Donald Danforth Plant Science Center

Continued growth and intensification of aquaculture production depends upon the development of sustainable protein sources to replace fish meal in aquafeeds. This document reviews various plant feedstuffs, which currently are or potentially may be incorporated into aquafeeds to support the sustainable production of various fish species in aquaculture. The plant feedstuffs considered include oilseeds, legumes and cereal grains, which traditionally have been used as protein or energy concentrates as well as novel products developed through various processing technologies. The nutritional composition of these various feedstuffs are considered along with the presence of any bioactive compounds that may positively or negatively affect the target organism. Lipid composition of these feedstuffs is not specifically considered although it is recognized that incorporating lipid supplements in aquafeeds to achieve proper fatty acid profiles to meet the metabolic requirements of fish and maximize human health benefits are important aspects. Specific strategies and techniques to optimize the nutritional composition of plant feedstuffs and limit potentially adverse effects of bioactive compounds are also described. Such information will provide a foundation for developing strategic research plans for increasing the use of plant feedstuffs in aquaculture to reduce dependence of animal feedstuffs and thereby enhance the sustainability of aquaculture.

Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.

Plant growth and development are regulated by internal signals and by external environmental conditions. One important regulator that coordinates growth and development with responses to the environment is the sesquiterpenoid hormone abscisic acid (ABA). ABA plays important roles in many cellular processes including seed development, dormancy, germination, vegetative growth, and environmental stress responses. These diverse functions of ABA involve complex regulatory mechanisms that control its production, degradation, signal perception, and transduction. Because of the key role of ABA in plant stress responses, understanding these regulatory mechanisms will help devise rational strategies to breed or genetically engineer crop plants with increased tolerance to adverse environmental conditions. Since the discovery of ABA in the early 1960s, much effort has been devoted to understanding how ABA is synthesized. Through genetic and biochemical studies, the pathway for ABA biosynthesis in higher plants is now understood in great detail. Recently, all the major genes for the enzymes in the biosynthesis pathway have been identified (Schwartz et al., 2003). The new challenge is to understand how these biosynthesis genes, and the biosynthetic pathway as a whole, are regulated. Although much remains to be learned about the regulatory mechanism, evidence thus far indicates that ABA biosynthesis is subject to complex regulation during plant development and in response to environmental stresses. In this Update, we first present a brief overview of the functions of ABA and the biosynthesis pathway. We then focus on the regulation of ABA production and attempt to provide some future directions in ABA biosynthesis studies. Under non-stressful conditions, ABA in plant cells is maintained at low levels. Some low levels of ABA may be required for normal plant growth, as evidenced by reduced vigor observed in ABA-deficient mutant plants that can be restored to the wild-type level of growth by exogenous ABA (Finkelstein and Rock, 2002). Because all ABA-deficient mutants still have certain basal levels of ABA that are not dramatically lower than those in the wild type under normal growth conditions, it is difficult to uncover the cellular processes that require a very small amount of ABA. As a consequence, our knowledge of ABA functions has been gained mainly from observations with ABA at elevated levels, either from endogenous or exogenous sources. ABA levels can increase dramatically during seed maturation and in response to environmental stresses. Thus, ABA functions have been most extensively studied in these two processes. During seed development, ABA is known to initiate the following programs: embryo maturation, synthesis of storage reserves and late embryogenesis-abundant (LEA) proteins, and initiation of seed dormancy, although