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bioRxiv2018

Stable Carbon Isotopes in Zea mays

The increasing demand for food production and predicted climate change scenarios highlight the need for improvements in crop sustainability. The efficient use of water will become increasingly important for rainfed agricultural crops even in fertile regions that have historically received ample precipitation. Improvements in water-use efficiency in Zea mays have been limited, and warrants a renewed effort aided by molecular breeding approaches. Progress has been constrained by the difficulty of measuring water-use in a field environment. The stable carbon isotope composition ({delta}13C) of the leaf has been proposed as an integrated signature of carbon fixation with a link to stomatal conductance. However, additional factors affecting leaf {delta}13C exist, and a limited number of studies have explored this trait in Z. mays. Here we present an extensive characterization of leaf {delta}13C in Z. mays. Significant variation in leaf {delta}13C exists across diverse lines of Z. mays, which we show to be heritable across several environments.\n\nFurthermore, we examine temporal and spatial variation in leaf {delta}13C to determine the optimum sampling time to maximize the use of leaf {delta}13C as a trait. Finally, our results demonstrate the relationship between transpiration and leaf {delta}13C in the field and the greenhouse. Decreasing transpiration and soil moisture are associated with decreasing leaf {delta}13C. Taken together these results outline a strategy for using leaf {delta}13C and reveal its usefulness as a measure of transpiration efficiency under well-watered conditions rather than a predictor of performance under drought.\n\nSignificance StatementThis study identifies sources of variation in stable carbon isotopes of maize leaves and establishes the framework for connecting leaf {delta}13C and transpiration efficiency.

plant biology↗

bioRxiv2018

Genome based QTL and meta-QTL analyses of thousand-kernel weight in tetraploid wheat

The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTLs) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession Zavitan and durum wheat variety Svevo. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.

plant biology↗

bioRxiv2018

Characterization of the early response of Arabidopsis thaliana to Dickeya dadantii infection using expression profiling

To draw a global view of plant responses to interactions with the phytopathogenic enterobacterale Dickeya dadantii, a causal agent of soft rot diseases on many plant species, we analysed the early Arabidopsis responses to D. dadantii infection. We performed a genome-wide analysis of the Arabidopsis thaliana transcriptome during D. dadantii infection and conducted a genetic study of identified responses.\n\nA limited set of genes related to plant defence or interactions with the environment were induced at an early stage of infection, with an over-representation of genes involved in both the metabolism of indole glucosinolates (IGs) and the jasmonate (JA) defence pathway. Bacterial type I and type II secretion systems are required to trigger the induction of IG and JA-related genes while the type III secretion system appears to partially inhibit these defence pathways. Using Arabidopsis mutants impaired in JA biosynthesis or perception, we showed that induction of some IG metabolism genes was COI1-dependent but, surprisingly, JA-independent. Moreover, characterisation of D. dadantii disease progression in Arabidopsis mutants impaired in JA or IG pathways showed that JA triggers an efficient plant defence response that does not involve IGs.\n\nThe induction of the IG pathway by bacterial pathogens has been reported several times in vitro. This study shows for the first time, that this induction does indeed occur in planta, but also that this line of defence is ineffective against D. dadantii infection, in contrast to its role to counteract herbivorous or fungal pathogen attacks.

plant biology↗

bioRxiv2018

Arginine culture turns on the elusive nitrogen starvation signal during robust phototrophic growth in Chlamydomonas

Under nitrogen (N) starvation, microalgae increase carbon storage in the form of lipid droplets while also downregulating photosynthesis and eventually terminating growth. To improve lipid yield, we asked whether lipid droplets and N starvation responses can be induced without limiting growth or photosynthesis. In the chlorophyte Chlamydomonas reinhardtii, gametogenesis is induced either by N starvation or by growth with arginine as the sole N source. We showed that arginine cultures supported robust phototrophic growth, constitutively turned on N starvation-induced genes, and increased lipid droplets. The lipids accumulated in arginine cultures exhibited strong enrichment of saturated and monounsaturated fatty acids, a preferred characteristic of biodiesel precursors. The diatom Phaeodactylum tricornutum also accumulated lipid droplets in arginine culture without growth impairment. We document a system wherein N starvation responses are induced without compromising photosynthesis or growth, thereby suited to the producing valuable chemicals and biofuel precursors without requiring stressors in microalgae.

