (light black in print version): Aus, Oryza nivara and O. rufipogon in South Asia. Genes
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