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Results for “Plant Biology”

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bioRxiv2019

Reallocation to lateral and early-emerging axial roots allows maize (Zea mays L.) with reduced nodal root number to more efficiently forage for nitrate

Previous simulations indicated reduced nodal root number (NRN) was promising for maize (Zea mays L.) breeding, and were partially confirmed using variation in NRN among inbreds. However, the exact mechanism was unknown, therefore manipulative experiments were conducted in hydroponics and tall solid-media mesocosms with treatments involving no nodal root excision (0% NRE) or excising either 33% or 67% of the nodal roots (NR) as they emerged under high or low levels of nitrogen (N). Reduced NRN was hypothesized to increase elongation of all remaining root classes, increase N acquisition under low N, and increase shoot mass. In both experiments, plants with 67% NRE had 12% and 19% less root fraction of total biomass, 61% and 91% greater lateral-to-axial root length ratio regardless of N levels; and 61% and 182% greater biomass of embryonic roots under low N, compared to 0% NRE for hydroponics and mesocosms studies, respectively. In hydroponics, regardless of NRE level, specific root respiration under high N was 2.6 times of low N, and was greatest at depth. Under low N in mesocosms, plants with 67% NRE had 52% greater shoot biomass, 450% greater root length at depth, and 232% greater deep-injected 15N content in the shoot relative to 0% NRE, however biomass in hydroponics did not differ based on NRE. These results reveal the mechanism by which plants with fewer nodal roots increase N capture and shoot mass by reallocation of biomass to lateral, embryonic, and first whorl nodal roots that increases foraging efficiency in solid media. SummaryReallocating root biomass from nodal roots to lateral and early-emerging axial roots allows grasses to capture more nitrogen under limiting conditions, including by increasing foraging at depth.

plant biology↗

bioRxiv2019

Soybean Haplotype Map (GmHapMap): A Universal Resource for Soybean Translational and Functional Genomics

Here we describe the first worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 Glycine max accessions and yielding 15 million variants. The number of unique haplotypes plateaued within this collection (4.3 million tag SNPs) suggesting extensive coverage of diversity within the cultivated germplasm. We imputed GmHapMap variants onto 21,618 previously genotyped (50K array/210K GBS) accessions with up to 96% success for common alleles. A GWAS performed with imputed data enabled us to identify a causal SNP residing in the NPC1 gene and to demonstrate its role in controlling seed oil content. We identified 405,101 haplotypes for the 55,589 genes and show that such haplotypes can help define alleles. Finally, we predicted 18,031 putative loss-of-function (LOF) mutations in 10,662 genes and illustrate how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for soybean genomics and breeding.

plant biology↗

bioRxiv2019

Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

mRNA translation is a critical step in gene expression, but our understanding of the landscape and control of translation in diverse crops remains lacking. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato roots. Taking advantage of the 3-nucleotide periodicity displayed by translating ribosomes, we identified 354 novel small ORFs (sORFs) translated from previously unannotated transcripts, as well as 1329 upstream ORFs (uORFs) translated within the 5 UTRs of annotated protein-coding genes. Proteomic analysis confirmed that some of these novel uORFs and sORFs generate stable proteins in planta. Compared with the annotated ORFs, the uORFs use more flexible Kozak sequences around translation start sites. Interestingly, uORF-containing genes are enriched for protein phosphorylation/dephosphorylation and signaling transduction pathways, suggesting a regulatory role for uORFs in these processes. We also demonstrated that ribosome profiling is useful to facilitate the annotation of translated ORFs and noncanonical translation initiation sites. In addition to defining the translatome, our results revealed the global control of mRNA translation by uORFs and microRNAs in tomato. In summary, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved translational features, and identifies new regulatory mechanisms hidden in a crop genome. SignificanceSeveral studies have shown that altering mRNA translation is a powerful way of improving crop performance. However, due to limited genomic resources and methods, translational regulation remains poorly understood in crops. By leveraging de novo transcriptome assembly and ribosome profiling, we mapped and quantified translating ribosomes across the entire transcriptome in tomato roots. This is the first experiment-based survey to systematically identify actively translated ORFs in a crop. Our results reveal numerous unannotated translation events and uncover new regulatory mechanisms of gene expression in tomato. Our approach not only facilitates our understanding of the tomato translational landscape but also provides a practical strategy to study the translatomes of other species. O_LIThe raw RNA-seq and Ribo-seq data have been deposited in the Gene Expression Omnibus (GEO) database under accession no. GSE124962. C_LIO_LIProteomics raw data files and MaxQuant Search results have been deposited at the MassIVE repository with dataset identifier: MSV000083363. C_LI

plant biology↗

bioRxiv2019

The systemin signaling cascade as derived from phosphorylation time courses under stimulation by systemin and its inactive Thr17Ala (A17) analog