plant biology↗

bioRxiv2018

Heat-shock inducible CRISPR/Cas9 system generates heritable mutations in rice

Transient expression of CRISPR/Cas9 is an effective approach for limiting its activities and improving its precision in genome editing. Here, we describe the heat-shock inducible CRISPR/Cas9 system for controlled genome editing, and demonstrate its efficiency in the model crop, rice. Using a soybean heat-shock protein gene promoter and the rice U3 promoter to express Cas9 and sgRNA, respectively, we developed the heat-shock (HS) inducible CRISPR/Cas9 system, and tested its efficacy in targeted mutagenesis. Two loci were targeted by transforming rice with HS-CRISPR/Cas9 vectors, and the presence of targeted mutations was determined before and after the HS treatment. We found only a low rate of targeted mutagenesis before HS, but an increased rate of mutagenesis after HS treatment among the transgenic lines. Specifically, only [~]11% of transformants showed characteristic insertions-deletions at the ambient room temperature, but a higher percentage ([~]45%) of callus lines developed mutations after a few days of HS treatment. Analysis of regenerated plants harboring HS-CRISPR/Cas9 revealed that targeted mutagenesis was suppressed in the plants but induced by HS, which was detectable by Sanger sequencing after several weeks of HS treatments. Most importantly, the HS-induced mutations were transmitted to the progeny at a high rate, generating monoallelic and biallelic mutant lines that independently segregated from Cas9. Taken together, this work shows that HS-CRISPR/Cas9 is a controlled and reasonably efficient platform for genome editing, and therefore, a promising tool for limiting genome-wide off-target effects and improving the precision of genome editing.\n\nSignificance StatementA method for the temporal control on gene editing based on the use of heat-shock induced expression of CRISPR/Cas9 is described, which was efficient in producing heritable mutations in the rice genome. We assume this method will be useful for targeting essential genes and improving the precision of CRISPR/Cas9.

plant biology↗

bioRxiv2018

Arabidopsis class I formin FH1 relocates between membrane compartments during root cell ontogeny and associates with plasmodesmata

Formins are evolutionarily conserved eukaryotic proteins engaged in actin nucleation and other aspects of cytoskeletal organization. Angiosperms have two formin clades with multiple paralogs; typical plant Class I formins are integral membrane proteins that can anchor cytoskeletal structures to membranes. For the main Arabidopsis housekeeping Class I formin, FH1 (At3g25500), plasmalemma localization was documented in heterologous expression and overexpression studies. We previously showed that loss of FH1 function increases cotyledon epidermal pavement cell shape complexity via modification of actin and microtubule organization and dynamics. Here we employ transgenic Arabidopsis expressing green fluorescent protein-tagged FH1 (FH1-GFP) from its native promoter to investigate in vivo behaviour of this formin using advanced microscopy techniques. The fusion protein is functional, since its expression complements the fh1 loss-of-function mutant phenotype. Accidental overexpression of FH1-GFP results in a decrease in trichome branch number, while fh1 mutation has the opposite effect, indicating a general role of this formin in controlling cell shape complexity. Consistent with previous reports, FH1-GFP associates with membranes. However, the protein exhibits surprising actin- and secretory pathway-dependent dynamic localization and relocates between cellular endomembranes and the plasmalemma during cell division and differentiation in root tissues, with transient tonoplast localization at the transition/elongation zones border. FH1-GFP also accumulates in actin-rich regions of cortical cytoplasm and associates with plasmodesmata in both the cotyledon epidermis and root tissues. Together with previous reports from metazoan systems, this suggests that formins might have an ancestral role at cell-cell junctions.

plant biology↗

bioRxiv2018

Chemical composition of essential oil from Folium nelumbinis and its antioxidant activity

This study is aim to determine the chemical composition and antioxidant activity of the essential oil from lotus leaves. The different methods and solvents were selected to extract oils from lotus leaves. About 38 components were found by GC-MS analysis, representing as 12, 15-octadecatrienoic acid (34.99%), linoleic acid and hexadecanoic acid. TBARS value, AV value and IV value reflected the various physicochemical indexes and lipid properties of Folium nelumbinis oil. Furthermore, antioxidant activities of the leaf samples were examined by FRAP and DPPH assays. In all systems, twice methanol-decolorized and ultrasonic-assisted essential oil using hexane solvent exhibited a higher potential activitythan than that of other extracts (ethanol, ethyl acetate and petroleum ether). These results provide a clear picture of the essential oils of Folium nelumbinis and demonstrate that the lotus leaves oil has an huge potential as a kind of chemical additive for the food industry owing to the strong antioxidant capacity.

