Global warming threatens food security. Rice (Oryza sativa L.), a vital food crop, is vulnerable to heat stress, especially at the reproductive stage. Here we summarize putative mechanisms of high-temperature perception (via RNA secondary structure, the phyB gene, and phase separation) and response (membrane fluidity, heat shock factors, heat shock proteins, and ROS (reactive oxygen species) scavenging) in plants. We describe how rice responds to heat stress at different cell-component levels (membrane, endoplasmic reticulum, chloroplasts, and mitochondria) and functional levels (denatured protein elimination, ROS scavenging, stabilization of DNA and RNA, translation, and metabolic flux changes). We list temperature-sensitive genetic male sterility loci available for use in rice hybrid breeding and explain the regulatory mechanisms associated with some of them. Breeding thermotolerant rice species without yield penalties via natural alleles mining and transgenic editing should be the focus of future work.
Salinity is one of the major abiotic stresses which impose constraints to plant growth and production. Rice (Oryza sativa L.) is one of the most important staple food crops and a model monocot plant. Its production is expanding into regions that are affected by soil salinity, requiring cultivars more tolerant to saline conditions. Understanding the molecular mechanisms of such tolerance could lay a foundation for varietal improvement of salt tolerance in rice. In spite of extensive studies exploring the mechanism of salt tolerance, there has been limited progress in breeding for increased salinity tolerance. In this review, we summarize the information about the major molecular mechanisms underlying salinity tolerance in rice and further discuss the limitations in breeding for salinity tolerance. We show that numerous gene families and interaction networks are involved in the regulation of rice responses to salinity, prompting a need for a comprehensive functional analysis. We also show that most studies are based on whole-plant level analyses with only a few reports focused on tissue- and/or cell-specific gene expression. More details of salt-responsive channel and transporter activities at tissue- and cell-specific level still need to be documented before these traits can be incorporated into elite rice germplasm. Thus, future studies should focus on diversity of available genetic resources and, particular, wild rice relatives, to re-incorporate salinity tolerance traits lost during domestication.
As a consequence of industrial development, soil Cd pollution leads to crop contamination by Cd, posing a threat to food safety and human health. Excessive accumulation of Cd in plants also inhibits their growth via oxidative stress damage to their photosynthetic systems. Through evolutionary selection, plants have developed a set of efficient strategies to respond to Cd in their environments. These include the accumulation and detoxification of heavy metals. Cd is absorbed by plant roots through the apoplastic and symplastic pathways and then translocated to plant shoots via xylem loading, long-distance transport, and phloem redistribution. Simultaneously, plants initiate a series of mechanisms to reduce Cd toxicity, including cell wall adsorption, cytoplasmic chelation, and vacuolar sequestration. This review summarizes current knowledge of Cd accumulation and detoxification in plants.
Amino acids are essential plant compounds serving as the building blocks of proteins, the predominant forms of nitrogen (N) distribution, and signaling molecules. Plant amino acids derive from root acquisition, nitrate reduction, and ammonium assimilation. Many amino acid transporters (AATs) mediating transfer processes of amino acids have been functionally characterized in Arabidopsis, whereas the function and regulation of the vast majority of AATs in rice (Oryza sativa L.) and other crops remain unknown. In this review, we summarize the current understanding of amino acids in the rhizosphere and in metabolism. We describe their function as signal molecules and in regulating plant architecture, flowering time, and defense against abiotic stress and pathogen attack. AATs not only function in root acquisition and translocation of amino acids from source to sink organs, regulating N uptake and use efficiency, but also as transporters of non-amino acid substrates or as amino acid sensors. Several AAT genes show natural variations in their promoter and coding regions that are associated with altered uptake rate of amino acids, grain N content, and tiller number. Development of an amino acid transfer model in plants will advance the manipulation of AATs for improving rice architecture, grain yield and quality, and N-use efficiency.
Global food security is threatened by rice blast disease caused by the filamentous fungus Magnaporthe oryzae. An understanding of rice resistance mechanisms is fundamental to developing strategies for disease control. In this review, we summarize recent advances in pathogen-associated molecular pattern-triggered immunity, effector-triggered immunity, defense regulator-mediated immunity, and effects of nutrient elements on rice blast resistance. We outline strategies used for breeding rice cultivars with improved disease resistance. We also present the major research challenges for rice blast disease resistance and propose approaches for future investigation.
Plants and viruses coexist in the natural ecosystem for extended periods of time, interacting with each other and even coevolving, maintaining a dynamic balance between plant disease resistance and virus pathogenicity. During virus-host interactions, plants often exhibit abnormal growth and development. However, plants do not passively withstand virus attacks but have evolved sophisticated and effective defense mechanisms to resist, limit, or undermine virus infections. It is widely believed that the initial stage of infection features the most intense interactions between the virus and the host and the greatest variety of activated signal transduction pathways. This review describes the most recent findings in rice antiviral research and discusses a variety of rice antiviral molecular mechanisms, including those based on R genes and recessive resistance, RNA silencing, phytohormone signaling, autophagy and WUS-mediated antiviral immunity. Finally, we discuss the challenges and future prospects of breeding rice for enhanced virus resistance.
