Temporal and spatial expression pattern of the OSVP1 and OSEM genes during seed development in rice

The aleurone layer of cereal grains: Development, genetic regulation, and breeding applications

Cereal aleurone cells are differentiated from triploid endosperm cells and exhibit distinct cytological, physiological, and biochemical characteristics that distinguish them from the starchy endosperm cells of cereals. Aleurone cells maintain viability throughout seed development, whereas starchy endosperm cells undergo programmed cell death during maturation. Despite variations in aleurone-related traits among cereal species, the aleurone layer plays a crucial role in regulating many aspects of seed development, including the accumulation of storage reserves, the acquisition of dormancy, and germination. Given that many nutrients-such as lipids, dietary fibers, vitamins, and minerals like iron and zinc-are predominantly accumulated in the aleurone cells of cereal grains, this layer has attracted considerable attention aimed at improving the nutritional value of cereals. This review provides a comprehensive overview of the developmental, genetic, and molecular basis of aleurone cell differentiation and proliferation. It focuses on the improvement of aleurone-related traits informed by knowledge of the molecular networks governing aleurone development and presents a detailed discussion on the challenges and potential solutions associated with cereal improvement through the manipulation of aleurone-related traits.

Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (Cyperus esculentus L.)

LEA_5 domain-containing proteins constitute a small family of late embryogenesis-abundant proteins that are essential for seed desiccation tolerance and dormancy. However, their roles in non-seed storage organs such as underground tubers are largely unknown. This study presents the first genome-scale analysis of the LEA_5 family in tigernut (Cyperus esculentus L.), a Cyperaceae plant producing desiccation-tolerant tubers. Four LEA_5 genes identified from the tigernut genome are twice of two present in model plants Arabidopsis thaliana and Oryza sativa. A comparison of 86 members from 34 representative plant species revealed the monogenic origin and lineage-specific family evolution in Poales, which includes the Cyperaceae family. CeLEA5 genes belong to four out of five orthogroups identified in this study, i.e., LEA5a, LEA5b, LEA5c, and LEA5d. Whereas LEA5e is specific to eudicots, LEA5b and LEA5d appear to be Poales-specific and LEA5c is confined to families Cyperaceae and Juncaceae. Though no syntenic relationship was observed between CeLEA5 genes, comparative genomics analyses indicated that LEA5b and LEA5c are more likely to arise from LEA5a via whole-genome duplication. Additionally, local duplication, especially tandem duplication, also played a role in the family expansion in Juncus effuses, Joinvillea ascendens, and most Poaceae plants examined in this study. Structural variation (e.g., fragment insertion) and expression divergence of LEA_5 genes were also observed. Whereas LEA_5 genes in A. thaliana, O. sativa, and Zea mays were shown to be preferentially expressed in seeds/embryos, CeLEA5 genes have evolved to be predominantly expressed in tubers, exhibiting seed desiccation-like accumulation during tuber maturation. Moreover, CeLEA5 orthologs in C. rotundus showed weak expression in various stages of tuber development, which may explain the difference in tuber desiccation tolerance between these two close species. These findings highlight the lineage-specific evolution of the LEA_5 family, which facilitates further functional analysis and genetic improvement in tigernut and other species.

Progress of ABA function in endosperm cellularization and storage product accumulation

Seed development is a complex process and co-regulated by genetic and environmental factors, which significantly affects the seed vigor, yield and quality of crops, especially in cereal crops. Abscisic acid (ABA) regulates various biological processes in seed development, including endosperm and embryo development, accumulation of storage materials, achievement of desiccation tolerance and dormancy. Compared to the functional investigation of ABA in germination and stress response, the role of ABA in early seed development and storage product accumulation has not been collectively elucidated. Here, ABA origin in seed was concluded: both maternal source and de novo synthesis of ABA in seed play an important role in seed development. This review also provided an overview of the current knowledge on ABA in early seed development, mainly in endosperm cellularization. ABA promotes endosperm cellularization in Arabidopsis, but this notion has not been spread into cereal crops. Besides, the increasing importance of ABA in seed reserve accumulation was also emphatically described. In the last section, the key problems and challenges (e.g., where dose ABA come from at each stage of seed development? whether same regulators in response to ABA in Arabidopsis apply equally to cereal crops) were addressed.