plant biology↗

bioRxiv2018

Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis

Bacterial CRISPR systems have been widely adopted to create operator-specified site-specific nucleases. Such nuclease action commonly results in loss-of-function alleles, facilitating functional analysis of genes and gene families We conducted a systematic comparison of components and T-DNA architectures for CRISPR-mediated gene editing in Arabidopsis, testing multiple promoters, terminators, sgRNA backbones and Cas9 alleles. We identified a T-DNA architecture that usually results in stable (i.e. homozygous) mutations in the first generation after transformation. Notably, the transcription of sgRNA and Cas9 in head-to-head divergent orientation usually resulted in highly active lines. Our Arabidopsis data may prove useful for optimization of CRISPR methods in other plants.

plant biology↗

bioRxiv2018

Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants

The Anthropocene epoch is associated with the spreading of metals in the environment increasing oxidative and genotoxic stress on living organisms1,2. Once regarded as a curiosity, plants hyperaccumulating metals are now envisioned as an opportunity to remediate metal contaminated soils. About 500 plant species adapted to metalliferous soils acquired the capacity to hyperaccumulate (>0.1% of dry weight) nickel in their shoot3. The phylogenetic distribution of these hyperaccumulators in 50 families suggest that this complex trait evolved multiple times independently from basic mechanisms involved in metal homeostasis. However, the exact nature of these mechanisms and whether they are shared between various lineages is not known. Here, using cross-species transcriptomic analyses in different plant families, we have identified convergent functions that may represent major nodes in the evolution of nickel hyperaccumulation. In particular, our data point out that constitutive high expression of IREG/Ferroportin transporters recurrently emerged as a mechanism involved in nickel hyperaccumulation.

plant biology↗

bioRxiv2018

Photosynthetic CO2 assimilation: the last gap in the structural proteome is closed

In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga Chlamydomonas reinhardtii (CrPRK) and the land plant Arabidopsis thaliana (AtPRK). PRK is an elongated homodimer characterized by a large central {beta}-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 [A] apart and connected by a flexible region exclusive to photosynthetic eukaryotes--the clamp loop--which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both AtPRK and CrPRK have a strongly reduced dimer interface and increased number of random coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes. Significance StatementIn chloroplasts, five enzymes of the Calvin-Benson (CB) cycle are regulated by thioredoxins (TRXs). These enzymes have all been structurally characterized with the notable exception of phosphoribulokinase (PRK). Here, we determined the crystal structure of chloroplast PRK from two model photosynthetic organisms. Regulatory cysteines appear distant from each other and are linked by a long loop that is present only in plant-type PRKs and allows disulfide bond formation and subsequent conformational rearrangements. Structural comparisons with ancient PRKs indicate that the presence of flexible regions close to regulatory cysteines is a unique feature that is shared by TRX-dependent CB cycle enzymes, suggesting that the evolution of the PRK structure has resulted in a global increase in protein flexibility for photosynthetic eukaryotes.

plant biology↗

bioRxiv2018

Anthranilic acid regulates subcellular localization of auxin transporters during root gravitropism

O_LIDistribution of auxin within plant tissues is of great importance for developmental plasticity, including root gravitropic growth. Auxin flow is directed by the subcellular polar distribution and dynamic relocalization of auxin transporters such as the PIN-FORMED (PIN) efflux carriers, which can be influenced by the main natural plant auxin indole-3-acetic acid (IAA). Anthranilic acid (AA) is an important early precursor of IAA and previously published studies with AA analogues suggested that AA may also regulate PIN localization.\nC_LIO_LIUsing Arabidopsis thaliana as a model species, we studied an AA-deficient mutant displaying agravitropic root growth, treated seedlings with AA and AA analogues and transformed lines to over-produce AA while inhibiting its conversion to downstream IAA precursors.\nC_LIO_LIWe showed that AA rescues root gravitropic growth in the AA-deficient mutant at concentrations that do not rescue IAA levels. Overproduction of AA affects root gravitropism without affecting IAA levels. Treatments with, or deficiency in, AA result in defects in PIN polarity and gravistimulus-induced PIN relocalization in root cells.\nC_LIO_LIOur results reveal a previously unknown role for AA in the regulation of PIN subcellular localization and dynamics involved in root gravitropism, which is independent of its better-known role in IAA biosynthesis.\nC_LI