ABA is not the sole regulator of these processes. In particular, the induction of LEA protein synthesis to preserve the viability of embryos in the extremely dry condition of seeds is related to the role of ABA in promoting synthesis of LEA-like proteins in vegetative tissues to tolerate dehydration stress. Embryos from ABA antibody-expressing plants lose their viability as a result of desiccation intolerance (Phillips et al., 1997). In vegetative tissues, ABA levels increase when plants encounter adverse environmental conditions such as drought, salt, and to a lesser extent, low temperatures. Although a higher level of exogenous ABA inhibits plant growth under non-stressful conditions, an increased ABA content is beneficial for plants under environmental stress as a result of ABA-induced changes at the cellular and whole-plant levels. ABA promotes the closure of stomata to minimize transpirational water loss. It also mitigates stress damage through the activation of many stress-responsive genes that encode enzymes for the biosynthesis of compatible osmolytes and LEA-like proteins, which collectively increase plant stress tolerance (Hasegawa et al., 2000; Bray, 2002; Finkelstein et al., 2002). In addition, ABA has been shown to offset the inhibitory effect of stress-induced ethylene on plant growth (Sharp, 2002). Plant mutants defective in ABA biosynthesis are more susceptible to the environmental stresses and have been isolated in stress sensitivity screens (Xiong et al., 2002b). Importantly, manipulating ABA levels by changing the expression of key ABA biosynthetic genes provides an effective means to increase plant stress resistance. ABA-deficient mutants have been instrumental for revealing the pathway of ABA biosynthesis. By virtue of their precocious germination of seeds and the wilty appearance of the plants, mutants defective in ABA biosynthesis were isolated from a number of plant species including maize (Zea mays), tomato (Lycopersicon esculentum), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), barley (Hordeum vulgare), and Arabidopsis. Before the molecular identities of the affected genes were known, a major route for ABA biosynthesis was revealed by profiling ABA biosynthetic intermediates in combination with feeding assays using these mutants. These studies suggested that ABA in higher plants is synthesized from an “indirect” pathway through the cleavage of a C40 carotenoid precursor, followed by a two-step conversion of the intermediate xanthoxin to ABA via ABA-aldehyde (Fig. 1; Taylor et al., 2000; Finkelstein and Rock, 2002; Seo and Koshiba, 2002; Schwartz et al., 2003). By now, major ABA-deficient mutants, genes, and enzymes have been characterized in Arabidopsis (Schwartz et al., 2003). The information from Arabidopsis is applicable to other plant species because the pathway and the respective genes are highly conserved in angiosperms. To avoid confusion, in this Update, genes are named after their products instead of the respective genetic loci. Regulation of ABA biosynthesis. ABA is derived from C40 epoxycarotenoid precursors through an oxidative cleavage reaction in plastids. The C15 intermediate xanthoxin is converted to ABA by a two-step reaction via ABA-aldehyde in cytosol. Abiotic stresses such as drought and salt activate the biosynthetic genes (italicized), probably through a Ca2+-dependent phosphorelay cascade as shown on the left. ABA feedback stimulates the expression of the biosynthetic genes, which is also likely through a Ca2+-dependent phosphoprotein cascade. Among the biosynthetic genes, NCED is strongly upregulated by stress (indicated with a thick arrow), whereas SDR is regulated by sugar. ABA biosynthetic enzymes are shown in small ovals. The NCED step probably limits ABA biosynthesis in leaves (indicated with a dashed arrow). ZEP, zeaxanthin epoxidase; NCED, 9-cis-epoxycarotenoid dioxygenase; AAO, ABA-aldehyde oxidase; MCSU, MoCo sulfurase. The first step that is more specific to the ABA biosynthesis pathway is the epoxidation of zeaxanthin and antheraxanthin to violaxanthin, which occurs in plastids. This step is catalyzed by a zeaxanthin epoxidase (ZEP), whose molecular identity was first revealed in tobacco (Marin et al., 1996). After a series of structural modifications, violaxanthin is converted to 9-cis-epoxycarotenoid. Oxidative cleavage of the major epoxycarotenoid 9-cis-neoxanthin by