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bioRxiv2018

Increased temperatures may safeguard the nutritional quality of crops under future elevated CO2 concentrations

Iron (Fe) and zinc (Zn) deficiencies are a global human health problem that may worsen by growth of crops at elevated atmospheric CO2 concentration (eCO2). However, climate change will also involve higher temperature, but it is unclear how the combined effect of eCO2 and higher temperature will affect the nutritional quality of food crops. To begin to address this question, we grew soybean (Glycine max) in a Temperature by Free-Air CO2 Enrichment (T-FACE) experiment in 2014 and 2015 under ambient (400 mol mol-1) and elevated (600 mol mol-1) CO2 concentration and under ambient and elevated temperatures (+2.7 {degrees}C day and +3.4 {degrees}C at night). In our study, eCO2 significantly decreased Fe concentration in soybean seeds in both seasons (-8.7% and -7.7%) and Zn concentration in one season (-8.9%) while higher temperature (at ambient CO2 concentration) had the opposite effect. The combination of eCO2 with elevated temperature generally restored seed Fe and Zn concentrations to levels obtained under ambient CO2 and temperature conditions, suggesting that the potential threat to human nutrition by increasing CO2 concentration may not be realized. In general, seed Fe concentration was negatively correlated with yield suggesting inherent limitations to increasing seed Fe. In addition, we confirm our previous report that the concentration of seed storage products and several minerals varies with node position at which the seeds developed. Overall, these results demonstrate the complexity of predicting climate change effects on food security when various environmental parameters change in an interactive manner.

plant biology↗

bioRxiv2018

Competitive tolerance and yield response of maize, cowpea and tomato in mixed culture and pure stand

This study investigated the competitive effect and yield response of maize, cowpea and tomato in mixed and pure stand.\n\nThe experiment was carried out under a screenhouse to minimize extraneous factors such as pests and rodents using a randomized complete block design (RCBD). The treatments where T1 = sole maize (SM); T2 = Maize intercrop with cowpea (MC); T3 = Maize intercrop with tomato (MT); T4 = Sole tomato (ST); T5 = Tomato intercrop with Cowpea (TC); T6 = Sole cowpea (SC); T7 = Maize intercrop with cowpea and tomato (MCT). At harvest the yields parameters of maize, tomato and cowpea were taken. Some of the indices for intensity of competition were computed using standard formulas and statistical analysis was performed using statistical analytical software SAS version 9.12.\n\nThe result showed that the yield of maize, cowpea and tomato were enhanced in the intercropped than the sole crops. Most of the intensity of competition indices of maize, tomato and cowpea in the mixed cultured were greater than 1, while that of the sole culture equals 1.\n\nThe study concluded that competition for shared resources in the mixed culture of tomato, maize and cowpea enhanced their yield.

plant biology↗

bioRxiv2018

The MoT3 assay does not distinguish between Magnaporthe oryzae wheat and rice blast isolates from Bangladesh

The blast fungus Magnaporthe oryzae is comprised of lineages that exhibit varying degrees of specificity on about 50 grass hosts, including rice, wheat and barley. Reliable diagnostic tools are essential given that the pathogen has a propensity to jump to new hosts and spread to new geographic regions. Of particular concern is wheat blast, which has suddenly appeared in Bangladesh in 2016 before spreading to neighboring India. In these Asian countries, wheat blast strains are now co-occurring with the destructive rice blast pathogen raising the possibility of genetic exchange between these destructive pathogens. We assessed the recently described MoT3 diagnostic assay and found that it did not distinguish between wheat and rice blast isolates from Bangladesh. The assay is based on primers matching the WB12 sequence corresponding to a fragment of the M. oryzae MGG_02337 gene annotated as a short chain dehydrogenase. These primers could not reliably distinguish between wheat and rice blast isolates from Bangladesh based on DNA amplification experiments performed in separate laboratories in Bangladesh and in the UK. In addition, comparative genomics of the WB12 sequence revealed a complex underlying genetic structure with related sequences across M. oryzae strains and in both rice and wheat blast isolates. We, therefore, caution against the indiscriminate use of this assay to identify wheat blast.

plant biology↗

bioRxiv2018

The Mechanical of Organic Acids Secreted by Roots of Tartary Buckwheat under the Effects of Low Nitrogen Stress

