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Background Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa.Result In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns.Conclusions Taken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.

Pits are regions in the cell walls of plant tracheary elements that lack secondary walls. Each pit consists of a space within the secondary wall called a pit chamber, and a modified primary wall called the pit membrane. The pit membrane facilitates transport of solutions between vessel cells and restricts embolisms during drought. Here we analyzed the role of an angiosperm-specific TPX2-like microtubule protein MAP20 in pit formation using Brachypodium distachyon as a model system. Live cell imaging was used to analyze the interaction of MAP20 with microtubules and the impact of MAP20 on microtubule dynamics. MAP20-specific antibody was used to study expression and localization of MAP20 in different cell types during vascular bundle development. We used an artificial microRNAs (amiRNA) knockdown approach to determine the function of MAP20. MAP20 is expressed during the late stages of vascular bundle development and localizes around forming pits and under secondary cell wall thickenings in metaxylem cells. MAP20 suppresses microtubule depolymerization; however, unlike the animal TPX2 counterpart, MAP20 does not cooperate with the γ-tubulin ring complex in microtubule nucleation. Knockdown of MAP20 causes bigger pits, thinner pit membranes, perturbed vasculature development, lower reproductive potential and higher drought susceptibility. We conclude that MAP20 may contribute to drought adaptation by modulating pit size and pit membrane thickness in metaxylem.

Association of plastic particles with plant roots could represent a pathway for human consumption of plastic and plastic-associated organic contaminants. Here, we investigated the uptake of spherical, negatively-charged, polystyrene nano- and microparticles by plant roots. We used negatively-charged, 40 nm and 1 μm fluorescently-labeled polystyrene spheres and two plant species: Arabidopsis (Arabidopsis thaliana) and wheat (Triticum aestivum). Plants were grown from seeds to 5 days for wheat and 12 days for Arabidopsis, in agar growth media containing plastic spheres (0.029 g L−1), and plant uptake of spheres was investigated by laser scanning confocal microscopy and pyrolysis gas chromatography-mass spectrometry (GC-MS). The confocal images of both plant species showed no evidence for active uptake of nano- and microsized polystyrene spheres during plant growth up to the 1 to 2 leaf growth stage. Pyrolysis GC-MS was unsuccessful because of the occurrence of natural styrene monomers in plant roots and insufficient detection limits. Both 40 nm and 1 μm polystyrene spheres accumulated at the root surface of each species, particularly at the root tip, and were still found attached to the root surface after washing. However, there was no evidence of plastic particles in the internal root structure. Our results demonstrate the association and accumulation of plastics at root surface and cap cells.

Background Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. ResultIn the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in Arabidopsis thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance.ConclusionsTaken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.

The direct root-zone irrigation system is a new technique to deliver water directly to the root zone of grapevines at specific irrigation rates and delivery depths. The response of Vitis vinifera L. cv. Cabernet Sauvignon to direct root-zone deficit irrigation was investigated in a commercial vineyard with loamy sand soil in the semi-arid lower Columbia Basin of southcentral Washington State, USA. Three irrigation rates and three delivery depths were compared for effects on grape yield and crop water use efficiency during three consecutive growing seasons. Furthermore, we investigated the influence of irrigation rate on grape quality, and used an in situ root imaging system for root phenotyping under different delivery depths for two years. Results showed that delivery depth had no significant effect on grape yield and crop water use efficiency; however, increases in delivery depth from 30 cm to 90 cm resulted in 60–70% decreased root number and 46–59% decreased root length in the upper soil profile (0–60 cm). Moderate irrigation rates (35% less water use on average) improved crop water use efficiency by 14–23% and only reducing grape yield 15–18% per individual grapevine, without sacrificing grape quality or inducing early defoliation for the first two years. Surprisingly, no significant reduction of grape yield was found in the third year, which can be attributed to cooler and wetter weather and potentially vine acclimation to the direct root-zone irrigation strategy. We conclude that direct root-zone deficit irrigation could be a convenient and efficient subsurface irrigation method to improve crop water use efficiency without reducing grape quality under seasonal drought. Future studies should compare the economic and environmental returns of direct root-zone deficit irrigation with other traditional irrigation strategies under different environmental conditions to optimize the direct root-zone deficit irrigation method.