the 9-cis-epoxycarotenoid dioxygenase (NCED) yields a C15 intermediate, xanthoxin (Schwartz et al., 1997). This step was considered the first committed step in the ABA biosynthesis pathway. The ZmNCED gene was isolated using the maize vp14 mutant (Tan et al., 1997). The product xanthoxin is then exported to the cytosol, where it is converted to ABA through a two-step reaction via ABA-aldehyde. A short-chain alcohol dehydrogenase/reductase (SDR), encoded by the AtABA2 gene (Rook et al., 2001; Cheng et al., 2002; Gonzalez-Guzman et al., 2002), catalyzes the first step of this reaction and generates ABA aldehyde. ABA aldehyde oxidase (AAO) then catalyzes the last step in the biosynthesis pathway. Mutations in either the aldehyde oxidase apoprotein (e.g. Seo et al., 2000b) or molybdenum cofactor (MoCo) synthase (e.g. Ataba3 mutant) would impair ABA biosynthesis. The AtABA3 gene encodes a MoCo sulfurase that catalyzes the sulfurylation of a dioxo form of MoCo to a sulfurylated mono-oxo form (Bittner et al., 2001; Xiong et al., 2001b). This form of MoCo is required by aldehyde oxidase and xanthine dehydrogenase for their activities. Seed maturation and germination expose the young embryo to dramatic osmotic stresses. ABA is the major factor that is required to escort the embryo upon entering and exiting its quiescent state. ABA in developing seeds can either be derived from maternal tissues or be synthesized de novo in the embryo. Studies in Arabidopsis suggest that during seed development, there appear to be two peaks of ABA accumulation (for review, see Bentsink and Koornneef, 2002; Finkelstein et al., 2002). The first one occurs about halfway during seed development (approximately 10 d after pollination). This ABA is likely to be derived from maternal tissues because in reciprocal crosses, the peak only occurred when the wild-type but not ABA-deficient mutants were used as the female. ABA at this stage promotes the synthesis of storage proteins. Embryos from ABA antibody-expressing plants either did not accumulate or accumulated a much lower level of storage proteins relative to the wild-type embryos (Phillips et al., 1997). The second peak with less significant ABA accumulation (about one-third of the first peak) is from biosynthesis in the embryo and may activate the synthesis of LEA proteins that prepare the embryo for desiccation. This peak of ABA also initiates seed dormancy. ABA levels fall rapidly in the later stage of seed maturation and are very low in dry seeds. During seed imbibition, de novo ABA biosynthesis in the embryo is a determinant of seed dormancy (Bentsink and Koornneef, 2002; Finkelstein et al., 2002). ABA at this stage also maintains, within a narrow time window, the imbibed embryo in a reversible state between dormancy and germination by regulating the basic Leu Zip transcription factor ABI5 (Lopez-Molina et al., 2001). These important roles of ABA and its dynamics of accumulation in the embryo suggest that ABA biosynthesis is under tight developmental regulation in the embryo. Transcripts for all the ABA biosynthetic genes are detected in embryos/developing seeds, although more detailed analysis of the expression of individual genes during seed development has not been reported except for AtZEP1. In situ hybridization detected AtZEP expression in the embryo from globular to desiccation stages (Audran et al., 2001), which indicates that the ZEP gene was during the first peak of ABA accumulation in developing seeds. In to a role of ABA in it also an which ZEP other ABA biosynthetic in developing Although the of a developmental signal that one or more of the ABA biosynthetic genes be evidence that osmotic and ABA are likely to be the signals that activate ABA biosynthesis in developing seeds. ABA has been shown to be required for the first peak accumulation of ABA in developing seeds, it is not the ABA was derived from maternal tissues or that maternal ABA only as a signal for de novo synthesis of ABA in developing This is because ABA can its biosynthesis by ABA biosynthetic genes Because ZEP, and genes are all by to et al., 2002), levels may ABA biosynthesis in the embryo. This is more important for because is not by either osmotic stress or ABA. the of seed maturation, osmotic stress may more important in de novo ABA which is for embryo desiccation tolerance and dormancy. The activation of individual genes in seeds