A pot experiment was conducted to study the effects of two different low nitrogen tolerant tartary buckwheat varieties (Diqing buckwheat (DQ, low nitrogen resistance) and Heifeng 1 (HF, low nitrogen sensitive) response mechanism of organic acids to low nitrogen stress. The results showed that the soil moisture of HF and DQ under low nitrogen treatment decreased 24.2% and 14.32%, respectively when compared with normal nitrogen treatment, and the water consumption of DQ was significantly higher than that of HF at seedling stage. Under low nitrogen treatment, the soil pH value of DQ was 1.44% and 8.44% lower than that of HF at seedling and flowering stages, respectively, the content of NH4+ in DQ soil was 8.2% lower than that of HF at maturity stage, the content of NO3- was significantly higher than that HF 49.2%, 12.9%, and 16.6% in each growth period, respectively. Split plot analysis showed that nitrogen treatment significantly affected the organic acids content in the soil of the buckwheat. The secretion content of organic acids are different among buckwheat cultivars under low nitrogen stress. In the soil of DQ, the content of malonic acid was higher than that of HF by 34.39% at maturity stage; the content of oxalic acid was respectively higher than that of HF by 24.86% and 24.52% at seedling and flowering stages; the content of propionic acid was significantly higher than that of HF by 7.36%, 9.44% and23.47% in each growth period, respectively; and tartaric acid acetic acid also showed the same trend at flowering and maturity stages. In summary, tartary buckwheat may regulate the nutrient availability of rhizosphere soil through the secretion of organic acids in the root system to cope with the low nitrogen stress environment. For the cultivation of tartary buckwheat on poor soil should consider the differences cultivaring barren resistance varieties to increase efficiency in the future.

plant biology↗

bioRxiv2018

GONST2 transports GDP-Mannose for sphingolipid glycosylation in the Golgi apparatus of Arabidopsis

The Golgi lumen is the site of many different glycosylation events, including cell wall polysaccharide biosynthesis and lipid glycosylation. Transporters are necessary for the import of the substrates required for glycosylation (nucleotide sugars) from the cytosol where they are synthesized. Plants use four GDP-linked sugars to glycosylate macromolecules: GDP-L-Fucose, GDP-D-Mannose, GDP-L-Galactose and GDP-D-Glucose. Of the predicted fifty-one members of the nucleotide sugar transporter/triose phosphate transporter family in Arabidopsis, only four appear to contain the conserved motif needed for the transport of GDP-linked sugars, GOLGI LOCALIZED NUCLEOTIDE SUGAR TRANSPORTER (GONST) 1-4. Previously, we have demonstrated that GONST1 provides GDP-D-Mannose for glycosylation of a class of sphingolipids, the glycosylinositolphosphorylceramides (GIPCs). Here, we characterize its closest homologue, GONST2, and conclude that it also specifically provides substrate for GIPC glycosylation. Expression of GONST2 driven by the GONST1 promoter is able to rescue the severe growth phenotype of gonst1. Loss of GONST2 exacerbates the gonst1 constitutive hypersensitive response, as well as the reduced cell wall cellulose content. The gonst2 mutant grows normally under standard conditions, but has enhanced resistance to the powdery mildew-causing fungus Golovinomyces orontii.

plant biology↗

bioRxiv2018

NADP-dependent malic enzyme 1 participates in the abscisic acid response in Arabidopsis thaliana

Arabidopsis thaliana possesses three cytosolic (NADP-ME1-3) and one plastidic (NADP-ME4) NADP-dependent malic enzymes. NADP-ME2 and-ME4 show constitutive expression, in contrast to NADP-ME1 and-ME3, which are restricted to particular tissues. Here, we show that NADP-ME1 transcript and protein were almost undetectable during normal vegetative growth, but gradually increased and reached levels higher than those of the other isoforms in the latest stages of seed development. Accordingly, in knockout nadp-me1 mature seeds the total NADP-ME activity was significantly lower than in wild type mature seeds. The phenotypic analysis of nadp-me1 plants indicated alterations of seed viability and germination. Besides, the treatment with abscisic acid (ABA), NaCl and mannitol specifically induced the accumulation of NADP-ME1 in seedlings. In line with this, nadp-me1 plants show a weaker response of primary and lateral root length and stomatal opening to the presence of ABA.\n\nThe results suggest that NADP-ME1 plays a specialized role, linked to ABA signalling during the seed development as well as in the response to saline and osmotic stress.

plant biology↗

bioRxiv2018

Effects of planting density on the growth and photosynthetic characteristics of Alternanthera philoxeroides under different nutrient conditions

