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bioRxiv2018

The complete plastid genomes of four species from Brassicales

Brassicales is a diverse angiosperm order with about 4,700 recognized species. Here, we assembled and described the complete plastid genomes from four species of Brassicales: Capparis urophylla F.Chun (Capparaceae), Carica papaya L. (Caricaceae), Cleome rutidosperma DC. (Cleomaceae), and Moringa oleifera Lam. (Moringaceae), including two plastid genomes newly assembled for two families (Capparaceae and Moringaceae). The four plastid genomes are 159,680 base pairs on average in length and encode 78 protein-coding genes. The genomes each contains a typical structure of a Large Single-Copy (LSC) region and a Small Single-Copy (SSC) region separated by two Inverted Repeat (IR) regions. We performed the maximum-likelihood (ML) phylogenetic analysis using three different data sets of 66 protein-coding genes (ntAll, ntNo3rd and AA). Our phylogenetic results from different dataset are congruent, and are consistent with previous phylogenetic studies of Brassiales.

plant biology↗

bioRxiv2018

The interaction between genotype and maternal nutritional environments affects tomato seed and seedling quality

Seed and seedling traits are affected by the conditions of the maternal environment, such as light, temperature and nutrient availability. In this study, we have investigated whether different maternally applied nitrate and phosphate concentrations affect the seed and seedling performance of two tomato genotypes: Solanum lycopersicum cv. Money maker and Solanum pimpinellifolium accession CGN14498. We observed large differences for seed and seedling traits between the two genotypes. Additionally, we have shown that for nitrate most of the seed and seedling traits were significantly affected by genotype by environment interactions (GxE). The effect of the maternal environment was clearly visible in the primary metabolites of the dry seeds. For example, we could show that the amount of {gamma}-aminobutyric acid (GABA) in Money maker seeds was affected by the differences in the maternal environments and was positively correlated with seed germination under high temperature. Overall, compared to phosphate, nitrate had a larger effect on seed and seedling performance in tomato. In general, the different responses to the maternal environments of the two tomato genotypes show a major role of genotype by environment interactions in shaping seed and seedling traits.\n\nHighlightThe presented data specifically provides knowledge towards understanding a multi-level effect of the maternal nutritional environment on seed and seedling characteristics in tomato. We show a clear genotype by environment interactions (GxE) especially for maternal growth on different nitrate concentrations. Additionally we identified metabolites with either positive or negative correlations with maternal environment affected phenotypical traits.

plant biology↗

bioRxiv2018

Efficient reverse breeding by VIGS-mediated transient crossover reduction

F1 heterozygotes are traditionally generated by crossing homozygous parental lines. The opposite is achieved through reverse breeding, in which parental lines are generated from a heterozygote. Reverse breeding can be used to develop new F1 hybrid varieties without having prior access to homozygous breeding lines. For successful reverse breeding, the heterozygotes homologous chromosomes must be divided over two haploid complements, which is achieved by suppression of meiotic crossover (CO) recombination. We here show two innovations that facilitate efficient reverse breeding. Firstly, we demonstrate that downregulation of CO rates can be accomplished using virus-induced gene silencing (VIGS). We obtain transgene-free parental lines for a heterozygote in just two generations. Secondly, we show that incomplete CO suppression opens up several alternative strategies for the preservation of hybrid phenotypes through reverse breeding.

plant biology↗

bioRxiv2018

Taxonomy, ecology and distribution of Juniperus oxycedrus L. group in the Mediterranean Region using morphometric, phytochemical and bioclimatic approaches.