Systemin is a small peptide with important functions in plant wound response signaling. Although transcriptional responses of systemin action are well described, the precise signaling cascades involved in its perception and signal transduction are poorly understood at the protein level. Here we use a phosphoproteomic profiling study involving stimulation time courses with systemin and its inactive analogon A17 to reconstruct a systemin-specific kinase/phosphatase signaling network. The time course analysis of systemin-induced phosphorylation patterns revealed early events at the plasma membrane, such dephosphorylation of H+-ATPase, rapid phosphorylation of NADPH-oxidase and Ca2+-ATPase. Later responses involved transient phosphorylation of small GTPases and vesicle trafficking proteins, as well as transcription factors. Based on a correlation analysis of systemin-specific phosphorylation profiles, we predict substrate candidates for 56 systemin specific kinases and 18 phosphatases. Among the kinases are several systemin-specific receptor kinases as well as kinases with downstream signaling functions, such as MAP-kinases. A regulatory circuit for plasma membrane H+-ATPase was predicted and confirmed by in-vitro activity assays. In this regulatory model we propose that upon systemin treatment, H+-ATPase LHA1 is rapidly de-phosphorylated at its C-terminal regulatory residue T955 by phosphatase PLL5, resulting in the alkalization of the growth medium within 2 minutes of systemin treatment. We further propose that the H+-ATPase LHA1 is re-activated by MAP-Kinase MPK2 later in the systemin response. MPK2 was identified with increased phosphorylation at its activating TEY-motif at 15 minutes of treatment and the predicted interaction with LHA1 was confirmed by in-vitro kinase assays. Our data set provides a valuable resource of proteomic events involved in the systemin signaling cascade with a focus on predictions of substrates to systemin-specific kinases and phosphatases.

plant biology↗

bioRxiv2019

The striking flower-in-flower phenotype of Arabidopsis thaliana Nossen (No-0) is caused by a novel LEAFY allele

SummaryThe transition to reproduction is a crucial step in the life cycle of any organism. In Arabidopsis thaliana the establishment of reproductive growth can be divided into two phases: In the first phase, cauline leaves with axillary meristems are formed and internode elongation begins. In the second phase, lateral meristems develop into flowers with defined organs. Floral shoots are usually determinate and suppress the development of lateral shoots. Here, we describe a Ds transposon insertion mutant in the Nossen (No-0) accession with severe defects in floral development and flower morphology. The most striking aspect is the outgrowth of stems from the axillary bracts of the primary flower carrying terminal secondary flowers. Therefore, we named this mutant flower-in-flower (fif). However, the insertion of the transposon in the annotated gene is not responsible for the fif phenotype. By means of classical and genome sequencing-based mapping, the mutation responsible for the fif phenotype was found to be in the LEAFY (LFY) gene. The mutation, a G-to-A exchange in the second exon of LFY, creates a novel lfy allele and causes a cysteine-to-tyrosine exchange in the 1-helix of the LFY DNA-binding domain. Whereas subcellular localization and homomerization are not affected, the DNA-binding of LFYFIF is abolished. We propose that the amino acid exchange interferes with the cooperative binding of LFY to its target DNA. To generate the strong fif phenotype, LFYFIF may act dominant-negatively by either forming non-binding LFY/LFYFIF heteromers or by titrating out the interaction partners, required for LFY function as transcription factor. Significant StatementThe fif phenotype of Arabidopsis thaliana No-0 is caused by a novel allele of the LEAFY gene

plant biology↗

bioRxiv2019

Maturity2, a novel regulator of flowering time in Sorghum bicolor, increases expression of SbPRR37 and SbCO in long days delaying flowering