Current Insights into Weak Seed Dormancy and Pre-Harvest Sprouting in Crop Species

During the domestication of crops, seed dormancy has been reduced or eliminated to encourage faster and more consistent germination. This alteration makes cultivated crops particularly vulnerable to pre-harvest sprouting, which occurs when mature crops are subjected to adverse environmental conditions, such as excessive rainfall or high humidity. Consequently, some seeds may bypass the normal dormancy period and begin to germinate while still attached to the mother plant before harvest. Grains affected by pre-harvest sprouting are characterized by increased levels of α-amylase activity, resulting in poor processing quality and immediate grain downgrading. In the agriculture industry, pre-harvest sprouting causes annual economic losses exceeding USD 1 billion worldwide. This premature germination is influenced by a complex interplay of genetic, biochemical, and molecular factors closely linked to environmental conditions like rainfall. However, the exact mechanism behind this process is still unclear. Unlike pre-harvest sprouting, vivipary refers to the germination process and the activation of α-amylase during the soft dough stage, when the grains are still immature. Mature seeds with reduced levels of ABA or impaired ABA signaling (weak dormancy) are more susceptible to pre-harvest sprouting. While high seed dormancy can enhance resistance to pre-harvest sprouting, it can lead to undesirable outcomes for most crops, such as non-uniform seedling establishment after sowing. Thus, resistance to pre-harvest sprouting is crucial to ensuring productivity and sustainability and is an agronomically important trait affecting yield and grain quality. On the other hand, seed color is linked to sprouting resistance; however, the genetic relationship between both characteristics remains unresolved. The identification of mitogen-activated protein kinase kinase-3 (MKK3) as the gene responsible for pre-harvest sprouting-1 (Phs-1) represents a significant advancement in our understanding of how sprouting in wheat is controlled at the molecular and genetic levels. In seed maturation, Viviparous-1 (Vp-1) plays a crucial role in managing pre-harvest sprouting by regulating seed maturation and inhibiting germination through the suppression of α-amylase and proteases. Vp-1 is a key player in ABA signaling and is essential for the activation of the seed maturation program. Mutants of Vp-1 exhibit an unpigmented aleurone cell layer and exhibit precocious germination due to decreased sensitivity to ABA. Recent research has also revealed that TaSRO-1 interacts with TaVp-1, contributing to the regulation of seed dormancy and resistance to pre-harvest sprouting in wheat. The goal of this review is to emphasize the latest research on pre-harvest sprouting in crops and to suggest possible directions for future studies.

Underlying Biochemical and Molecular Mechanisms for Seed Germination

With the burgeoning population of the world, the successful germination of seeds to achieve maximum crop production is very important. Seed germination is a precise balance of phytohormones, light, and temperature that induces endosperm decay. Abscisic acid and gibberellins—mainly with auxins, ethylene, and jasmonic and salicylic acid through interdependent molecular pathways—lead to the rupture of the seed testa, after which the radicle protrudes out and the endosperm provides nutrients according to its growing energy demand. The incident light wavelength and low and supra-optimal temperature modulates phytohormone signaling pathways that induce the synthesis of ROS, which results in the maintenance of seed dormancy and germination. In this review, we have summarized in detail the biochemical and molecular processes occurring in the seed that lead to the germination of the seed. Moreover, an accurate explanation in chronological order of how phytohormones inside the seed act in accordance with the temperature and light signals from outside to degenerate the seed testa for the thriving seed’s germination has also been discussed.