The ecology, taxonomy and distribution of the Juniperus oxycedrus L. group of taxa are studied. From an ecological aspect, this work proposes a new ombroedaphoxeric index to explain the presence of populations of Juniperus in ombrotypes that are not the optimum for these taxa. The controversy among various authors on the taxonomy of the oxycedrus group with regard to J. oxycedrus subsp. badia and J. oxycedrus subsp. lagunae is clarified. The phytochemical differences in essential oils are addressed, and their similarities analysed; greater similarities are observed between oxycedrus and badia (H. Gay) Debeaux, and between navicularis Grand. and macrocarpa (Sm.) Ball. The phytochemical, molecular and distribution differences allow J. macrocarpa and J. navicularis to be maintained as species.

plant biology↗

bioRxiv2018

Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.

plant biology↗

bioRxiv2018

Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network

Artificial selection experiments are designed to investigate phenotypic evolution of complex traits and its genetic bases. Here we focused on flowering time, a trait of key importance for plant adaptation and life-cycle shifts. We undertook divergent selection experiments (Saclay DSEs) from two maize inbred lines. After 13 generations of selection, we obtained we obtained a time-lag of roughly two weeks between Early- and Late-populations. We used this material to characterize the genome-wide transcriptomic response to selection in the shoot apical meristem (SAM) before, during and after floral transition in realistic field conditions during two consecutive years. We validated the reliability of performing RNA-sequencing in uncontrolled conditions. We found that roughly half of maize genes were expressed in the SAM, 59.3% of which were differentially expressed. We detected a majority of genes with differential expression between inbreds and across meristem status, and retrieved a subset of 2,451 genes involved in the response to selection. Among these, we found a significant enrichment for genes with known function in maize flowering time. Furthermore, they were more often shared between inbreds than expected by chance, suggesting convergence of gene expression. We discuss new insights into the expression pattern of key players of the underlying gene regulatory network including ZCN8, RAP2.7, ZMM4, KN1, GA2ox1, as well as alternative scenarios for genetic convergence.

plant biology↗

bioRxiv2018

Nitric oxide is important for sensing and survival under hypoxia in Arabidopsis

Nitric oxide (NO) is a free radical molecule that plays an important role in hypoxic stress. We studied the impact of hypoxia-induced NO production on the expression of genes and production of metabolites involved in carbon, oxygen sensing, nitrogen, and antioxidant metabolism using wild type (WT), non-symbiotic haemoglobin-overexpressing (Hb+) and nitrate reductase double mutant (nia1,2) of Arabidopsis. Futher application of NO scavenger cPTIO was used to confirm NO role. We found that imposing hypoxia leads to the increaseof NO and reactive oxygen species (ROS) levels in WT, while the reduced levels of NO and higher levels of ROS were observed in roots of Hb+ and nia1,2 mutant. Expression of the genes encoding oxygen sensing and the enzymes involved in fermentative pathways, their activities and metabolite levels were highly induced in WT suggesting that NO plays a role in the induction of fermentation. Several genes and metabolites involved in the TCA cycle were also induced in WT in comparison to Hb+ and nia mutant line suggesting that NO can accelerate TCA cycle to regenerate reducing equivalents under hypoxia. Interestingly, we found that the genes and metabolites involved in the ascorbate-glutathione cycle were modulated by NO under hypoxia. The alternative oxidasegene (AOX1A) was induced under hypoxia in WTdue to increased levels of NO rather than ROS. Futher, we found that NO improves plant survival. Overall these findings suggest that NO is a major player in plant survival under hypoxia by modulating gene expression and metabolite levels of carbon, nitrogen, oxygen sensing and antioxidant metabolism.\n\nHighlightHypoxia-induced nitric oxide plays a central role in activation of genes and metabolites involved in fermentation, TCA cycle, nitrogen and antioxidant metabolism

plant biology↗

bioRxiv2018

Moisture adsorption isotherms and quality of seeds stored in conventional packaging materials and hermetic Super Bag