Density and nutrient level are important factors that might affect the growth of invasive plants. To reveal the effects of plant density on the performance of invasive plant Alternanthera philoxeroides under different nutrient conditions, a greenhouse experiment was conducted in which A. philoxeroides was planted at three densities (low, medium and high) under three nutrient levels (low, medium and high). The results showed that both planting density and nutrient levels had significant effects on the growth of the plant. The biomass of individual plant and all plants in one pot under medium nutrient level were the highest while the photosynthetic rate and total chlorophyll content were the highest at the high nutrient level. Under different nutrient levels, the photosynthetic rate was the highest at medium planting density. The biomass of single plant decreased with the increase of population density, while the total biomass in the whole pot increased with the increase of density. These characteristics might contribute to the invasion of A. philoxeroides and help the plant to form monodominant community.

plant biology↗

bioRxiv2018

Plant aquaporins: the origin of NIPs

Many of the aquaporin genes in Cyanobacteria belong to the AqpN-clade. This clade was also the cradle of plant NIPs (nodulin-26 like intrinsic proteins) whose members are transporters for glycerol and several hydroxylated metalloids. The superphylum of Archaeplastida acquired the primordial NIP-gene most likely from the cyanobacterium that, some 1500 million years ago, became the ancestor of all plastids.

plant biology↗

bioRxiv2018

Polyploidy and elevation contribute to opposing latitudinal gradients in diversification and species richness in lady ferns (Athyriaceae)

O_LIIn ferns, the temperate-tropical sister clades Athyrium and Diplazium present an opportunity to study a latitudinal contrast in diversification dynamics.\nC_LIO_LIWe generated a taxonomically expanded molecular chronogram and used macroevolutionary models to analyze how diversification rates have changed through time, across lineages, and in concert with changes in elevation and ploidy. We tested a novel model of cladogenetic state-change in which polyploidy can arise as an infraspecific polymorphism, with diversification parameters distinct from those of pure diploids and polyploids.\nC_LIO_LIBoth Athyrium and Diplazium accelerated their diversification near the Oligocene-Miocene transition. In Diplazium, the rate shift is older, with subsequent net diversification somewhat slower and suggestive of diversity-dependence. In Athyrium, diversification is faster and associated with higher elevations. In both clades, polyploids have the highest rate of net accumulation but lowest (negative) net diversification, while the converse is true for polymorphic species; diploids have low rates of both net accumulation and diversification.\nC_LIO_LIDiversification in Athyrium may have responded to ecological opportunities in expanding temperate habitats during the Neogene, especially in mountains, while the pattern in Diplazium suggests saturation in the tropics. Neopolyploids are generated rapidly, primarily through accelerated cladogenesis in polymorphic species, but are evolutionary dead ends.\nC_LI

plant biology↗

bioRxiv2018

The genome and metabolome of the tobacco tree, Nicotiana glauca: a potential renewable feedstock for the bioeconomy

BackgroundGiven its tolerance to stress and its richness in particular secondary metabolites, the tobacco tree, Nicotiana glauca, has been considered a promising biorefinery feedstock that would not be competitive with food and fodder crops.\n\nResultsHere we present a 3.5 Gbp draft sequence and annotation of the genome of N. glauca spanning 731,465 scaffold sequences, with an N50 size of approximately 92 kbases. Furthermore, we supply a comprehensive transcriptome and metabolome analysis of leaf development comprising multiple techniques and platforms.\n\nThe genome sequence is predicted to cover nearly 80% of the estimated total genome size of N. glauca. With 73,799 genes predicted and a BUSCO score of 94.9%, we have assembled the majority of gene-rich regions successfully. RNA-Seq data revealed stage-and/or tissue-specific expression of genes, and we determined a general trend of a decrease of tricarboxylic acid cycle metabolites and an increase of terpenoids as well as some of their corresponding transcripts during leaf development.\n\nConclusionThe N. glauca draft genome and its detailed transcriptome, together with paired metabolite data, constitute a resource for future studies of valuable compound analysis in tobacco species and present the first steps towards a further resolution of phylogenetic, whole genome studies in tobacco.