may be for ABA biosynthesis and accumulation in seeds. the expression of its between one-third and of seed development, which with increased ABA accumulation during this (Audran et al., seeds from plants a higher ABA level and dormancy et al., that may ABA biosynthesis in seeds and during seed in NCED may also ABA levels in the seeds. of the gene increased ABA levels in imbibed seeds and seed dormancy et al., These suggest that ABA biosynthesis in developing and seeds may be regulated at environmental signals such as have been suggested to ABA biosynthesis or The environmental conditions that most dramatically activate ABA are drought and salt stress. ABA levels under these stresses result mainly from increased de novo biosynthesis. The of ABA to be by stress and by ABA and stress and salt stresses ABA biosynthesis through regulation of ABA biosynthetic genes because transcription by using transcription stress-induced ABA biosynthesis. regulation of ABA biosynthetic genes the key to understanding how ABA biosynthesis is although regulation of the specific of ABA biosynthesis enzymes also ZEP was the first gene in the ABA biosynthesis pathway to be and its expression and regulation have been in a number of plant ZEP genes were in plant with a higher basal expression in leaves (Audran et al., Xiong et al., It was that ZEP not ABA biosynthesis in tissues because on a the amount of 9-cis-epoxycarotenoid of the in tissues such as leaves is higher than the amount of ABA during stress. In tobacco and tomato plants, the levels of ZEP genes in leaves were also not regulated by drought stress but were to be regulated with levels in the which may regulation by the (Audran et al., et al., than the of water changes in the in levels, in the level of ZEP protein was The regulation be related to the of ZEP products in the complex but not to the role of ZEP proteins in ABA biosynthesis. In to the amount of epoxycarotenoid precursors is lower in where ZEP, may ABA biosynthesis. with this ZEP genes in were regulated by drought stress. levels increased after drought stress in tobacco and tomato plants (Audran et al., et al., The regulation of ABA biosynthetic genes may not only between plant and developmental stages but also between plant the ZEP genes in tobacco and the Arabidopsis ZEP gene also a basal level under non-stressful conditions. drought, salt, and increased its expression level in the and in the (Xiong et al., that the AtZEP gene is under stress in the regulation of the ZEP genes observed in may be related to the relative basal levels. A basal level may stress of the studies with other ABA biosynthetic genes MCSU, and are less the that the cleavage step is in ABA the expression of NCED has stress were shown to NCED expression in maize (Tan et al., tomato et al., and Arabidopsis et al., 2001), et al., and and in NCED levels can be detected within to after or dehydration and et al., that the activation of NCED genes can be In with the of whose expression not to be regulated by stress et al., 2002; Gonzalez-Guzman et al., 2002), all the other ABA biosynthetic genes are by drought and salt stress et al., et al., 2001; Xiong et al., Xiong et al., although their protein levels have not been in most Because ABA biosynthesis increase dramatically upon stress it is that the protein levels of these genes increase after the levels, as was with the NCED gene and a with suggested that its protein levels did not as the levels et al., it is not this is only an the conditions In to the regulation of these genes by drought and salt the expression of AtZEP (Xiong et al., NCED and and (Xiong et al., was not by This is with the that the of increase in ABA in plants to was much less than that in plants The regulation of the SDR gene is was detected mainly in Thus, its expression tissues appear to be from those for other ABA biosynthetic genes that are more et al., 2002). The gene is at a low level and is not by drought stress. its expression is by sugar. During seed development, changes in levels in the seeds may have an on ABA as levels also and are by stress. stress under conditions effect on et al., 2002). biosynthetic are regulated by their ABA has been to ABA accumulation by its enzymes and The of a ABA which catalyzes the first step of ABA degradation, was by exogenous ABA (e.g. and Studies with tobacco NCED gene under an that ABA with the of the acid and 2002). These