Seed moisture content (SMC) is an important attribute to seed quality. Maintaining seed dryness throughout supply chain (The Dry Chain) prevents seed germination and quality losses. Ambient relative humidity (RH) and temperature affect seed moisture and thereof seed moisture isotherm. Present study was conducted to compare the moisture adsorption isotherms of wheat, maize, cotton and quinoa seeds packed in hermetic Super Bag and traditional packaging materials including paper, polypropylene (PP), jute and cloth bags. Seeds were incubated at 60, 70, 80 and 90% static RH. Nearly straight line moisture isotherms for all crop seeds were obtained in Super Bag. Seed moisture contents increased in traditional packaging materials with increasing RH. At higher level of RH, moisture contents increased slightly (1-2%) in Super Bag, whereas this increase was much higher in traditional packaging materials ({approx}9% higher than original SMC at 90% RH). In second study, seeds were dried to 8 and 14% initial seed moisture contents using zeolite drying beads and were stored in hermetic and traditional bags for a period of 18 months. For all crop seeds, germination was severely affected in all packaging materials both at 8 and 14% initial SMC except storage in Super Bag at 8% SMC. Wheat seed stored in Super Bag at 8% SMC almost maintained initial germination while germination of cotton, maize and quinoa seeds declined 7%, 14% and 30% respectively in Super Bag at 8% SMC. Seed storage in Super Bag can help to prevent the significant increase in seed moisture at higher RH as is evident from moisture isotherm study, thus helps to preserve quality of maize, wheat, cotton and quinoa seeds by maintaining The Dry Chain throughout the storage period.

plant biology↗

bioRxiv2018

A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance

The introgression of a small segment of wheat chromosome 1BS in the distal region of the rye 1RS arm translocation in wheat (henceforth 1RSrw) was previously associated with reduced grain yield, carbon isotope discrimination and stomatal conductance, suggesting reduced access to soil moisture. In this study, we show that the 1RS/1RSRW polymorphism causes differences in root length in field and hydroponic experiments. In the latter, differences in seminal root length were associated with a developmentally regulated arrest of the root apical meristem (RAM). Approximately 10 days after germination, the seminal roots of the 1RSRW plants showed a gradual reduction in elongation rate and stopped growing a week later. Seventeen days after germination, the roots of the 1RSRW plants showed altered gradients of reactive oxygen species and emergence of lateral roots close to the RAM, suggesting a loss of apical dominance. The 1RS/1RSRW isogenic lines also differed in plant biomass and grain yield under normal, terminal drought, and waterlogging field conditions. The differences were larger in fields with reduced or excessive irrigation. These results suggest that this polymorphism may be useful to modulate root architecture and mitigate the negative impacts of excess or reduced water in wheat production.\n\nHIGHLIGHTA wheat/rye polymorphism in chromosome one affects seminal root length and apical dominance and is associated with differences in drought and waterlogging tolerance in the field.

plant biology↗

bioRxiv2018

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation

BackgroundNext-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to specific types of cells that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ.\n\nResultsHere, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. Furthermore, we employed a unique molecular identifier to reduce amplification bias in the cDNA libraries. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells into stem cells in excised tissues of the moss Physcomitrella patens, identifying 6,382 DEGs between cells at 0 h and 24 h after excision. We found substantial variations in both the transcript levels of previously reported reprogramming factors and the overall expression profiles between cells, which appeared to be related to their different reprogramming abilities or the estimated states of the cells according to the pseudotime based on the transcript profiles.\n\nConclusionsWe developed 1cell-DGE with microcapillary manipulation, a technique that can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.

plant biology↗

bioRxiv2018

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped specialized metabolite diversity, which drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating specialized metabolite diversity in an evolutionary context have been limited by the impossibility to identify chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here, we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites, and apply it for over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5 % based on spectral library matches alone to 42.6 % of total MS/MS molecular features extending annotations from well-known plant compound classes into the dark plant metabolomics matter. To gain insights in substructural diversity within the plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations towards the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.

plant biology↗

bioRxiv2018

ARF5/MONOPTEROS directly regulates miR390 expression in theArabidopsis thaliana primary root meristem