Sorghum bicolor is a drought-resilient facultative short-day C4 grass that is grown for grain, forage, and biomass. Adaptation of sorghum for grain production in temperate regions resulted in the selection of mutations in Maturity loci (Ma1 - Ma6) that reduced photoperiod sensitivity and resulted in earlier flowering in long days. Prior studies identified the genes associated with Ma1 (PRR37), Ma3 (PHYB), Ma5 (PHYC) and Ma6 (GHD7) and characterized their role in the flowering time regulatory pathway. The current study focused on understanding the function and identity of Ma2. Ma2 delayed flowering in long days by selectively enhancing the expression of SbPRR37 (Ma1) and SbCO, genes that co-repress the expression of SbCN12, a source of florigen. Genetic analysis identified epistatic interactions between Ma2 and Ma4 and located QTL corresponding to Ma2 on SBI02 and Ma4 on SBI10. Positional cloning and whole genome sequencing identified a candidate gene for Ma2, Sobic.002G302700, which encodes a SET and MYND (SYMD) domain lysine methyltransferase. Nine sorghum genotypes previously identified as recessive for Ma2 contained the mutated version of Sobic.002G302700 present in 80M (ma2).

plant biology↗

bioRxiv2019

\"Low-cost\" initial burst of root development in whole Fagus crenata seedlings: The key to survival?

Terrestrial plants are rooted in one place, and therefore their metabolism must be flexible to adapt to continuously changing environments. This flexibility is probably influenced by the divergent metabolic traits of plant organs. However, direct measurements on organ-specific metabolic rates are particularly scarce and little is known about their roles in determining whole-individual meatabolism. To reveal this on seedlings of Fagus crenata, which is one of the most widespread dominant genus in temperate deciduous broad leaf forests in the circum-polar Northern Hemisphere, we measured respiration, fresh mass and surface area for total leaves, stems and roots of 55 individuals in two years from germination and analyzed their relationships with individual metabolism. Proportion of roots to whole plant in mass increased from approximately 17% to 74%, and that in surface area increased from about 11% to 82% in the two years. Nonetheless, the increment of the proportion of root respiration to whole-plant respiration was from 9.2% to only 40%, revealing that the increment in mass and surface area of roots was much larger than the increment in energetic cost. As a result, only the roots showed a substantial decline in both respiration/surface area and respiration/mass among the three organs; roots had about 90% decline in their respiration/surface area, and 84% decline in their respiration/mass, while those in leaves and stems were relatively constant. The low-cost and rapid root development is specific to the two years after germination and would be effective for avoiding water and nutrient deficit, and possibly helps seedling survival. This drastic shift in structure and function with efficient energy use in developmental change from seeds to seedlings may underpin the establishment of F. crenata forests. We discuss significance of lowering energetic cost for various individual organisms to effectively acquire resources from a wide perspective of view.

plant biology↗

bioRxiv2019

Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize

Rapid development and adoption of biofortified, provitamin A-dense orange maize (Zea mays L.) varieties could be facilitated by a greater understanding of the natural variation underlying kernel color, including as relates to carotenoid biosynthesis and retention in maize grain. Greater abundance of carotenoids in maize kernels is generally accompanied by deeper orange color, useful for distinguishing provitamin A-dense varieties to consumers. While kernel color can be scored and selected with high-throughput, low-cost phenotypic methods within breeding selection programs, it remains to be well established as to what would be the logical genetic loci to target for selection for kernel color. We conducted a genome-wide association study of maize kernel color, as determined by colorimetry, in 1,651 yellow and orange inbreds from the Ames maize inbred panel. Associations were found with y1, encoding the first committed step in carotenoid biosynthesis, and with dxs2, which encodes the enzyme responsible for the first committed step in the biosynthesis of the isoprenoid precursors of carotenoids. These genes logically could contribute to overall carotenoid abundance and thus kernel color. The lcyE and zep1 genes, which can affect carotenoid composition, were also found to be associated with colorimeter values. A pathway-level analysis, focused on genes with a priori evidence of involvement in carotenoid biosynthesis and retention, revealed associations for dxs3 and dmes1, involved in isoprenoid biosynthesis; ps1 and vp5, within the core carotenoid pathway; and vp14, involved in cleavage of carotenoids. Collectively, these identified genes appear relevant to the accumulation of kernel color.

plant biology↗

bioRxiv2019

Turning a green alga red: engineering astaxanthin biosynthesis by intragenic pseudogene revival in Chlamydomonas reinhardtii.