plant biology↗

bioRxiv2018

IRON MAN, a ubiquitous family of peptides that control iron transport in plants

Iron (Fe) is an essential mineral nutrient which severely affects the growth, yield and nutritional quality of plants if not supplied in sufficient quantities. We here report that a short C-terminal amino acid sequence consensus motif (IRON MAN; IMA) conserved across numerous, highly diverse peptides in angiosperms, is essential for Fe uptake in plants. Overexpression of the IMA sequence in Arabidopsis induced Fe uptake genes in roots, causing accumulation of Fe and manganese in all plant parts including seeds. Silencing of all eight IMA genes harbored by the Arabidopsis genome abolished Fe uptake and caused severe chlorosis; increasing the Fe supply or overexpressing IMA1 restored the wild-type phenotype. IMA1 is predominantly expressed in the phloem, preferentially in leaves, and reciprocal grafting showed that IMA1 peptides in shoots positively regulate Fe uptake in roots. IMA homologs are highly responsive to the Fe status and functional wh ...

plant biology↗

bioRxiv2018

Ancestry of the two subgenomes of maize

Maize (Zea mays ssp. mays) is not only one of the worlds most important crops, but it also is a powerful tool for studies of genetics, genomics, and cytology. The genome of maize shows the unmistakable signature of an ancient hybridization event followed by whole genome duplication (allopolyploidy), but the parents of this event have been a mystery for over a century, since studies of maize cytogenetics began. Here we show that the whole genome duplication event preceded the divergence of the entire genus Zea and its sister genus Tripsacum. One genome was donated, in whole or in part, by a plant related to the modern African genera Urelytrum and Vossia, although genomic rearrangement has been extensive. The other genome donor is less well-supported, but may have been related to the modern Rottboellia-Hemarthria clade, which is also African. Thus Zea and Tripsacum together represent a New World radiation derived from African ancestors.

plant biology↗

bioRxiv2018

Three-dimensional refractive index distributions of individual angiosperm pollen grains

Three-dimensional (3D) refractive index (RI) imaging and quantitative analyses of angiosperm pollen grains are presented. Using optical diffraction tomography, the 3D RI structures of individual angiosperm pollen grains were measured without using labeling or other preparation techniques. Various physical quantities, including volume, surface area, exine volume, and sphericity, were determined from the measured RI tomograms of pollen grains. Exine skeletons, the distinct internal structures of angiosperm pollen grains, were identified and systematically analyzed.

plant biology↗

bioRxiv2018

Effects of different pretreatments on flavonoids and antioxidant activity of Dryopteris erythrosora leave

Flavonoids with wide bioactivity for medcine are vital secondary metabolite of plant. The factors influenced on flavonoids had been reported. However, as the key processes lead to metabolite alterations, the influences of the different pretreatments of samples on flavonoids and antioxidant activity of ferns were with little information. Therefore, Dryopteris erythrosora leaves were chosen as the materials for analyzing flavonoids alterations, which would not only provide the significant basic data for flavonoid metabolism of fern, but also for further developing fern resources. The results showed that a) The total flavonoids contents of D. erythrosora leaves with different pretreatments were obviously different. The total flavonoid contents of samples, which was dried in shade firstly and then dried at 75 {degrees}C in oven, finally smashed, was the highest (7.6%), but that of samples, which was quickly dried at 75 {degrees}C in oven directly after cleaning and then smashed, was the lowest (2.17%); b) Antioxidant activities of D. erythrosora leaves with different pretreatments were variant. Samples, which were dried in shade firstly and then dried at 75 {degrees}C in oven, finally smashed and samples which were firstly dried in the sun and then dried at 75 {degrees}C in oven, ultimately smashed, both showed stronger antioxidant activity; c) Total twenty-three flavonoids with four different pretreatments were tentatively identified by HPLC-ESI-TOF-MS. In conlusion, a) The influences of different pretreatments on flavonoids and antioxidant activity of D. erythrosora Leaves were obvious. b) The best pretreatment in respect to conserving fern medical application was drying in shade firstly and then drying at 75 {degrees}C in oven, finally smashed.

plant biology↗

bioRxiv2018

Light dynamically regulates growth rate and cellular organisation of the Arabidopsis root meristem.