Selenium and zinc oxide nanoparticles modulate the molecular and morpho-physiological processes during seed germination of Brassica napus under salt stress

The advent of the nanotechnology era offers a unique opportunity for sustainable agriculture, and the contribution of nanoparticles (NPs) to ameliorate abiotic stresses became the new area of interest for researchers due to their special physiochemical characteristics in the biological system. Salinity is a key devastating abiotic factor that hinders the development and yield of rapeseed. On the flip side, the impact of nanoparticles on plant hormones upon salt stress during seed imbibition and germination has been poorly understood. Hence, we aimed to study the influence of nanopriming on plant hormones and germination processes using selenium and zinc oxide nanoparticles (SeNPs and ZnONPs) during seed imbibition and the early seedling stage upon salinity stress. Nanopriming showed a positive effect on final germination percentage, germination rate, seed microstructure, and antioxidant enzyme activity of two rapeseed cultivars under salt stress. Moreover, nano-treatment decreased the expression of abscisic acid related genes BnCYP707A1, 3, and 4 during the priming time and after sowing, where the levels of BnCYP707A1, and 3 genes showed a slightly significant difference between the nanopriming and hydropriming, which gave an evidence that the nanopriming influenced the ABA levels then elevated the seed germination with SeNPs and ZnONPs. Likewise, nanoparticles significantly elevated the expression levels of BnGA20ox, BnGA3ox and BnCPS genes during the germination stage, especially at 24 h after being sown in salt stress. That confirms the positive role of SeNPs and ZnONPs in regulating gibberellic acid level, which increases the germination in primed seeds as compared to unprimed seeds and hydroprimed seeds. Additionally, our results demonstrated that nanopriming regulated the expression level of BnCAM and BnPER during priming time and after sowing, along with the various levels of expression remarkably in BnEXP4 and BnRAB28, especially at 24 h of being sown under salt stress, which promoted seed germination and early seedling growth. Overall, this work provides new insights into mechanisms underlying the interactions of SeNPs and ZnONPs with plant hormones during the seed imbibition and early seedling stage, consequently enhanced plant growth and development. Additionally, these findings portrayed that the application of SeNPs and ZnONPs could be a new strategy and useful approach to enhance tolerance against salinity in rapeseed plants.

High-resolution spatiotemporal transcriptome analyses during cellularization of rice endosperm unveil the earliest gene regulation critical for aleurone and starchy endosperm cell fate specification

The major tissues of the cereal endosperm are the starchy endosperm (SE) in the inner and the aleurone layer (AL) at the outer periphery. The fates of the cells that comprise these tissues are determined according to positional information; however, our understanding of the underlying molecular mechanisms remains limited. Here, we conducted a high-resolution spatiotemporal analysis of the rice endosperm transcriptome during early cellularization. In rice, endosperm cellularization proceeds in a concentric pattern from a primary alveolus cell layer, such that developmental progression can be defined by the number of cell layers. Using laser-capture microdissection to obtain precise tissue sections, transcriptomic changes were followed through five histologically defined stages of cellularization from the syncytial to 3-cell layer (3 L) stage. In addition, transcriptomes were compared between the inner and the outermost peripheral cell layers. Large differences in the transcriptomes between stages and between the inner and the peripheral cells were found. SE attributes were expressed at the alveolus-cell-layer stage but were preferentially activated in the inner cell layers that resulted from periclinal division of the alveolus cell layer. Similarly, AL attributes started to be expressed only after the 2 L stage and were localized to the outermost peripheral cell layer. These results indicate that the first periclinal division of the alveolus cell layer is asymmetric at the transcriptome level, and that the cell-fate-specifying positional cues and their perception system are already operating before the first periclinal division. Several genes related to epidermal identity (i.e., type IV homeodomain-leucine zipper genes and wax biosynthetic genes) were also found to be expressed at the syncytial stage, but their expression was localized to the outermost peripheral cell layer from the 2 L stage onward. We believe that our findings significantly enhance our knowledge of the mechanisms underlying cell fate specification in rice endosperm.

Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling

Rice, a staple food worldwide, contains varying amounts of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly investigated. Here, an optimized rapid laser capture microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis-elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.

Diverse Roles of MAX1 Homologues in Rice

Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.

WRKY Transcription Factor OsWRKY29 Represses Seed Dormancy in Rice by Weakening Abscisic Acid Response

For efficient plant reproduction, seed dormancy delays seed germination until the environment is suitable for the next generation growth and development. The phytohormone abscisic acid (ABA) plays important role in the induction and maintenance of seed dormancy. Previous studies have identified that WRKY transcription factors can regulate ABA signaling pathway. Here, we identified an Oswrky29 mutant with enhanced dormancy in a screen of T-DNA insertion population. OsWRKY29 is a member of WRKY transcription factor family which located in the nuclear. The genetic analyses showed that both knockout and RNAi lines of OsWRKY29 had enhanced seed dormancy whereas its overexpression lines displayed reduced seed dormancy. When treated with ABA, OsWRKY29 knockout and RNAi lines showed greater sensitivity than its overexpression lines. In addition, the expression levels of ABA positive response factors OsVP1 and OsABF1 were higher in the OsWRKY29 mutants but were lower in its overexpression lines. Further assays showed that OsWRKY29 could bind to the promoters of OsABF1 and OsVP1 to inhibit their expression. In summary, we identified a new ABA signaling repressor OsWRKY29 that represses seed dormancy by directly downregulating the expression of OsABF1 and OsVP1.

A new Em-like protein from Lactuca sativa, LsEm1, enhances drought and salt stress tolerance in Escherichia coli and rice

Late embryogenesis abundant (LEA) proteins are closely related to abiotic stress tolerance of plants. In the present study, we identified a novel Em-like gene from lettuce, termed LsEm1, which could be classified into group 1 LEA proteins, and shared high homology with Cynara cardunculus Em protein. The LsEm1 protein contained three different 20-mer conserved elements (C-element, N-element, and M-element) in the C-termini, N-termini, and middle-region, respectively. The LsEm1 mRNAs were accumulated in all examined tissues during the flowering and mature stages, with a little accumulation in the roots and leaves during the seedling stage. Furthermore, the LsEm1 gene was also expressed in response to salt, dehydration, abscisic acid (ABA), and cold stresses in young seedlings. The LsEm1 protein could effectively reduce damage to the lactate dehydrogenase (LDH) and protect LDH activity under desiccation and salt treatments. The Escherichia coli cells overexpressing the LsEm1 gene showed a growth advantage over the control under drought and salt stresses. Moreover, LsEm1-overexpressing rice seeds were relatively sensitive to exogenously applied ABA, suggesting that the LsEm1 gene might depend on an ABA signaling pathway in response to environmental stresses. The transgenic rice plants overexpressing the LsEm1 gene showed higher tolerance to drought and salt stresses than did wild-type (WT) plants on the basis of the germination performances, higher survival rates, higher chlorophyll content, more accumulation of soluble sugar, lower relative electrolyte leakage, and higher superoxide dismutase activity under stress conditions. The LsEm1-overexpressing rice lines also showed less yield loss compared with WT rice under stress conditions. Furthermore, the LsEm1 gene had a positive effect on the expression of the OsCDPK9, OsCDPK13, OsCDPK15, OsCDPK25, and rab21 (rab16a) genes in transgenic rice under drought and salt stress conditions, implying that overexpression of these genes may be involved in the enhanced drought and salt tolerance of transgenic rice. Thus, this work paves the way for improvement in tolerance of crops by genetic engineering breeding.