The green alga Chlamydomonas reinhardtii does not synthesize high-value ketocarotenoids like canthaxanthin and astaxanthin, however, a {beta}-carotene ketolase (CrBKT) can be found in its genome. CrBKT is poorly expressed, contains a long C-terminal extension not found in homologues and likely represents a pseudogene in this alga. Here, we used synthetic re-design of this gene to enable its constitutive overexpression from the nuclear genome of C. reinhardtii. Overexpression of the optimized CrBKT extended native carotenoid biosynthesis to generate ketocarotenoids in the algal host causing noticeable changes the green algal colour to a reddish-brown. We found that up to 50% of native carotenoids could be converted into astaxanthin and more than 70% into other ketocarotenoids by robust CrBKT overexpression. Modification of the carotenoid metabolism did not impair growth or biomass productivity of C. reinhardtii, even at high light intensities. Under different growth conditions, the best performing CrBKT overexpression strain was found to reach ketocarotenoid productivities up to 4.5 mg L-1 day-1. Astaxanthin productivity in engineered C. reinhardtii shown here is competitive with that reported for Haematococcus lacustris (formerly pluvialis) which is currently the main organism cultivated for industrial astaxanthin production. In addition, the extractability and bio-accessibility of these pigments was much higher in cell wall deficient C. reinhardtii than the resting cysts of H. lacustris. Engineered C. reinhardtii strains could thus be a promising alternative to natural astaxanthin producing algal strains and may open the possibility of other tailor-made pigments from this host.

plant biology↗

bioRxiv2019

The Arabidopsis thaliana pan-NLRome

Disease is both among the most important selection pressures in nature and among the main causes of yield loss in agriculture. In plants, resistance to disease is often conferred by Nucleotide-binding Leucine-rich Repeat (NLR) proteins. These proteins function as intracellular immune receptors that recognize pathogen proteins and their effects on the plant. Consistent with evolutionarily dynamic interactions between plants and pathogens, NLRs are known to be encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define the majority of the Arabidopsis thaliana species-wide "NLRome". From NLR sequence enrichment and long-read sequencing of 65 diverse A. thaliana accessions, we infer that the pan-NLRome saturates with approximately 40 accessions. Despite the high diversity of NLRs, half of the pan-NLRome is present in most accessions. We chart the architectural diversity of NLR proteins, identify novel architectures, and quantify the selective forces that act on specific NLRs, domains, and positions. Our study provides a blueprint for defining the pan-NLRome of plant species.

plant biology↗

bioRxiv2019

Effectiveness of Genomic Selection by Response to Selection for Winter Wheat Variety Improvement

The genomic revolution opened up the possibility for predicting un-tested phenotypes in schemes commonly referred as genomic selection (GS). Considering the practicality of applying GS in the line development stage of a hard red winter (HRW) wheat variety development program (VDP), effectiveness of GS was evaluated by prediction accuracy, as well as by the response to selection across field seasons that demonstrated challenges for crop improvement under significant climate variability. Important breeding targets for HRW wheat improvement in the southern Great Plains of USA, including Grain Yield, Kernel Weight, Wheat Protein content, and Sodium Dodecyl Sulfate (SDS) Sedimentation Volume as a rapid test for predicting bread-making quality, were used to estimate GSs effectiveness across harvest years from 2014 (drought) to 2016 (normal). In general, nonparametric algorithms RKHS and RF produced higher accuracies in both same-year/environment cross validations and cross-year/environment predictions, for the purpose of line selection in this bi-parental doubled haploid (DH) population. Further, the stability of GS performance was greatest for SDS Sedimentation Volume but least for Wheat Protein content. To ensure long-term genetic gain, our study on selection response suggested that across this sample of environmental variability, and though there are cases where phenotypic selection (PS) might be still preferential, training conducted under drought stress or in suboptimal conditions could still provide an encouraging prediction outcome, when selection decisions were made in normal conditions. However, it is not advisable to use training information collected from a normal field season to predict trait performance under drought conditions. Further, the superiority of response to selection was most evident if the training population can be optimized. Core IdeasO_LIPrediction performance for winter wheat grain yield and end-use quality traits. C_LIO_LIPrediction accuracy evaluated by cross validations significantly overestimated. C_LIO_LINon-parametric algorithms outperform, when considering cross-year predictions. C_LIO_LIStrategically designing training population improves response to selection. C_LIO_LIResponse to selection varied across growing seasons/environments. C_LI

plant biology↗

bioRxiv2019

Conservation of N-hydroxy-pipecolic acid-mediated systemic acquired resistance in crop plants