studies the that ABA its accumulation by its degradation, at under non-stressful conditions. the other ABA can or its biosynthesis was Because the NCED gene product has been suggested to the step in the ABA biosynthesis or not this gene is regulated by ABA is very to the of ABA can its biosynthesis. In tomato plants, it was that the NCED gene was not by exogenous ABA et al., in ABA was to activate NCED genes et al., These observations would the that ABA may its but not its when the expression of ABA biosynthetic genes was genetic a To our we have that ZEP, and in Arabidopsis are all by in to regulated by stress. ABA the expression of these genes (Xiong et al., these genes appear also to be regulated by endogenous ABA. It was observed that in of the ABA-deficient mutants or the levels for all the ABA biosynthetic genes under stress conditions were lower than those in the wild-type plants (Xiong et al., although their basal levels were in these mutants under non-stressful conditions (Audran et al., 2001; Xiong et al., Thus, ABA in the Arabidopsis mutants may not be a of the in the biosynthetic enzymes but also may be because of the reduced expression of other ABA biosynthetic genes as a result of the it was that the NCED gene was by ABA in certain genetic (e.g. ABA-deficient mutants and certain such as Xiong et al., Recently, Cheng et also reported that the gene AtZEP and be by ABA in the In addition, levels under drought and salt stress were reduced in the ABA-deficient mutants and as with those in wild-type that ABA is required for activation of by osmotic stress (Xiong et al., these observations strongly suggest a feedback regulation of ABA biosynthesis by ABA. This may a stress where an induction of ABA biosynthesis rapidly stimulates biosynthesis of ABA through this feedback (Fig. To understand this feedback regulatory it is important to which may this of ABA biosynthetic One such is to ABA and drought A in to exogenous ABA during seed germination, vegetative growth, and in gene expression (Xiong et al., mutant plants are also in ABA biosynthesis. of that the mutant was defective in the because the ABA regulation of the and genes (Xiong et al., gene products are required for the last step of ABA the conversion of ABA aldehyde to ABA (Fig. a feeding that the conversion of ABA-aldehyde to ABA was in the mutant (Xiong et al., This may be for the ABA biosynthesis in the It is likely that an small that is to be in and degradation, may the for the of an early ABA The may in the feedback One such is likely to be an protein because stress induction of this gene was in (Xiong et al., Although a in the protein also reduced the expression of this was not ABA et al., 2001). Thus, at some of the including may be in this as Arabidopsis and are protein that may ABA The and ABA in seed germination, vegetative growth, and the expression of certain genes (Finkelstein et al., 2002). In the of ABA biosynthesis is because in this ABA to activate the expression of the NCED gene and this reduced the levels of ZEP and under ABA all these genes were in (Xiong et al., their and and are to have roles in ABA it was shown that ABA-induced species production was in but not in In and closure in but not in et al., 2001). Because is in ABA and probably also in regulating ABA biosynthesis et al., 2001), it is that this of ABA biosynthetic genes may be by through a protein cascade (Fig. In the of in the feedback that for ABA biosynthesis is ABA and that there is between the pathway for ABA biosynthesis and the pathway for ABA studies are to the between these two and the of of ABA biosynthesis in ABA accumulation under stress conditions. in ABA biosynthesis either as a or a gene and the may be to regulation as whose has been the of ABA biosynthetic genes are known It that ZEP, MCSU, and SDR are genes, whereas NCED and to gene suggest that for those to gene is regulated by stresses. In addition, may be in a and developmental was in leaves but not in the and was mainly in et al., whereas may be less in seeds. Thus, mutant seeds were not in dormancy et al., which is from other known ABA-deficient mutants whose seeds are much less This may mutants were not isolated in germination It is also likely that may be regulated by stresses or may have of stress ABA biosynthetic genes and their regulation in Arabidopsis all the genes are in ABA those known to be are in are in ABA