The root meristem is organized around a quiescent centre surrounded by stem cells that generate all cell types of the root. In the transit amplifying compartment progeny of stem cells further divide prior to differentiation. Auxin controls the size of this transit-amplifying compartment via Auxin Response Factors (ARF) that interact with Auxin Response Elements (AuxRE) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3 and ARF4 by triggering the production of trans-acting (ta)-siRNA from TAS3. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to auxin. A single AuxRE bound by ARF5/MONOPTEROS (MP) in miR390 promoter is necessary for miR390 expression in this compartment. We show that interfering with ARF5/MP dependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment. Our results show that ARF5/MP regulates directly the expression of miR390 in the basal root meristem. We propose that ARF5, miR390 and the ta-siRNAs-regulated ARFs are necessary to maintain the size of the transit-amplifying region of the meristem.\n\nOne sentence summaryThe expression of miR390 in the Arabidopsis basal root meristem is controlled by ARF5/MONOPTEROS.

plant biology↗

bioRxiv2018

Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of Radiation Use Efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programs in an attempt to alleviate this, however their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE we applied genome-wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31traits over two years under optimal growing conditions and genotyped using the 35K Wheat Breeders array. Marker-trait-association identified 94 SNPs significantly associated with yield, agronomic and phenology related traits along with RUE and biomass at various growth stages that explained 7-17 % of phenotypic variation. Common SNP markers were identified for grain yield, final biomass and RUE on chromosomes 5A and 7A. Additionally we show that landrace and synthetic derivative lines showed higher thousand grain weight (TGW), biomass and RUE but lower grain number (GNO) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker assisted breeding to systematically increase biomass, RUE and TGW and avoid the TGW/GNO and BM/HI trade-off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.

plant biology↗

bioRxiv2018

Subdivision of light signalling networks contributes to cellular partitioning of C4 photosynthesis in maize

Plants coordinate the expression of genes required to conduct photosynthesis in response to growth and environmental changes. In species that conduct two-cell C4 photosynthesis, the expression of photosynthesis genes is partitioned such that leaf mesophyll and vascular sheath cells accumulate different components of the photosynthetic pathway. The identity of the regulatory networks that facilitate this partitioning are unknown. Here we show that differences in light perception between mesophyll and bundle sheath cells facilitate differential regulation and accumulation of photosynthesis genes in the C4 crop Zea mays (maize). We show that transcripts encoding photoreceptors differentially accumulate in mesophyll and bundle sheath cells in a manner that is consistent with biophysical light filtration. We further show the blue light (but not red) is necessary and sufficient to activate photosystem II assembly in etiolated maize mesophyll cells, while both red and blue produce the same effect in C3 Hordeum vulgare (barley). Finally, we demonstrate that changes in abundance of >20% of genes that differentially accumulate between mesophyll and bundle sheath cells can be recapitulated by spectrum specific deetiolation of maize seedlings. These findings provide evidence that subdivision of light signalling networks is a key component of cellular partitioning of C4 photosynthesis in maize.

plant biology↗

bioRxiv2018

First Report of Recurrent Genomic Selection with Real Data in Popcorn and Genetic Gain Increases

Recurrent Selection increases the frequencies of favorable alleles for economically important traits, which in the case of popcorn are popping expansion and grain yield. However, is time-consuming, since each selection cycle consists of three stages: progeny development and evaluation, and recombination of the best families. With the Recurrent Genomic Selection use, the time required for each selection cycle can be shortened, as it allows the evaluation and recombination phases to be performed simultaneously, reducing the time needed to complete one selection cycle to only one growing season. In this respect, the objective of this study was to determine the selection accuracy and genetic gains for different selection strategies: PhEN = estimates based exclusively on the phenotypic data of 98 plants; PhEN + GEN = estimates based exclusively on the phenotypic and genotypic data of 98 plants; and GEN = estimates based exclusively on SNP marker genotyping. The following traits were evaluated: 100-grain weight, ear height, grain yield, popping expansion, plant height, and popcorn volume. Field trials were carried out with 98 S1 progenies, at two locations, in an incomplete block design with three replications. The parents of these progenies were genotyped with a panel of ~ 21K SNPs. From the results based on the predictions by strategy GEN, at different selection intensities, the average annual genetic gain for the different traits was 29.1% and 25.2% higher than that by the strategies PhEN and GEN + PhEN for 98 selection candidates; 148.3% and 140.9% higher for 500; and 187.9% and 179.4% higher for 1,000 selection candidates, respectively. Therefore, recurrent genomic selection may result in a high genetic gain, provided that: i) phenotyping is accurate; ii) selection intensity is explored by genotyping several plants, increasing the number of selection candidates, and iii) genomic selection is used for early selection in recurrent selection.