Domestication of crops is one of the greatest inventions of the human race and has played a vital role in the progress of human civilization. Understanding the genetic mechanisms of crop domestication could shed light on its history and would advance crop breeding. Cultivated rice species, which were domesticated from wild rice species, are important food crops worldwide. Morphological traits, physiological characteristics, and ecological adaptability of cultivated rice are very different from those characters of wild rice. In this review, we summarize current knowledge of the genetic mechanisms underlying these differences between wild and cultivated rice and discuss the application of wild rice species in modern breeding.
Rice grain yield is determined by three major “visible” morphological traits: grain weight, grain number per panicle, and effective tiller number, which are affected by a series of “invisible” physiological factors including nutrient use efficiency and photosynthetic efficiency. In the past few decades, substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation, laying a solid foundation for improving rice yield by molecular breeding. This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency. It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.
Rice panicle architecture affects grain number per panicle and thereby grain yield. Many genes involved in control of panicle architecture have been identified in the past decades. According to their effect on phenotype, these genes are divided into three categories: panicle branch and lateral spikelets, multifloret spikelets, and panicle type. We review these genes, describe their genetic regulatory network, and propose a strategy for using them in rice breeding. These findings on rice panicle architecture may facilitate related studies in other crops.
Anthocyanins are a major subclass of flavonoids that have diverse biological functions and benefit human health. In rice (Oryza sativa), the various colors shown by organs are due mainly to the accumulation of anthocyanins and are traits associated with domestication. Elucidating the genetic basis of anthocyanin biosynthesis in rice would support the engineering of anthocyanins as well as shedding light on the evolutionary history of O. sativa. We summarize recent progress in rice anthocyanin biosynthesis research, including gene cloning, biosynthetic pathway discovery, and study of the domestication process. We discuss the application of anthocyanin biosynthesis genes in rice breeding. Our object is to broaden knowledge of the genetic basis of anthocyanin biosynthesis in rice and support the breeding of novel rice cultivars.
Rice is one of cereal crops and a model species for monocots. Since the release of the first draft rice genome sequences in 2002, considerable progress has been achieved in rice genomic researches, thanks to rapid development and efficient utilization of bioinformatics methods and tools. In this review, we summarize the progress of studies of rice genome sequencing and other omics and introduce the well-maintained bioinformatics databases and tools developed for rice genome resources and breeding. After reviewing the history of rice bioinformatics, we use single-cell sequencing and machine learning as examples showing how bioinformatics integrates emerging technologies and how it continues to develop for future rice research.
The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement. Pan-genomics has revolutionized genomic research in plants. However, rice pan-genomic studies so far have been limited mostly to cultivated accessions, with only a few close wild relatives. Advances in sequencing technologies have permitted the assembly of high-quality rice genome sequences at low cost, making it possible to construct genus-level pan-genomes across all species. In this review, we summarize progress in current research on genetic and genomic resources in Oryza, and in sequencing and computational technologies used for rice genome and pan-genome construction. For future work, we discuss the approaches and challenges in the construction of, and data access to, Oryza pan-genomes based on representative high-quality genome assemblies. The Oryza pan-genomes will provide a basis for the exploration and use of the extensive genetic diversity present in both cultivated and wild rice populations.
With the rapid development of genetic analysis techniques and crop population size, phenotyping has become the bottleneck restricting crop breeding. Breaking through this bottleneck will require phenomics, defined as the accurate, high-throughput acquisition and analysis of multi-dimensional phenotypes during crop growth at organism-wide levels, ranging from cells to organs, individual plants, plots, and fields. Here we offer an overview of crop phenomics research from technological and platform viewpoints at various scales, including microscopic, ground-based, and aerial phenotyping and phenotypic data analysis. We describe recent applications of high-throughput phenotyping platforms for abiotic/biotic stress and yield assessment. Finally, we discuss current challenges and offer perspectives on future phenomics research.
Future demands for increased productivity and resilience to abiotic/biotic stresses of major crops require new technologies of breeding by design (BBD) built on massive information from functional and population genomics research. A novel strategy of breeding by selective introgression (BBSI) has been proposed and practiced for simultaneous improvement, genetic dissection and allele mining of complex traits to realize BBD. BBSI has three phases: a) developing large numbers of trait-specific introgression lines (ILs) using backcross breeding in elite genetic backgrounds as the material platform of BBD; b) efficiently identifying genes or quantitative trait loci (QTL) and mining desirable alleles affecting different target traits from diverse donors as the information platform of BBD; and c) developing superior cultivars by BBD using designed QTL pyramiding or marker-assisted recurrent selection. Phase (a) has been implemented massively in rice by many Chinese research institutions and IRRI, resulting in the development of many new green super rice cultivars plus large numbers of ILs in 30 + elite genetic backgrounds. Phase (b) has been demonstrated in a series of proof-of-concept studies of high-efficiency genetic dissection of rice yield and tolerance to abiotic stresses using ILs and DNA markers. Phase (c) has also been implemented by designed QTL pyramiding, resulting in a prototype of BBD in several successful cases. The BBSI strategy can be easily extended for simultaneous trait improvement, efficient gene and QTL discovery and allele mining of complex traits using advanced breeding lines from crosses between a common “backbone” parent and a set of elite parents in conventional pedigree breeding programs. BBSI can be relatively easily adopted by breeding programs with small budgets, but the BBSI-based BBD strategy can be fully and more efficiently implemented by large seed companies with sufficient capacity.