biosynthetic genes and their regulation in Arabidopsis all the genes are in ABA those known to be are in are in Because the ABA biosynthesis pathway gene there be a step in the pathway. this step is important for genetic of the pathway. the complex regulation mechanisms for individual ABA biosynthetic genes that may plant with the of ABA or its it would be difficult to a the regulatory of these genes or the step for ABA biosynthesis in the it was that the step catalyzed by NCED, the oxidative cleavage of is (Tan et al., and Taylor et al., 2000; et al., This may be in where most studies on ABA biosynthesis are with this or of the NCED genes in increased ABA biosynthesis and reduced water et al., 2001; and 2002; et al., the step is at the NCED, then one would that of other ABA biosynthetic genes would not increase ABA at not in the evidence that the AtZEP whose product catalyzes the step considered in the result in an increased stress gene induction in Arabidopsis (Xiong et al., of to increased seed dormancy and seed germination in tobacco et al., as a result of increased ABA biosynthesis in imbibed These observations would suggest that ZEP ABA biosynthesis in tissues such as seeds and It would be to see the expression level of other ABA biosynthetic genes can ABA biosynthesis. The that of the ABA biosynthetic genes probably have an on ABA biosynthesis may in have to with the in the This is because a increase in ABA biosynthesis from a ABA biosynthetic gene may result in a increased induction of other ABA biosynthetic genes through the (Fig. This can be by the expression of other ABA biosynthetic genes in the In addition, the that are either not upregulated or by ABA may the NCED step to late in ABA biosynthesis in As a consequence, regulating NCED genes may have a more significant on ABA biosynthesis. the regulation of ABA biosynthesis is of great in ABA level and plant stress responses and developmental Because ABA biosynthetic genes the and in their (Xiong et al., Bray, 2002), it is that these genes may be regulated as the of stress-responsive genes (Xiong et al., 2002b). evidence has suggested that the signal for stress-induced ABA biosynthesis may involve and protein and biochemical or genetic studies of of these processes in to ABA biosynthesis have been In the molecular studies the in ABA biosynthetic genes and the respective transcription that are for the activation of these genetic analysis will also be to such a complex signal screens of seed germination, either in the of synthesis or of salt, have identified in ABA biosynthesis in ABA These mutants also were in screens for sensitivity to (Finkelstein et al., 2002; et al., 2002). In some were identified in more than that ABA biosynthesis has in these Because and ABA biosynthesis have a in seed germination and in some other processes et al., 2000; and 2000; Gonzalez-Guzman et al., 2002), there is a that some of the in other hormone response may be in ABA biosynthesis regulation but have our One such may be response to ABA plants have a basal ABA level of that in the wild which is probably to increased biosynthesis because the ZEP level was also higher in et al., the effect of the on ABA biosynthesis be a of the complex between than a specific regulation of ABA biosynthesis. from genetic of the regulatory the in regulatory in screens may also have to with the that these screens are not for the of the To uncover the regulatory for ABA one may the roles of ABA in stress responses at the vegetative screens on stress responses in vegetative tissues would likely new that are important in regulating ABA biosynthesis or to the in manipulating drought stress in a and screens for drought tolerance have not been screens such as those for regulation (e.g. et al., and (e.g. sensitivity to may that ABA accumulation or Because gene expression is more to stress regulation than are some of the molecular genetic such as the one used in the for stress signal mutants et al., may be more in signal In this the of ABA biosynthetic genes particular, and can be to a mutants with gene in response to stress can be These screens may uncover regulatory mechanisms in ABA biosynthesis. the of the information of Arabidopsis and of expression also the of new regulatory in the pathway to ABA biosynthesis. A understanding of the regulation of ABA biosynthesis will require a combination of molecular and biochemical

Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild pineapple relative. Their analysis supports the use of the pineapple as a reference genome for monocot comparative genomics and provides insight into the evolution of crassulacean acid metabolism photosynthesis. Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

Anticipated population growth, shifting demographics, and environmental variability over the next century are expected to threaten global food security. In the face of these challenges, crop yield for food and fuel must be maintained and improved using fewer input resources. In recent years, genetic tools for profiling crop germplasm has benefited from rapid advances in DNA sequencing, and now similar advances are needed to improve the throughput of plant phenotyping. We highlight recent developments in high-throughput plant phenotyping using robotic-assisted imaging platforms and computer vision-assisted analysis tools.

Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.

Trillions of microbes inhabit the distal gut of adult humans. They have evolved to compete efficiently for nutrients, including a wide array of chemically diverse, complex glycans present in our diets, secreted by our intestinal mucosa, and displayed on the surfaces of other gut microbes. Here, we review how members of the Bacteroidetes, one of two dominant gut-associated bacterial phyla, process complex glycans using a series of similarly patterned, cell envelope-associated multiprotein systems. These systems provide insights into how gut, as well as terrestrial and aquatic, Bacteroidetes survive in highly competitive ecosystems.

Small GTP-binding proteins regulate diverse processes in eukaryotic cells such as signal transduction, cell proliferation, cytoskeletal organization, and intracellular membrane trafficking. These proteins function as molecular switches that cycle between "active" and "inactive" states, and this cycle is linked to the binding and hydrolysis of GTP. The Arabidopsis genome contains 93 genes that encode small GTP-binding protein homologs. Phylogenetic analysis of these genes shows that plants contain Rab, Rho, Arf, and Ran GTPases, but no Ras GTPases. We have assembled complete lists of these small GTPases families, as well as accessory proteins that control their activity, and review what is known of the functions of individual members of these families in Arabidopsis. We also discuss the possible roles of these GTPases in relation to their similarity to orthologs with known functions and localizations in yeast and/or animal systems.

Potassium (K(+)) is an essential nutrient required by plants in large quantities, but changes in soil concentrations may limit K(+) acquisition by roots. It is not known how plant root cells sense or signal the changes that occur after the onset of K(+) deficiency. Changes in the kinetics of Rb(+) uptake in Arabidopsis roots occur within 6 h after K(+) deprivation. Reactive oxygen species (ROS) and ethylene increased when the plants were deprived of K(+). ROS accumulated in a discrete region of roots that has been shown to be active in K(+) uptake and translocation. Suppression of an NADPH oxidase in Arabidopsis (rhd2), which is involved in ROS production, prevented the up-regulation of genes that are normally induced by K(+) deficiency, but the induction of high-affinity K(+) transport activity was unchanged. Application of H(2)O(2) restored the expression of genes induced by K(+) deficiency in rhd2 and was also sufficient to induce high-affinity K(+) transport activity in roots grown under K(+)-sufficient conditions. ROS production is an early root response to K(+) deficiency that modulates gene expression and physiological changes in the kinetics of K(+) uptake.

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

We determined the role of Phospholipase Dalpha1 (PLDalpha1) and its lipid product phosphatidic acid (PA) in abscisic acid (ABA)-induced production of reactive oxygen species (ROS) in Arabidopsis thaliana guard cells. The pldalpha1 mutant failed to produce ROS in guard cells in response to ABA. ABA stimulated NADPH oxidase activity in wild-type guard cells but not in pldalpha1 cells, whereas PA stimulated NADPH oxidase activity in both genotypes. PA bound to recombinant Arabidopsis NADPH oxidase RbohD (respiratory burst oxidase homolog D) and RbohF. The PA binding motifs were identified, and mutation of the Arg residues 149, 150, 156, and 157 in RbohD resulted in the loss of PA binding and the loss of PA activation of RbohD. The rbohD mutant expressing non-PA-binding RbohD was compromised in ABA-mediated ROS production and stomatal closure. Furthermore, ABA-induced production of nitric oxide (NO) was impaired in pldalpha1 guard cells. Disruption of PA binding to ABI1 protein phosphatase 2C did not affect ABA-induced production of ROS or NO, but the PA-ABI1 interaction was required for stomatal closure induced by ABA, H(2)O(2), or NO. Thus, PA is as a central lipid signaling molecule that links different components in the ABA signaling network in guard cells.

BACKGROUND: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. RESULTS: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. CONCLUSIONS: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.