plant biology↗

bioRxiv2018

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering

Molecular tools adapted from bacterial CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) systems for adaptive immunity have become widely used for plant genome engineering, both to investigate gene functions and to engineer desirable traits. A number of different Cas (CRISPR-associated) nucleases are now used but, as most studies performed to date have engineered different targets using a variety of plant species and molecular tools, it has been difficult to draw conclusions about the comparative performance of different nucleases. Due to the time and effort required to regenerate engineered plants, efficiency is critical. In addition, there have been several reports of mutations at sequences with less than perfect identity to the target. While in some plant species it is possible to remove these so-called off-targets by backcrossing to a parental line, the specificity of genome engineering tools is important when targeting specific members of closely-related gene families, especially when recent paralogues are co-located in the genome and unlikely to segregate. Specificity is also important for species that take years to reach sexual maturity or that are clonally propagated. Here, we directly compare the efficiency and specificity of Cas nucleases from different bacterial species together with engineered variants of Cas9. We find that the nucleotide content correlates with efficiency and that Cas9 from Staphylococcus aureus is comparatively most efficient at inducing mutations. We also demonstrate that high-fidelity variants of Cas9 can reduce off-target mutations in plants. We present these molecular tools as standardised DNA parts to facilitate their re-use.

plant biology↗

bioRxiv2018

Hormonal balance finely tunes dormancy status in sweet cherry flower buds

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiological, transcriptional analyses, quantification of abscisic acid (ABA) and gibberellins (GAs), and modelling to further investigate how these signaling pathways are associated with dormancy progression in the flower buds of two sweet cherry cultivars. Our results demonstrated that GA-associated pathways have distinct functions and may be differentially related with dormancy. In addition, ABA levels rise at the onset of dormancy, associated with enhanced expression of ABA biosynthesis PavNCED genes, and decreased prior to dormancy release. Following the observations that ABA levels are correlated with dormancy depth, we identified PavUG71B6, a sweet cherry UDP-GLYCOSYLTRANSFERASE gene that up-regulates active catabolism of ABA to ABA-GE and may be associated with low ABA content in the early cultivar. Subsequently, we modelled ABA content and dormancy behavior in three cultivars based on the expression of a small set of genes regulating ABA levels. These results strongly suggest the central role of ABA pathway in the control of dormancy progression and open up new perspectives for the development of molecular-based phenological modelling.

plant biology↗

bioRxiv2018

Multiple C2 domains and Transmembrane region Proteins (MCTPs) tether membranes at plasmodesmata

AO_SCPLOWBSTRACTC_SCPLOWIn eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved unique MCS, the plasmodesmata intercellular pores, which combine endoplasmic reticulum (ER) - plasma membrane (PM) contacts with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remains unknown.\n\nHere we show that the Multiple C2 domains and Transmembrane region Protein (MCTP) family, key regulators of cell-to-cell signalling in plants, act as ER - PM tethers specifically at plasmodesmata. We report that MCTPs are core plasmodesmata proteins that insert into the ER via their transmembrane region whilst their C2 domains dock to the PM through interaction with anionic phospholipids. A mctp3/4 loss-of-function mutant induces plant developmental defects while MCTP4 expression in a yeast {Delta}tether mutant partially restores ER-PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER-PM contacts and cell-cell signalling.

plant biology↗

bioRxiv2018

Flavor-Cyber-Agriculture: Optimization of plant metabolites in an open-source control environment through surrogate modeling

Food production in conventional agriculture faces numerous challenges such as reducing waste, meeting demand, maintaining flavor, and providing nutrition. Contained environments under artificial climate control, or cyber-agriculture, could in principle be used to meet many of these challenges. Through such environments, phenotypic expression of the plant---mass, edible yield, flavor, and nutrients---can be actuated through a "climate recipe," where light, water, nutrients, temperature, and other climate and ecological variables are optimized to achieve a desired result. This paper describes a method for doing this optimization for the desired result of flavor by combining cyber-agriculture, metabolomic phenotype (chemotype) measurements, and machine learning. In a pilot experiment, (1) environmental conditions, i.e. photoperiod and ultraviolet (UV) light (known to affect production of flavor-active molecules in edible plants) were applied under different regimes to basil plants (Ocimum basilicum) growing inside a hydroponic farm with an open-source design; (2) flavor-active volatile molecules were measured in each plant using gas chromatography-mass spectrometry (GC-MS); and (3) symbolic regression was used to construct a surrogate model of this chemistry from the input environmental variables, and this model was used to discover new combinations of photoperiod and UV light to increase this chemistry. These new combinations, or climate recipes, were then implemented in the hydroponic farm, and several of them resulted in a marked increase in volatiles over control. The process also led to two important insights: it demonstrated a "dilution effect", i.e. a negative correlation between weight and desirable chemical species, and it discovered the surprising effect that a 24-hour photoperiod of photosynthetic-active radiation, the equivalent of all-day light, induces the most flavor molecule production in basil. In this manner, surrogate optimization through machine learning can be used to discover effective recipes for cyber-agriculture that would be difficult and time-consuming to find using hand-designed experiments.

