Publications by authors named "Mark G Aarts"

72 Publications

Isotopic signatures reveal zinc cycling in the natural habitat of hyperaccumulator Dichapetalum gelonioides subspecies from Malaysian Borneo.

BMC Plant Biol 2021 Sep 27;21(1):437. Epub 2021 Sep 27.

Industry Environments Program, CSIRO Land and Water, Environmental Assessment and Technologies, Adelaide, South Australia, Australia.

Background: Some subspecies of Dichapetalum gelonioides are the only tropical woody zinc (Zn)-hyperaccumulator plants described so far and the first Zn hyperaccumulators identified to occur exclusively on non-Zn enriched 'normal' soils. The aim of this study was to investigate Zn cycling in the parent rock-soil-plant interface in the native habitats of hyperaccumulating Dichapetalum gelonioides subspecies (subsp. pilosum and subsp. sumatranum). We measured the Zn isotope ratios (δZn) of Dichapetalum plant material, and associated soil and parent rock materials collected from Sabah (Malaysian Borneo).

Results: We found enrichment in heavy Zn isotopes in the topsoil (δZn 0.13 ‰) relative to deep soil (δZn -0.15 ‰) and bedrock (δZn -0.90 ‰). This finding suggests that both weathering and organic matter influenced the Zn isotope pattern in the soil-plant system, with leaf litter cycling contributing significantly to enriched heavier Zn in topsoil. Within the plant, the roots were enriched in heavy Zn isotopes (δZn ~ 0.60 ‰) compared to mature leaves (δZn ~ 0.30 ‰), which suggests highly expressed membrane transporters in these Dichapetalum subspecies preferentially transporting lighter Zn isotopes during root-to-shoot translocation. The shoots, mature leaves and phloem tissues were enriched in heavy Zn isotopes (δZn 0.34-0.70 ‰) relative to young leaves (δZn 0.25 ‰). Thisindicates that phloem sources are enriched in heavy Zn isotopes relative to phloem sinks, likely because of apoplastic retention and compartmentalization in the Dichapetalum subspecies.

Conclusions: The findings of this study reveal Zn cycling in the rock-soil-plant continuum within the natural habitat of Zn hyperaccumulating subspecies of Dichapetalum gelonioides from Malaysian Borneo. This study broadens our understanding of the role of a tropical woody Zn hyperaccumulator plant in local Zn cycling, and highlights the important role of leaf litter recycling in the topsoil Zn budget. Within the plant, phloem plays key role in Zn accumulation and redistribution during growth and development. This study provides an improved understanding of the fate and behaviour of Zn in hyperaccumulator soil-plant systems, and these insights may be applied in the biofortification of crops with Zn.
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http://dx.doi.org/10.1186/s12870-021-03190-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8474765PMC
September 2021

Quantification of spatial metal accumulation patterns in Noccaea caerulescens by X-ray fluorescence image processing for genetic studies.

Plant Methods 2021 Aug 3;17(1):86. Epub 2021 Aug 3.

Laboratory of Genetics, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands.

Background: Hyperaccumulation of trace elements is a rare trait among plants which is being investigated to advance our understanding of the regulation of metal accumulation and applications in phytotechnologies. Noccaea caerulescens (Brassicaceae) is an intensively studied hyperaccumulator model plant capable of attaining extremely high tissue concentrations of zinc and nickel with substantial genetic variation at the population-level. Micro-X-ray Fluorescence spectroscopy (µXRF) mapping is a sensitive high-resolution technique to obtain information of the spatial distribution of the plant metallome in hydrated samples. We used laboratory-based µXRF to characterize a collection of 86 genetically diverse Noccaea caerulescens accessions from across Europe. We developed an image-processing method to segment different plant substructures in the µXRF images. We introduced the concentration quotient (CQ) to quantify spatial patterns of metal accumulation and linked that to genetic variation.

Results: Image processing resulted in automated segmentation of µXRF plant images into petiole, leaf margin, leaf interveinal and leaf vasculature substructures. The harmonic means of recall and precision (F1 score) were 0.79, 0.80, 0.67, and 0.68, respectively. Spatial metal accumulation as determined by CQ is highly heritable in Noccaea caerulescens for all substructures, with broad-sense heritability (H) ranging from 76 to 92%, and correlates only weakly with other heritable traits. Insertion of noise into the image segmentation algorithm barely decreases heritability scores of CQ for the segmented substructures, illustrating the robustness of the trait and the quantification method. Very low heritability was found for CQ if randomly generated substructures were compared, validating the approach.