Progress in plant breeding depends on the development of genetic resources, genetic knowledge, and breeding techniques. The core of plant breeding is the use of naturally occurring variation. At the beginning of the post-genomic era, a new concept of “breeding by design” was proposed, which aims to control all allelic variation for all genes of agronomic importance. In the past two decades, we have applied a three-step strategy for research on rice breeding by design. In the first step, we constructed a single-segment substitution line (SSSL) library using Huajingxian 74 (HJX74), an elite xian (indica) rice cultivar, as the recipient in which to assemble genes from the rice AA genome. In the second step, we identified a series of desirable genes in the SSSL library. In the third step, we designed new rice lines, and achieved the breeding goals by pyramiding target genes in the HJX74-SSSL library. This review introduces the background, concept, and strategy of breeding by design, as well as our achievements in rice breeding by design using the HJX74-SSSL platform. Our practice shows that target chromosome-segment substitution is a way to breeding by design.
Rice (Oryza sativa) provides a staple food source for more than half the world population. However, the current pace of rice breeding in yield growth is insufficient to meet the food demand of the ever-increasing global population. Genomic selection (GS) holds a great potential to accelerate breeding progress and is cost-effective via early selection before phenotypes are measured. Previous simulation and experimental studies have demonstrated the usefulness of GS in rice breeding. However, several affecting factors and limitations require careful consideration when performing GS. In this review, we summarize the major genetics and statistical factors affecting predictive performance as well as current progress in the application of GS to rice breeding. We also highlight effective strategies to increase the predictive ability of various models, including GS models incorporating functional markers, genotype by environment interactions, multiple traits, selection index, and multiple omic data. Finally, we envision that integrating GS with other advanced breeding technologies such as unmanned aerial vehicles and open-source breeding platforms will further improve the efficiency and reduce the cost of breeding.
With the ever-increasing human population and deteriorating environmental conditions, there is an urgent need to breed environmentally friendly and resource-conserving rice cultivars to achieve sustainable agricultural development and food security. However, conventional rice improvement strategies, such as hybrid breeding, are time-consuming and laborious processes and may not be able to keep pace with increasing food demand in the future. Targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas), permit efficient targeted genome modification and offer great promise for the creation of desired plants with higher yield, improved grain quality, and resistance to herbicides, diseases, and insect pests. There is also great potential for tapping heterosis using the CRISPR/Cas technology. In this review, we focus on the most essential applications of CRISPR/Cas genome editing to rice genetic improvement, considering traits such as yield, quality, and herbicide, disease and insect-pest resistance. We discuss applications of CRISPR/Cas to the exploitation of heterosis. Finally, we outline perspectives for future rice breeding using genome-editing technologies.
Heterosis, which describes the superior vigor and yield of F1 hybrids with respect to their parents, is observed in many rice hybrid crosses. The exploitation of heterosis is a great leap in the history of rice breeding. With advances in genomics and genetics, high-resolution mapping and functional identification of heterosis-associated loci have been performed in rice. Here we summarize advances in understanding the genetic basis of grain yield heterosis in hybrid rice and provide a vision for the genetic study and breeding application of rice heterosis in the future.
The breeding and large-scale application of hybrid rice contribute significantly to the food supply worldwide. Currently, hybrid seed production uses cytoplasmic male sterile (CMS) lines or photoperiod/thermo-sensitive genic male sterile (PTGMS) lines as female parent. Despite huge successes, both systems have intrinsic problems. CMS systems are mainly restricted by the narrow restorer resources that make it difficult to breed superior hybrids, while PTGMS systems are limited by conditional sterility of the male sterile lines that makes the propagation of both PTGMS seeds and hybrid seeds vulnerable to unpredictable climate changes. Recessive nuclear male sterile (NMS) lines insensitive to environmental conditions are widely distributed and are ideal for hybrid rice breeding and production, but the lack of effective ways to propagate the pure NMS lines in a large scale renders it impossible to use them for hybrid rice production. The development of “the third-generation hybrid rice technology” enables efficient propagation of the pure NMS lines in commercial scale. This paper discusses the establishment of “the third-generation hybrid rice technology” and further innovations. This new technology breaks the limitations of CMS and PTGMS systems and will bring a big leap forward in hybrid rice production.