A phosphoproteomic landscape of rice (Oryza sativa) tissues

Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nipponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4613 peptides were differentially phosphorylated (DP) among the tissues. Motif-X analysis revealed eight significantly enriched motifs, such as [sP], [Rxxs] and [tP] from the rice phosphosites. Hierarchical clustering analysis divided the DP peptides into 63 subgroups, which showed divergent spatial-phosphorylation patterns among tissues. These clustered proteins are functionally related to nutrition uptake in roots, photosynthesis in leaves and tissue differentiation in panicles. Phosphorylations were specific in the tissues where the target proteins execute their functions, suggesting that phosphorylation might be a key mechanism to regulate the protein activity in different tissues. This study greatly expands the rice phosphoproteomic dataset, and also offers insight into the regulatory roles of phosphorylation in tissue development and functions.

Alternative splicing enhances transcriptome complexity in desiccating seeds

Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are established during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing (AS). However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 34% of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.

Overexpression of OsEm1 encoding a group I LEA protein confers enhanced drought tolerance in rice

Drought is the greatest threat for crops, including rice. In an effort to identify rice genes responsible for drought tolerance, a drought-responsive gene OsEm1 encoding a group I LEA protein, was chosen for this study. OsEm1 was shown at vegetative stages to be responsive to various abiotic stresses, including drought, salt, cold and the hormone ABA. In this study, we generated OsEm1-overexpressing rice plants to explore the function of OsEm1 under drought conditions. Overexpression of OsEm1 increases ABA sensitivity and enhances osmotic tolerance in rice. Compared with wild type, the OsEm1-overexpressing rice plants showed enhanced plant survival ratio at the vegetative stage; moreover, over expression of OsEm1 in rice increased the expression of other LEA genes, including RAB16A, RAB16C, RAB21, and LEA3, likely protecting organ integrity against harsh environments. Interestingly, the elevated level of OsEm1 had no different phenotype compared with wild type under normal condition. Our findings suggest that OsEm1 is a positive regulator of drought tolerance and is potentially promising for engineering drought tolerance in rice.

The functions of the endosperm during seed germination

In angiosperms, a double fertilization event initiates the development of two distinct structures, the embryo and endosperm. The endosperm plays an important role in supporting embryonic growth by supplying nutrients, protecting the embryo and controlling embryo growth by acting as a mechanical barrier during seed development and germination. Its structure and function in the mature dry seed is divergent and specialized among different plant species. A subset of endospermic tissues are composed of living cells even after seed maturation, and play an active role in the regulation of seed germination. Transcriptome analysis has provided new insights into the regulatory functions of the endosperm during seed germination. It is well known that the embryo secretes signals to the endosperm to induce the degradation of the seed reserve and to promote endosperm weakening during germination. Recent advances in seed biology have shown that the endosperm is capable of sensing environmental signals, and can produce and secrete signals to regulate the growth of the embryo. Thus, germination is a systemic response that involves bidirectional interactions between the embryo and endosperm.

PLASTOCHRON3/GOLIATH encodes a glutamate carboxypeptidase required for proper development in rice

Most aerial parts of the plant body are products of the continuous activity of the shoot apical meristem (SAM). Leaves are the major component of the aerial plant body, and their temporal and spatial distribution mainly determines shoot architecture. Here we report the identification of the rice gene PLASTOCHRON3 (PLA3)/GOLIATH (GO) that regulates various developmental processes including the rate of leaf initiation (the plastochron). PLA3/GO encodes a glutamate carboxypeptidase, which is thought to catabolize small acidic peptides and produce small signaling molecules. pla3 exhibits similar phenotypes to pla1 and pla2- a shortened plastochron, precocious leaf maturation and rachis branch-to-shoot conversion in the reproductive phase. However, in contrast to pla1 and pla2, pla3 showed pleiotropic phenotypes including enlarged embryo, seed vivipary, defects in SAM maintenance and aberrant leaf morphology. Consistent with these pleiotropic phenotypes, PLA3 is expressed in the whole plant body, and is involved in plant hormone homeostasis. Double mutant analysis revealed that PLA1, PLA2 and PLA3 are regulated independently but function redundantly. Our results suggest that PLA3 modulates various signaling pathways associated with a number of developmental processes.