We report rampant homoeologous exchanges in progenies of a newly synthesized rice segmental allotetraploid and demonstrate their consequences to changes of gene expression and alternative splicing. Allopolyploidization is recurrent across the tree of angiosperms and known as a driving evolutionary force in both plants and animals. A salient feature of allopolyploidization is the induction of homoeologous exchange (HE) events between the constituent subgenomes, which may in turn cause changes in gene expression, transcript alternative splicing, and phenotypic novelty. However, this issue has been poorly studied, largely because lack of a system in which the exact parentage donating the subgenomes is known and the HE events are occurring in real time. Here, we employed whole-genome re-sequencing and RNA-seq-based transcriptome profiling in four randomly chosen progeny individuals (at the 10th-selfed generation) of segmental allotetraploids that were constructed by colchicine-mediated whole-genome doubling of F1 hybrids between the two subspecies (japonica and indica) of Asian cultivated Oryza sativa. We show that rampant HE events occurred in these tetraploid individuals, which converted most of the otherwise heterozygous genomic regions into a homogenized state of one parental subgenome. We demonstrate that genes within these homogenized genomic regions in the tetraploids showed high frequencies of altered expression and enhanced alternative splicing relative to their counterparts in the corresponding diploid parents in the embryo tissue. Intriguingly, limited overlaps between the differentially expressed genes and the differential alternative spliced genes were identified, which were partitioned to distinctly enriched gene ontology terms. Together, our results indicate that HE is a major mechanism to rapidly generate novelty in gene expression and transcriptome diversity, which may facilitate phenotypic innovation in nascent allopolyploids and relevant to allopolyploid crop breeding.

Plant cells sheath themselves in a complex lattice of polysaccharides, proteins and enzymes forming an integral matrix known as the cell wall. Cellulose microfibrils, the primary component of cell walls, are synthesized at the plasma membrane by CELLULOSE SYNTHASE A (CESA) proteins throughout cellular growth and are responsible for turgor-driven anisotropic expansion. Associations between hormone signaling and cell wall biosynthesis have long been suggested, but recently direct links have been found revealing hormones play key regulatory roles in cellulose biosynthesis. The radially swollen 1 (rsw1) allele of Arabidopsis thaliana CESA1 harbors a single amino acid change that renders the protein unstable at high temperatures. We used the conditional nature of rsw1 to investigate how auxin contributes to isotropic growth. We found that exogenous auxin treatment reduces isotropic swelling in rsw1 roots at the restrictive temperature of 30�C. We also discovered decreases in auxin influx between rsw1 and wild-type roots via confocal imaging of AUX1-YFP, even at the permissive temperature of 19�C. Moreover, rsw1 displayed mis-expression of auxin-responsive and CESA genes. Additionally, we found altered auxin maxima in rsw1 mutant roots at the onset of swelling using DII-VENUS and DR5:vYFP auxin reporters. Overall, we conclude disrupted cell wall biosynthesis perturbs auxin transport leading to altered auxin homeostasis impacting both anisotropic and isotropic growth that affects overall root morphology.

Direct root-zone irrigation (DRZ) is a novel subsurface irrigation strategy initially tested in vineyards for economizing water and securing grape production in arid regions with unstable climatic patterns. However, studies are lacking on the responses of grapevine leaf carbon assimilation and deep rooting patterns to the novel irrigation strategy, which are essential for optimizing grapevine growth and alleviating extreme water stress during periods of heat and drought. Thus, a two-year field study was conducted in a commercial vineyard of Cabernet Sauvignon (Vitis vinifera L.) under a semi-arid climate in Washington, USA to compare the differences in leaf gas exchange and root distribution along the 0-160 cm soil profile, combined with measurements of specific leaf area and total carbon and nitrogen content in leaves and shoots to compare DRZ and traditional surface drip irrigation (SD) under three watering regimes. Compared to SD, significantly higher rates of net CO2 assimilation, stomatal conductance and transpiration in leaves, which positively correlated to midday stem water potential, were found in grapevines irrigated through DRZ in both years. Meanwhile, DRZ reduced total root number by 50-60% and root length density (RLD) by 30-40% in the upper 60 cm soil at high (0.75-0.80 crop evapotranspiration) and moderate (0.60-0.65 crop evapotranspiration) irrigation rates, but no significant differences were found at low (0.45-0.50 crop evapotranspiration) irrigation rate between DRZ and SD. Higher root number and RLD were detected under DRZ within 60-160 cm soil depths, accompanied by a decreased ratio of total carbon to nitrogen content in leaves with slightly increased specific leaf area. Decreased rainfall and increased temperature in 2018 possibly amplified the positive effects of DRZ. Our study indicates that grapevines under DRZ could develop deeper roots for water uptake, which helps ameliorate water stress and improve the photosynthetic rate as well as enhance grapevine adaptation to semi-arid climates.