Signal propagation and the coordination of whole-organism responses in plants rely heavily on small molecules. Systemic acquired resistance (SAR) is one such process in which long-distance signaling activates immune responses in uninfected tissue as a way to limit the spread of a primary, localized infection. Recently, N-hydroxy pipecolic acid (NHP) was discovered and shown to coordinate SAR in Arabidopsis. Here, we provide metabolic and biochemical evidence that NHP is conserved across the plant kingdom and demonstrate a role for NHP in mediating SAR responses in tomato and pepper. We reconstituted the NHP biosynthetic pathway in planta and show that transient expression of two NHP biosynthetic genes in tomato induces enhanced resistance to a bacterial pathogen in distal tissue. Our results suggest engineering strategies to induce NHP-mediated SAR are a promising route to improve broad-spectrum pathogen resistance in crops. IN BRIEFEngineering NHP production is a promising strategy to enhance disease resistance in crops. HIGHLIGHTSO_LIArabidopsis N-hydroxy-pipecolic acid (NHP) pathway is conserved across the plant kingdom C_LIO_LIApplication of NHP to tomato and pepper plants induces a robust SAR response C_LIO_LIMetabolic engineering of the Arabidopsis NHP pathway in Solanum lycopersicum leads to enhanced NHP production and defense priming C_LIO_LIGenetic engineering for enhanced NHP production is a promising strategy to protect crop plants from multiple pathogens C_LI

plant biology↗

bioRxiv2019

A novel QTL conferring Fusarium crown rot resistance located on chromosome arm 6HL in barley

Fusarium crown rot (FCR), caused primarily by Fusarium pseudograminearum, is a devastating disease for cereal production in semi-arid regions worldwide. To identify and characterize loci conferring FCR resistance, we assessed a landrace AWCS799 which is among the top lines identified from a screening. Genetic control of its resistance was investigated by generating and analysing two populations of recombinant inbred lines. One of the populations was used for QTL detection and the other for validation. A novel QTL, located on the long arm of chromosome 6H (designated as Qcrs.caf-6H), was consistently detected in each of the four trials conducted against the mapping population. The QTL explained up to 29.1% of the phenotypic variance and its effect was confirmed in the validation population. Significant interactions between this resistance locus and either plant height or heading date were not detected, further facilitating its manipulation in breeding programs. Key MessageThis study identified and validated a novel and large-effect QTL conferring Fusarium crown rot resistance on the long arm of chromosome 6HL in barley.

plant biology↗

bioRxiv2019

A Stomata Classification and Detection System in Microscope Images of Maize Cultivars

Research on stomata, i.e., morphological structures of plants, has increased in popularity in the last years. These structures (pores) are in charge of the interaction between the internal plant system and the environment, working on different processes such as photosynthesis and transpiration stream. Besides, a better understanding of the pore mechanism plays a significant role when exploring the evolution process, as well as the behavior of plants. Although the study of stomata in dicots species of plants has advanced considerably in the past years, there is little information about stomata of cereal grasses. Also, automated detection of these structures have been considered in the literature, but some gaps are still uncovered. This fact is motivated by high morphological variation of stomata and the presence of noise from the image acquisition step. In this work, we propose a new methodology for automatic stomata classification and a new detection system in microscope images for maize cultivars. We have achieved an approximated accuracy of 97.1% in the identification of stomata regions using classifiers based on deep learning features, which figures out as a nearly perfect classification system.

plant biology↗

bioRxiv2019

DNA Nanostructures Coordinate Gene Silencing in Mature Plants

Plant bioengineering may generate high yielding and stress-resistant crops amidst a changing climate and a growing global population (1-3). However, delivery of biomolecules to plants relies on Agrobacterium infection (4) or biolistic particle delivery (5), the former of which is only amenable to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall which is absent in mammalian cells and poses the dominant physical barrier to exogenous biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells, however, nanoparticle-mediated delivery remains unexplored for passive biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver small interfering RNAs (siRNAs), and effectively silence a constitutively-expressed gene in Nicotiana benthamiana leaves. We show that nanostructure internalization into plant cells and the corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies, but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures, and details both the design parameters of importance for plant cell internalization, and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.

plant biology↗

bioRxiv2019

OsCYP71D8L as a key regulator involved in growth and stress response by mediating gibberellins and cytokinins homeostasis in rice

Phytohormones are pivotal in the regulation of plant growth and development, and acclimation to adverse environments. Multiple cytochrome P450 monooxygenases (CYP450s) are involved in the biosynthesis and catabolism of phytohormones. Here, we reported that a CYP450 member of CYP71 clan, OsCYP71D8L, participated in the control of multiple agronomic traits and abiotic stress responses by affecting gibberellin (GA) and cytokinin (CK) homeostasis in rice. We found that its gain-of-function mutant (cyp71d8l) and transgenic plants overexpressing OsCYP71D8L (OsCYP71D8L-OE) displayed similar phenotypes such as dwarfed plant, reduced panicle length and grain number per panicle. In OsCYP71D8L-OE seedlings, endogenous GAs and CKs was notably decreased and increased as compared with wild type (WT), respectively. Correspondingly, the dwarfed plant and less developed root of cyp71d8l and OsCYP71D8L-OE seedlings could be rescued by exogenous GA3, but more exacerbated by exogenous 6-BA. Importantly, cyp71d8l and OsCYP71D8L-OE seedlings maintained high chlorophyll contents and low reactive oxygen species level, and showed significantly enhanced tolerances to drought and high salt compared with WT. Thus, our results suggest that OsCYP71D8L plays roles in regulating rice growth and stress responses by coordinating GAs and CKs homeostasis, and it is useful to engineer stress-tolerant rice.