Overexpression of transcription factor OsLFL1 delays flowering time in Oryza sativa

Flowering time is regulated by genetic programs and environment signals in plants. Genetic analysis of flowering time mutants is instrumental in dissecting the regulatory pathways of flower induction. Genotype W378 is a rice (Oryza sativa) late-flowering mutant selected from our collections of T-DNA insertion line. The T-DNA flanking gene in mutant W378 codes OsLFL1 (O. sativa LEC2 and FUSCA3 Like 1), a putative B3 DNA-binding domain-containing transcription factor. In wild-type rice OsLFL1 is expressed exclusively in spikes and young embryos, while in mutant W378 it is ectopically expressed. Introduction of OsLFL1-RNAi into mutant W378 successfully down-regulated OsLFL1 expression and restored flowering to almost normal time, indicating that overexpression of OsLFL1 confers late flowering for mutant W378. The flowering-promoting gene Ehd1 and its downstream genes are all down-regulated in W378. Thus, overexpression of OsLFL1 might delay the flowering of W378 by repressing the expression of Ehd1.

Abscisic acid and stress signals induce Viviparous1 expression in seed and vegetative tissues of maize

Viviparous1 (Vp1) encodes a B3 domain-containing transcription factor that is a key regulator of seed maturation in maize (Zea mays). However, the mechanisms of Vp1 regulation are not well understood. To examine physiological factors that may regulate Vp1 expression, transcript levels were monitored in maturing embryos placed in culture under different conditions. Expression of Vp1 decreased after culture in hormone-free medium, but was induced by salinity or osmotic stress. Application of exogenous abscisic acid (ABA) also induced transcript levels within 1 h in a dose-dependent manner. The Vp1 promoter fused to beta-glucuronidase or green fluorescent protein reproduced the endogenous Vp1 expression patterns in transgenic maize plants and also revealed previously unknown expression domains of Vp1. The Vp1 promoter is active in the embryo and aleurone cells of developing seeds and, upon drought stress, was also found in phloem cells of vegetative tissues, including cobs, leaves, and stems. Sequence analysis of the Vp1 promoter identified a potential ABA-responsive complex, consisting of an ACGT-containing ABA response element (ABRE) and a coupling element 1-like motif. Electrophoretic mobility shift assay confirmed that the ABRE and putative coupling element 1 components specifically bound proteins in embryo nuclear protein extracts. Treatment of embryos in hormone-free Murashige and Skoog medium blocked the ABRE-protein interaction, whereas exogenous ABA or mannitol treatment restored this interaction. Our data support a model for a VP1-dependent positive feedback mechanism regulating Vp1 expression during seed maturation.

Rice mutants and genes related to organ development, morphogenesis and physiological traits

Recent advances in genomic studies and the sequenced genome information have made it possible to utilize phenotypic mutants for characterizing relevant genes at the molecular level and reveal their functions. Various mutants and strains expressing phenotypic and physiological variations provide an indispensable source for functional analysis of genes. In this review, we cover almost all of the rice mutants found to date and the variant strains that are important in developmental, physiological and agronomical studies. Mutants and genes showing defects in vegetative organs, i.e. leaf, culm and root, inflorescence reproductive organ and seeds with an embryo and endosperm are described with regards to their phenotypic and molecular characteristics. A variety of alleles detected by quantitative trait locus analysis, such as heading date, disease/insect resistance and stress tolerance, are also shown.

Rice plant development: from zygote to spikelet

Rice is becoming a model plant in monocotyledons and a model cereal crop. For better understanding of the rice plant, it is essential to elucidate the developmental programs of the life cycle. To date, several attempts have been made in rice to categorize the developmental processes of some organs into substages. These studies are based exclusively on the morphological and anatomical viewpoints. Recent advancement in genetics and molecular biology has given us new aspects of developmental processes. In this review, we first describe the phasic development of the rice plant, and then describe in detail the developmental courses of major organs, leaf, root and spikelet, and specific organs/tissues. Also, for the facility of future studies, we propose a staging system for each organ.