Key message We report a repertoire of diverse aneuploids harbored by a newly synthesized segmental allotetraploid rice population with fully sequenced sub-genomes and demonstrate their retention features and phenotypic consequences. Abstract Aneuploidy, defined as unequal numbers of different chromosomes, is a large-effect genetic variant and may produce diverse cellular and organismal phenotypes. Polyploids are more permissive to chromosomal content imbalance than their diploid and haploid counterparts, and therefore, may enable more in-depth investigation of the phenotypic consequences of aneuploidy. Based on whole-genome resequencing, we identify that ca. 40% of the 312 selfed individual plants sampled from an early generation rice segmental allotetraploid population are constitutive aneuploids harboring 55 distinct aneuploid karyotypes. We document that gain of a chromosome is more prevalent than loss of a chromosome, and the 12 rice chromosomes have distinct tendencies to be in an aneuploid state. These properties of aneuploidy are constrained by multiple factors including the number of genes residing on the chromosome and predicted functional connectivity with other chromosomes. Two broad categories of aneuploidy-associated phenotypes are recognized: those shared by different aneuploids, and those associated with aneuploidy of a specific chromosome. A repertoire of diverse aneuploids in the context of a segmental allotetraploid rice genome with fully sequenced sub-genomes provides a tractable resource to explore the roles of aneuploidy in nascent polyploid genome evolution and helps to decipher the mechanisms conferring karyotypic stabilization on the path to polyploid speciation and towards artificial construction of novel polyploid crops. Electronic supplementary material The online version of this article (10.1007/s00122-018-3077-7) contains supplementary material, which is available to authorized users.

Background Heavy metal toxicity has become a major threat to sustainable crop production worldwide. Thus, considerable interest has been placed on deciphering the mechanisms that allow plants to combat heavy metal stress. Strategies to deal with heavy metals are largely focused on detoxification, transport and/or sequestration. The P1B subfamily of the Heavy Metal-transporting P-type ATPases (HMAs) was shown to play a crucial role in the uptake and translocation of heavy metals in plants. Here, we report the locus-specific expression changes in the rice HMA genes together with several low-copy cellular genes and transposable elements upon the heavy metal treatment and monitored the transgenerational inheritance of the altered expression states. We reveal that plants cope with heavy metal stress by making heritable changes in gene expression and further determined gene-specific responses to heavy metal stress. Results We found most HMA genes were upregulated in response to heavy metal stress, and furthermore found evidence of transgenerational memory via changes in gene regulation even after the removal of heavy metals. To explore whether DNA methylation was also altered in response to the heavy metal stress, we selected a Tos17 retrotransposon for bisulfite sequencing and studied its methylation state across three generations. We found the DNA methylation state of Tos17 was altered in response to the heavy metal stress and showed transgenerational inheritance. Conclusions Collectively, the present study elucidates heritable changes in gene expression and DNA methylation in rice upon exposure to heavy metal stress and discusses implications of this knowledge in breeding for heavy metal tolerant crops. Electronic supplementary material The online version of this article (10.1186/s12870-019-1887-7) contains supplementary material, which is available to authorized users.