1Large-scale methods and robust algorithms are needed for a quantitative analysis of cells status/geometry in situ. It allows the understanding the cellular mechanisms that direct organ growth in response to internal and environmental cues. Using advanced whole-stack imaging in combination with pattern analysis, we have developed a new approach to investigate root zonation under different dark/light conditions. This method is based on the determination of 3 different parameters: cell length, cell volume and cell proliferation on the cell-layer level. This method allowed to build a precise quantitative 3D cell atlas of the Arabidopsis root tip. Using this approach we showed that the meristematic (proliferation) zone length differs between cell layers. Considering only the rapid increase of cortex cell length to determine the meristematic zone overestimates of the proliferation zone for epidermis/cortex and underestimates it for pericycle. The use of cell volume instead of cell length to define the meristematic zone correlates better with cell proliferation zone.

plant biology↗

bioRxiv2018

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight candidate host target genes associated with quantitative disease resistance

Plant pathogenic fungi secrete effector proteins and secondary metabolites to cause disease. Additionally, some produce small RNAs (sRNAs) that silence transcripts of host immunity genes through RNA interference. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about its molecular interactions with its hosts. In particular, the role of sRNAs in S. sclerotiorum pathogenicity has not been determined. By sequencing sRNAs in vitro and during infection of two host species, we found that S. sclerotiorum produces at least 374 highly abundant sRNAs. These sRNAs mostly originated from polymorphic repeat-rich genomic regions. Predicted gene targets of these sRNAs, from 10 different host species, were enriched for immunity-related functional domains. Predicted A. thaliana gene targets of S. sclerotiorum sRNAs were significantly more down-regulated during infection than other genes. A. thaliana gene targets were also more likely to contain single nucleotide polymorphisms (SNPs) associated with quantitative disease resistance. In conclusion, sRNAs produced by S. sclerotiorum are likely capable of silencing immunity components in multiple hosts. Prediction of fungal sRNA targets in host plant genomes can be combined with other global approaches, such as genome wide association studies and transcriptomics, to assist identification of plant genes involved in disease resistance.

plant biology↗

bioRxiv2018

Development of reduced gluten wheat enabled by determination of the genetic basis of the lys3a low hordein barley mutant

Celiac disease is the most common food-induced enteropathy in humans with a prevalence of approximately 1% world-wide [1]. It is induced by digestion-resistant, proline- and glutamine-rich seed storage proteins, collectively referred to as \"gluten,\" found in wheat. Related prolamins are present in barley and rye. Both celiac disease and a related condition called non-celiac gluten sensitivity (NCGS) are increasing in incidence [2] [3]. This has prompted efforts to identify methods of lowering gluten in wheat, one of the most important cereal crops. Here we used BSR-seq (Bulked Segregant RNA-seq) and map-based cloning to identify the genetic lesion underlying a recessive, low prolamin mutation (lys3a) in diploid barley. We confirmed the mutant identity by complementing the lys3a mutant with a transgenic copy of the wild type barley gene and then used TILLING (Targeting Induced Local Lesions in Genomes) [4] to identify induced SNPs (Single Nucleotide Polymorphisms) in the three homoeologs of the corresponding wheat gene. Combining inactivating mutations in the three sub-genomes of hexaploid bread wheat in a single wheat line lowered gliadin and low molecular weight glutenin accumulation by 50-60% and increased free and protein-bound lysine by 33%. This is the first report of the combination of mutations in homoeologs of a single gene that reduces gluten in wheat.

plant biology↗

bioRxiv2018

Scarification of Exotic and Indigenous Plant Seeds in Nigeria: Effect on Dormancy and Germination

Dormancy is exhibited in many seed producing plants. It could be endogenous or exogenous, depending on the plant and the type of seed the plant produce. A survival strategy, plant use to conserve their genetic materials during unfavourable conditions. Scarification treatments has been used in this work to break the dormancy of Anacardium occidentale, Annona muricata, Jatropha curcas, Tamarindus indica and Artocarpus heterophyllus using 65% Nitric acid (HNO3), 65% Sulphuric acid (H2SO4), 0.5% Potassium tetraoxosulphate(VI) (K2SO4), 0.5% Urea (CH4N2O), 43% Ethanol (C2H6O) and Distilled water. Nitric acid (65% HNO3) produced the best result for Anacardium occidentale with high numbers of seedlings and a germination period of 15 days. Jatropha curcas did not produce a favourable result from the treatments. Tamarindus indica, water treatment produced the best result with six days of germination shorter than the controlled value (16 days). Nitric acid (65% HNO3) and water favor Annona muricata with germination period of 19 days as against 24 days for control experiment. Water and Potassium sulphate are the best treatments for Artocarpus heterophyllus as they produce viable seedlings with short germination period of 14 and 15 days which give a good result better than the 18 days of the control experiment.

plant biology↗