plant biology↗

bioRxiv2018

Cis-regulatory code for predicting plant cell-type specific high salinity response

Multicellular organisms have diverse cell types with distinct roles in development and responses to the environment. At the transcriptional level, the differences in environmental response between cell types are due to differences in regulatory programs. In plants, although cell-type environmental responses have been examined, details on how these responses are regulated remain spotty. Here, we identify a set of putative cis-regulatory elements (pCREs) enriched in the promoters of genes responsive to high salinity stress in six Arabidopsis thaliana root cell types. Using machine learning with pCREs as predictors, we establish cis-regulatory codes, i.e. models predicting whether a gene is responsive to high salinity for each cell type. These pCRE-based models outperform models utilizing in vitro binding data of 758 A. thaliana transcription factors. Surprisingly, organ pCREs identified based on whole root high salinity response can predict cell-type responses as well as pCREs derived from cell-type data -because organ and cell-type pCREs predict complementary subsets of high salinity response genes. Our findings not only advance our understanding of the regulatory mechanisms of plant spatial transcriptional response through cis-regulatory codes, but also suggest broad applicability of the approach to any species, particularly those with little or no trans regulatory data.

plant biology↗

bioRxiv2018

Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis.

Many eukaryotic proteins regulating phosphate (Pi) homeostasis contain SPX domains. We have previously shown that these domains act as cellular receptors for inositol pyrophosphate (PP-InsP) signaling molecules, suggesting that PP-InsPs may regulate Pi homeostasis. Here we report that simultaneous deletion of two diphosphoinositol pentakisphosphate kinases VIH1 and 2 in Arabidopsis impairs plant growth and leads to constitutive Pi starvation responses. We demonstrate that VIH1 and VIH2 are bifunctional cytosolic enzymes able to generate and break-down PP-InsPs. Point-mutants targeting the kinase and phosphatase active sites have opposing effects on plant Pi content and Pi starvation responses, while VIH1 and VIH2 protein levels remain constant in different Pi growth conditions. Enzymatic assays reveal that ATP-Mg2+ substrate levels can shift the relative kinase and phosphatase activities of full-length diphosphoinositol pentakisphosphate kinases. Deletion of phosphate starvation response transcription factors rescues vih1 vih2 mutant phenotypes, placing diphosphoinositol pentakisphosphate kinases and PP-InsPs in plant phosphate signal transduction cascades. We propose that VIH1 and VIH2 relay changes in cellular ATP concentration to changes in PPInsP levels, allowing plants to maintain cellular Pi concentrations constant and to trigger Pi starvation responses.

plant biology↗

bioRxiv2018

Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana

FRIGIDA (FRI) as the major regulator of flowering time in Arabidopsis accessions can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. Besides FLC, other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatiotemporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets MADS AFFECTING FLOWERING4 (MAF4) and MAF5 in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as pro-embryo stage is enough to upregulate FLC expression to delay flowering. Together, our findings confirm the spatiotemporal effect of FRI on delaying flowering, and propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI.\n\nHighlightRoot FRIDIGA activated the novel targets MAF4/5 to delay flowering; Temporal expressing FRIGIDA at as early as pro-embryo stage is efficient to delay flowering.

plant biology↗