Annual plants are currently the dominant growth habit for grain production systems but often create agroecosystems with negative environmental consequences. Developing grains with a perennial growth habit provides an opportunity to produce staple crops in a more environmentally beneficial manner. Amphiploids of perennial tall wheatgrass (Thinopyrum elongatum) and common annual wheat (Triticum aestivum) have been produced for wheat-like traits while exhibiting post-sexual cycle regrowth (PSCR). Here we report results from two experiments at two locations in the Palouse region of the U.S. Pacific Northwest (PNW) designed to (1) evaluate a subset of the current perennial grain germplasm base and (2) test post-harvest management strategies on key perennial growth habit traits. The first experiment evaluated 18 putative perennial amphiploid lines, two annual wheat varieties, and one intermediate wheatgrass variety (Thinopyrum intermedium) for yield, PSCR, key agronomic traits, and grain quality characteristics. Results from this trial showed mean yields ranged from 713 to 2874 kg/ha among the amphiploids and 1,627 to 6,867 kg/ha with the annual wheat varieties. Variation across the amphiploids was found for key agronomic and quality traits, indicating potential for continued selection and improvement. When compared to the two annuals, the four highest-yielding amphiploids produced the same yield at one location but 50–60% less at the other. Amphiploids were generally taller with increased tiller number, flowered later, had lower leaf chlorophyll content, and decreased threshability, compared to annual varieties. Regarding grain qualities, amphiploids had lower test weights and thousand kernel weights, smaller kernel diameters, lower starch content, and higher protein, ash, and fiber. The second experiment investigated the effect of post-harvest residue management on PSCR and winter survival of two amphiploids using mowing, burning, and a control. Mowing the residue and PSCR significantly increased winter survival across both amphiploids at one location from 3% in the control to 63% in the mowed treatment. Burning the residue did not improve survival. Our results address three important challenges in perennial grain development in the Palouse region: selecting a stable perennial habit, increasing grain yield, and improving marketable grain quality traits. Each of these challenges will require significant research efforts by plant breeders and agronomists prior to widespread adoption of perennial grains in the Palouse region of the PNW.

Direct root-zone irrigation is a novel subsurface drip irrigation strategy for water conservation. However, a comparison with traditional irrigation methods is lacking to better define the potential advantages of direct root-zone irrigation. A two-year study was conducted to evaluate the performance of Vitis vinifera L. cv. Cabernet Sauvignon under direct root-zone irrigation and surface drip irrigation in a commercial vineyard with loamy sand soil in a semi-arid region of southcentral Washington State, USA. Plant water status, root traits, grape yield, berry morphology and composition, and crop water use efficiency were compared between irrigation methods under three irrigation rates. Compared to surface drip irrigation, direct root-zone irrigation improved grape yield by 9–12% and crop water use efficiency by 9–11% under varied climate conditions with minor effects on berry composition, which could be potentially adjusted by irrigation rate. Moreover, grapevines irrigated through direct root-zone irrigation had 48–67% and 50–54% decrease in root number, respectively, at high and moderate irrigation rates in the upper soil profile (0–60 cm) with a decrease in water stress as revealed by higher midday stem water potential. Irrigation rate was the major factor influencing berry morphology. In fact, reduced irrigation resulted in a decrease in weight, size and number of berries. We conclude that direct root-zone irrigation could be a successful tool for improving yield and crop water use efficiency, potentially encouraging deep rooting to alleviate the water stress in grapevine under seasonal drought, and offering the ability to modify berry morphology and composition by adjusting the amount of water use.

An understanding of the genes and mechanisms regulating environmental stress in crops is critical for boosting agricultural yield and safeguarding food security. Under adverse conditions, response pathways are activated for tolerance or resistance. In multiple species, the alternative oxidase (AOX) genes encode proteins which help in this process. Recently, this gene family has been extensively investigated in the vital crop plants, wheat, barley and rice. Cumulatively, these three species and/or their wild ancestors contain the genes for AOX1a, AOX1c, AOX1e, and AOX1d, and common patterns in the protein isoforms have been documented. Here, we add more information on these trends by emphasizing motifs that could affect expression, and by utilizing the most recent discoveries from the AOX isoform in Trypanosoma brucei to highlight clade-dependent biases. The new perspectives may have implications on how the AOX gene family has evolved and functions in monocots. The common or divergent amino acid substitutions between these grasses and the parasite are noted, and the potential effects of these changes are discussed. There is the hope that the insights gained will inform the way future AOX research is performed in monocots, in order to optimize crop production for food, feed, and fuel.