plant biology↗

bioRxiv2019

Genome-wide expression analysis identifies core components during iron starvation in hexaploid wheat

Iron is one of essential micronutrient for all organisms. Its deficiency causes a severe loss in crops yield. Nevertheless, our current understanding on major crops response to Fe deficiency remains limited. Herein, we investigated the effect of Fe deprivation at both transcriptomic and metabolic levels in hexaploid wheat. A genome-wide gene expression reprogramming was observed with a total of 5854 genes showing differential expression in roots of wheat subjected to Fe-starved medium. Subsequent, analysis revealed a predominance of strategy-II mode of Fe uptake, with induced genome bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc-induced facilitator-like protein was noticed. Our transcriptomic data were in agreement with the GC-MS analysis that showed an enhancement of accumulation of various metabolites such as fumarate, malonate, succinate and xylofuranose, which could be linked for enhancing Fe-mobilization. Interestingly, Fe starvation causes a significant temporal increase of glutathione-S-transferase both at transcriptional and enzymatic activity, which indicate the important role of glutathione in the response to Fe starvation in wheat roots. Taken together, our result provides new insight on wheat response to Fe starvation and lays foundation to design strategies to improve Fe nutrition in crops.

plant biology↗

bioRxiv2019

A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana

Field-grown plants have variable exposure to sunlight as a result of shifting cloud-cover, seasonal changes, canopy shading, and other environmental factors. As a result, they need to have developed a method for dissipating excess energy obtained from periodic excessive sunlight exposure. Non-photochemical quenching (NPQ) dissipates excess energy as heat, however the physical and molecular genetic mechanics of NPQ variation are not understood. In this study, we investigated the genetic loci involved in NPQ by first growing different Arabidopsis thaliana accessions in local and seasonal climate conditions, then measured their NPQ kinetics through development by chlorophyll fluorescence. We used genome-wide association studies (GWAS) to identify 15 significant quantitative trait loci (QTL) for a range of photosynthetic traits, including a QTL co-located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS promoter regions of the functional haplotypes and a significant difference in PsbS protein concentration. These findings parallel studies in rice showing recurrent regulatory evolution of this gene. The variation in the PSBS promoter and the changes underlying other QTLs could give insight to allow manipulations of NPQ in crops to improve their photosynthetic efficiency and yield. B.P. & J.B. conceived the project; B.P., J.B., P.W. and T.R. designed the research plan and analysis; P.W. supervised the experiments; T.R. performed most of the experiments and analysis; P.G., T.S., A.A. & E.A. designed and undertook experimental design, experiments and analysis for Figure 4; R.C. did the GWAS analysis; P.W., T.R. & A.A. wrote the article with contributions of all the authors. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/539379v1_fig4.gif" ALT="Figure 4"> View larger version (57K): org.highwire.dtl.DTLVardef@12ba2f9org.highwire.dtl.DTLVardef@1d88c15org.highwire.dtl.DTLVardef@1d4f21eorg.highwire.dtl.DTLVardef@16396aa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4:C_FLOATNO (A-D) Coverage tracks of the PSBS genomic regions from five low NPQ (A and B) and five high NPQ (C and D) Arabidopsis accessions aligned with the TAIR 10 Col-0 reference genome (low NPQ accession; A and C) and KBS-Mac-74 genome (high NPQ accession; B and D). Values along x-axes indicate the base pair distance relative to the PSBS transcription start site. Genes along the track are coloured green and the intergenic region is coloured pink. (E) Graphical view of the alignment of the TAIR 10 Col-0 and the KBS-Mac-74 PSBS genomic regions. Axis values refer to base pair positions within the respective tracks. (F) Comparison of the average relative PsbS protein abundance between low and high NPQ accessions. Error bars represent standard deviations. N=30; *** P < 0.001 with paired Students T test. C_FIG

plant biology↗