plant biology↗

bioRxiv2018

Genome-wide identification and expression analysis of the FAR gene family in hexaploid wheat (Triticum aestivum L.)

Fatty acyl-CoA reductase (FAR) is involved in the biosynthesis of primary alcohols, which are waxy constituents that play an important role in plant stress. Previous studies have shown that primary alcohol is the most important component in the wheat seeding stage and accounts for more than 80% of the total composition. To date, eight FAR genes have been identified in wheat, but there has not been a systematic analysis. In this study, a comprehensive overview of the TaFAR gene family was performed, including analyses of the phylogenetic relationship, the multiple sequence alignment, the conserved motif distribution and the expression pattern. The result showed that a total of 41 wheat FAR genes were identified and designated TaFAR1-A-TaFAR22-D; all FAR genes were divided into six classes according to their phylogenetic relationship, and most of the FAR genes might be related to wheat cuticular wax synthesis. The analysis of the promoter binding site showed that TaFAR genes could be regulated by the MYB transcription factor and could be used as target genes for hormone regulation under adverse conditions, especially during a drought. This study provides a basis for further analyses of the TaFAR gene function and of upstream regulatory genes.

plant biology↗

bioRxiv2018

An assessment of the interactions between climatic conditions and genetic characteristic on the agricultural performance of soybeans grown in Northeast Asia

Glycine max, commonly known as soybean or soya bean, is a species of legume native to East Asia. The interactions between climatic conditions and genetic characteristic affect the agricultural performance of soybean. Therefore, an investigation to identify the main elements affecting the agricultural performances of 11 soybeans was conducted in Northeast Asia, China [Harbin (45{degrees}12'N) Yanji (42{degrees}53'N) Dalian (39{degrees}30'N) Qingdao (36{degrees}26'N)] Republic of Korea [Suwon (37{degrees}16'N) and Jeonju (35{degrees}49'N)]. The days to flowering (DTF) of soybeans with the e1-nf and e1-as alleles and the E1e2e3e4 genotype, except Keumgangkong, Tawonkong, and Duyoukong, was relatively short compared to soybeans with other alleles. Although DTF of the soybeans was highly correlated to all climatic conditions, days to maturity (DTM) and 100-seed weight (HSW) of the soybeans showed no significant correlation with any climatic conditions. The soybeans with a dominant Dt1 allele, except Tawonkong, had the longest stem length (STL). Moreover, the STL of the soybeans grown at the test fields showed a positive correlation with only day length (DL) although the results of our chamber test showed that STL of soybean was positively affected by average temperature (AVT) and DL. Soybean yield (YLD) showed positive correlations with latitude and DL (except L62-667, OT89-5, and OT89-6) although the response of YLD to the climatic conditions was cultivar-specific. Our results show that DTF and STL of soybeans grown in Northeast Asia are highly affected by DL although AVT and genetic characteristic also affect DTF and STL. Along with these results, we confirmed that the DTM, HSW, and YLD of the soybeans vary in relation to their genetic characteristic.

plant biology↗

bioRxiv2018

The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Tetradesmus obliquus is a promising oleaginous microalga. We functionally annotated its genome and characterized the transcriptional landscape of T. obliquus adapted to 16:8h light dark (LD) cycles in turbidostat culture conditions at very high temporal resolution (1h intervals). Revealing a cycle of cellular events, six distinct expression profiles were obtained, each with transcriptional phenotypes correlating with measurements of biochemical composition.\n\nThe impact of starch deficiency was studied using the starchless mutant slm1. Significant changes in the transcriptional landscape were observed. Starch deficiency resulted in incapacity to supply energy during dark period, resulting in early or late time shift for energy demanding processes. Our study provides new perspectives on the role of starch and the adaptation to LD cycles of oleaginous microalgae.

plant biology↗