Grass biomass is comprised chiefly of secondary walls that surround fiber and xylem cells. A regulatory network of interacting transcription factors in part regulates cell wall thickening. We identified Brachypodium distachyon SECONDARY WALL ASSOCIATED MYB1 (SWAM1) as a potential regulator of secondary cell wall biosynthesis based on gene expression, phylogeny, and transgenic plant phenotypes. SWAM1 interacts with cellulose and lignin gene promoters with preferential binding to AC-rich sequence motifs commonly found in the promoters of cell wall-related genes. SWAM1 overexpression (SWAM-OE) lines had greater above-ground biomass with only a slight change in flowering time while SWAM1 dominant repressor (SWAM1-DR) plants were severely dwarfed with a striking reduction in lignin of sclerenchyma fibers and stem epidermal cell length. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. There was no reduction in bioconversion yield in SWAM1-OE lines; however, it was significantly increased for SWAM1-DR samples. Phylogenetic and syntenic analyses strongly suggest that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is not in the Brassicaceae. Collectively, these data suggest that SWAM1 is a transcriptional activator of secondary cell wall thickening and biomass accumulation in B. distachyon.

A comprehensive understanding of wheat responses to environmental stress will contribute to the long-term goal of feeding the planet. ALERNATIVE OXIDASE (AOX) genes encode proteins involved in a bypass of the electron transport chain and are also known to be involved in stress tolerance in multiple species. Here, we report the identification and characterization of the AOX gene family in diploid and hexaploid wheat. Four genes each were found in the diploid ancestors Triticum urartu, and Aegilops tauschii, and three in Aegilops speltoides. In hexaploid wheat (Triticum aestivum), 20 genes were identified, some with multiple splice variants, corresponding to a total of 24 proteins for those with observed transcription and translation. These proteins were classified as AOX1a, AOX1c, AOX1e or AOX1d via phylogenetic analysis. Proteins lacking most or all signature AOX motifs were assigned to putative regulatory roles. Analysis of protein-targeting sequences suggests mixed localization to the mitochondria and other organelles. In comparison to the most studied AOX from Trypanosoma brucei, there were amino acid substitutions at critical functional domains indicating possible role divergence in wheat or grasses in general. In hexaploid wheat, AOX genes were expressed at specific developmental stages as well as in response to both biotic and abiotic stresses such as fungal pathogens, heat and drought. These AOX expression patterns suggest a highly regulated and diverse transcription and expression system. The insights gained provide a framework for the continued and expanded study of AOX genes in wheat for stress tolerance through breeding new varieties, as well as resistance to AOX-targeted herbicides, all of which can ultimately be used synergistically to improve crop yield.

The mechanism of cellulose synthesis has been studied by characterizing the motility of cellulose synthase complexes tagged with a fluorescent protein; however, this approach has been used exclusively on the hypocotyl of Arabidopsis thaliana. Here we characterize cellulose synthase motility in the model grass, Brachypodium distachyon. We generated lines in which mEGFP is fused N-terminal to BdCESA3 or BdCESA6 and which grew indistinguishably from the wild type (Bd21-3) and had dense fluorescent puncta at or near the plasma membrane. Measured with a particle tracking algorithm, the average speed of GFP-BdCESA3 particles in the mesocotyl was 164 ± 78 nm min−1 (error gives standard deviation [SD], n = 1451 particles). Mean speed in the root appeared similar. For comparison, average speed in the A. thaliana hypocotyl expressing GFP-AtCESA6 was 184 ± 86 nm min−1 (n = 2755). For B. distachyon, we quantified root diameter and elongation rate in response to inhibitors of cellulose (dichlorobenylnitrile; DCB), microtubules (oryzalin), or actin (latrunculin B). Neither oryzalin nor latrunculin affected the speed of CESA complexes; whereas, DCB reduced average speed by about 50% in B. distachyon and by about 35% in A. thaliana. Evidently, between these species, CESA motility is well conserved.

Plant morphogenesis depends on the synchronized anisotropic expansion of individual cells in response to developmental and environmental cues. The magnitude of cell expansion depends on the biomechanical properties of the cell wall, which in turn depends on both its biosynthesis and extensibility. Although the control of cell expansion by the phytohormone auxin is well established, its regulation of cell wall composition, trafficking of H+-ATPases, and K+ influx that drives growth is still being elucidated. Furthermore, the maintenance of auxin fluxes via the interaction between the cytoskeleton and PIN protein recycling on the plasma membrane remains under investigation. This review proposes a model that describes how the cell wall, auxin, microtubule binding-protein CLASP and Kin7/separase complexes, and vesicle trafficking are co-ordinated on a cellular level to mediate cell wall loosening during cell expansion.

Embryogenesis in rice is unique from most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, the formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how it relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found via microarray analysis of embryo subdomains using in situ hybridization. Our study identified both homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatio-temporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.