Vitamin C (ascorbic acid) is essential to prevent disease associated with connective tissue (e.g., scurvy), improves cardiovascular and immune cell functions, and is used to regenerate alpha-tocopherol (vitamin E). In contrast to most animals, humans lack the ability to synthesize ascorbic acid as a result of a mutation in the last enzyme required for ascorbate biosynthesis. Vitamin C, therefore, must be obtained from dietary sources and, because it cannot be stored in the body, it must be obtained regularly. Once used, ascorbic acid can be regenerated from its oxidized form in a reaction catalyzed by dehydroascorbate reductase (DHAR). To examine whether overexpression of DHAR in plants would increase the level of ascorbic acid through improved ascorbate recycling, a DHAR cDNA from wheat was isolated and expressed in tobacco and maize, where DHAR expression was increased up to 32- and 100-fold, respectively. The increase in DHAR expression increased foliar and kernel ascorbic acid levels 2- to 4-fold and significantly increased the ascorbate redox state in both tobacco and maize. In addition, the level of glutathione, the reductant used by DHAR, also increased, as did its redox state. These results demonstrate that the vitamin C content of plants can be elevated by increasing expression of the enzyme responsible for recycling ascorbate.

We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.

Plants often grow in soils that contain very low concentrations of the macronutrients nitrogen, phosphorus, potassium, and sulfur. To adapt and grow in nutrient-deprived environments plants must sense changes in external and internal mineral nutrient concentrations and adjust growth to match resource availability. The sensing and signal transduction networks that control plant responses to nutrient deprivation are not well characterized for nitrogen, potassium, and sulfur deprivation. One branch of the signal transduction cascade related to phosphorus-deprivation response has been defined through the identification of a transcription factor that is regulated by sumoylation. Two different microRNAs play roles in regulating gene expression under phosphorus and sulfur deprivation. Reactive oxygen species increase rapidly after mineral nutrient deprivation and may be one upstream mediator of nutrient signaling. A number of molecular analyses suggest that both short-term and longer-term responses will be important in understanding the progression of signaling events when the external, then internal, supplies of nutrients become depleted.

Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.

Plant root sensing and adaptation to changes in the nutrient status of soils is vital for long-term productivity and growth. Reactive oxygen species (ROS) have been shown to play a role in root response to potassium deprivation. To determine the role of ROS in plant response to nitrogen and phosphorus deficiency, studies were conducted using wild-type Arabidopsis and several root hair mutants. The expression of several nutrient-responsive genes was determined by Northern blot, and ROS were quantified and localized in roots. The monitored genes varied in intensity and timing of expression depending on which nutrient was deficient. In response to nutrient deprivation, ROS concentrations increased in specific regions of the Arabidopsis root. Changes in ROS localization in Arabidopsis and in a set of root hair mutants suggest that the root hair cells are important for response to nitrogen and potassium. In contrast, the response to phosphorus deprivation occurs in the cortex where an increase in ROS was measured. Based on these results, we put forward the hypothesis that root hair cells in Arabidopsis contain a sensing system for nitrogen and potassium deprivation.

Drought stress is a common adverse environmental condition that seriously affects crop productivity worldwide. Due to the complexity of drought as a stress signal, deciphering drought tolerance mechanisms has remained a major challenge to plant biologists. To develop new approaches to study plant drought tolerance, we searched for phenotypes conferred by drought stress and identified the inhibition of lateral root development by drought stress as an adaptive response to the stress. This drought response is partly mediated by the phytohormone abscisic acid. Genetic screens using Arabidopsis (Arabidopsis thaliana) were devised, and drought inhibition of lateral root growth (dig) mutants with altered responses to drought or abscisic acid in lateral root development were isolated. Characterization of these dig mutants revealed that they also exhibit altered drought stress tolerance, indicating that this root response to drought stress is intimately linked to drought adaptation of the entire plant and can be used as a trait to access the elusive drought tolerance machinery. Our study also revealed that multiple mechanisms coexist and together contribute to whole-plant drought tolerance.