Conclusions: A strategy for segmenting µXRF images of Noccaea caerulescens is proposed and the concentration quotient is developed to provide a quantitative measure of metal accumulation pattern, which can be used to determine genetic variation for such pattern. The metric is robust to segmentation error and provides reliable H estimates. This strategy provides an avenue for quantifying XRF data for analysis of the genetics of metal distribution patterns in plants and the subsequent discovery of new genes that regulate metal homeostasis and sequestration in plants.
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http://dx.doi.org/10.1186/s13007-021-00784-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336263PMC
August 2021

Arabidopsis bZIP19 and bZIP23 act as zinc sensors to control plant zinc status.

Nat Plants 2021 02 16;7(2):137-143. Epub 2021 Feb 16.

Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark.

Zinc (Zn) is an essential micronutrient for plants and animals owing to its structural and catalytic roles in many proteins. Zn deficiency affects around 2 billion people, mainly those who live on plant-based diets relying on crops from Zn-deficient soils. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms involving Zn uptake, distribution and storage, but evidence of how they sense Zn status is lacking. Here, we use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, function as Zn sensors by binding Zn ions to a Zn-sensor motif. Deletions or modifications of this Zn-sensor motif disrupt Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. As the Zn-sensor motif is highly conserved in F-group bZIP proteins across land plants, the identification of this plant Zn sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackling the global Zn-deficiency health problem.
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http://dx.doi.org/10.1038/s41477-021-00856-7DOI Listing
February 2021

Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in .

Front Genet 2020 20;11:609117. Epub 2021 Jan 20.

Bioinformatics Group, Wageningen University, Wageningen, Netherlands.

Prediction of growth-related complex traits is highly important for crop breeding. Photosynthesis efficiency and biomass are direct indicators of overall plant performance and therefore even minor improvements in these traits can result in significant breeding gains. Crop breeding for complex traits has been revolutionized by technological developments in genomics and phenomics. Capitalizing on the growing availability of genomics data, genome-wide marker-based prediction models allow for efficient selection of the best parents for the next generation without the need for phenotypic information. Until now such models mostly predict the phenotype directly from the genotype and fail to make use of relevant biological knowledge. It is an open question to what extent the use of such biological knowledge is beneficial for improving genomic prediction accuracy and reliability. In this study, we explored the use of publicly available biological information for genomic prediction of photosynthetic light use efficiency (Φ ) and projected leaf area (PLA) in . To explore the use of various types of knowledge, we mapped genomic polymorphisms to Gene Ontology (GO) terms and transcriptomics-based gene clusters, and applied these in a Genomic Feature Best Linear Unbiased Predictor (GFBLUP) model, which is an extension to the traditional Genomic BLUP (GBLUP) benchmark. Our results suggest that incorporation of prior biological knowledge can improve genomic prediction accuracy for both Φ and PLA. The improvement achieved depends on the trait, type of knowledge and trait heritability. Moreover, transcriptomics offers complementary evidence to the Gene Ontology for improvement when used to define functional groups of genes. In conclusion, prior knowledge about trait-specific groups of genes can be directly translated into improved genomic prediction.
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http://dx.doi.org/10.3389/fgene.2020.609117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7855462PMC
January 2021

and Are Key Regulators of Flowering Time in the Biennial/Perennial Species .

Front Plant Sci 2020 11;11:582577. Epub 2020 Nov 11.

Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands.

The appropriate timing of flowering is crucial for plant reproductive success. Studies of the molecular mechanism of flower induction in the model plant showed long days and vernalization as major environmental promotive factors. has an obligate vernalization requirement that has not been studied at the molecular genetics level. Here, we characterize the vernalization requirement and response of four geographically diverse biennial/perennial accessions: Ganges (GA), Lellingen (LE), La Calamine (LC), and St. Felix de Pallières (SF). Differences in vernalization responsiveness among accessions suggest that natural variation for this trait exists within . Mutants which fully abolish the vernalization requirement were identified and were shown to contain mutations in the ( and ( genes, two key floral repressors in this species. At high temperatures, the non-vernalization requiring mutant reverts from flowering to vegetative growth, which is accompanied with a reduced expression of and . This suggested there is "crosstalk" between vernalization and ambient temperature, which might be a strategy to cope with fluctuations in temperature or adopt a more perennial flowering attitude and thus facilitate a flexible evolutionary response to the changing environment across the species range.
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http://dx.doi.org/10.3389/fpls.2020.582577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7686048PMC
November 2020

Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions.

Plant Cell Environ 2020 08 28;43(8):2000-2013. Epub 2020 Jun 28.

Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.

Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (Φ ) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in Φ upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in Φ in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.
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http://dx.doi.org/10.1111/pce.13811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497054PMC
August 2020

Rice F-bZIP transcription factors regulate the zinc deficiency response.

J Exp Bot 2020 06;71(12):3664-3677

Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg-C, Denmark.

The F-bZIP transcription factors bZIP19 and bZIP23 are the central regulators of the zinc deficiency response in Arabidopsis, and phylogenetic analysis of F-bZIP homologs across land plants indicates that the regulatory mechanism of the zinc deficiency response may be conserved. Here, we identified the rice F-bZIP homologs and investigated their function. OsbZIP48 and OsbZIP50, but not OsbZIP49, complement the zinc deficiency-hypersensitive Arabidopsis bzip19bzip23 double mutant. Ectopic expression of OsbZIP50 in Arabidopsis significantly increases plant zinc accumulation under control zinc supply, suggesting an altered Zn sensing in OsbZIP50. In addition, we performed a phylogenetic analysis of F-bZIP homologs from representative monocot species that supports the branching of plant F-bZIPs into Group 1 and Group 2. Our results suggest that regulation of the zinc deficiency response in rice is conserved, with OsbZIP48 being a functional homolog of AtbZIP19 and AtbZIP23. A better understanding of the mechanisms behind the Zn deficiency response in rice and other important crops will contribute to develop plant-based strategies to address the problems of Zn deficiency in soils, crops, and cereal-based human diets.
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http://dx.doi.org/10.1093/jxb/eraa115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7307843PMC
June 2020

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes.

Nat Plants 2020 01 13;6(1):13-21. Epub 2020 Jan 13.

Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands.

Assessment of the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear-derived variation (the nucleotype). Haploid-inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1,859 phenotypes under both stable and fluctuating conditions. We show that natural variation in the plasmotype results in both additive and epistatic effects across all phenotypic categories. Plasmotypes that induce more additive phenotypic changes also cause more epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average, epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multi-level nucleotype-plasmotype-environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation that is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a rapid and precise method for assessment of the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in these combinations and identify favourable combinations to enhance plant performance.
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http://dx.doi.org/10.1038/s41477-019-0575-9DOI Listing
January 2020

Spatially-resolved localization and chemical speciation of nickel and zinc in Noccaea tymphaea and Bornmuellera emarginata.

Metallomics 2019 12;11(12):2052-2065

Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Australia.

Hyperaccumulator plants present the ideal model system for studying the physiological regulation of the essential (and potentially toxic) transition elements nickel and zinc. This study used synchrotron X-ray Fluorescence Microscopy (XFM) elemental imaging and spatially resolved X-ray Absorption Spectroscopy (XAS) to elucidate elemental localization and chemical speciation of nickel and zinc in the hyperaccumulators Noccaea tymphaea and Bornmuellera emarginata (synonym Leptoplax emarginata). The results show that in the leaves of N. tymphaea nickel and zinc have contrasting localization, and whereas nickel is present in vacuoles of epidermal cells, zinc occurs mainly in the mesophyll cells. In the seeds Ni and Zn are similarly localized and strongly enriched in the cotyledons in N. tymphaea. Nickel is strongly enriched in the tip of the radicle of B. emarginata. Noccaea tymphaea has an Fe-rich provascular strand network in the cotyledons of the seed. The chemical speciation of Ni in the seeds of N. tymphaea is unequivocally associated with carboxylic acids, whereas Zn is present as the phytate complex. The spatially resolved spectroscopy did not reveal any spatial variation in chemical speciation of Ni and Zn within the N. tymphaea seed. The dissimilar ecophysiological behaviour of Ni and Zn in N. tymphaea and B. emarginata raises questions about the evolution of hyperaccumulation in these species.
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http://dx.doi.org/10.1039/c9mt00106aDOI Listing
December 2019

QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana.

BMC Plant Biol 2019 Sep 18;19(1):410. Epub 2019 Sep 18.

Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.

Background: Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability.

Results: Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus.

Conclusion: We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .
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http://dx.doi.org/10.1186/s12870-019-1996-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751748PMC
September 2019

Photosynthetic response to increased irradiance correlates to variation in transcriptional response of lipid-remodeling and heat-shock genes.

Plant Direct 2018 Jul 10;2(7):e00069. Epub 2018 Jul 10.

Laboratory of Genetics Wageningen University and Research Wageningen The Netherlands.

Plants have evolved several mechanisms for sensing increased irradiance, involving signal perception by photoreceptors (cryptochromes), and subsequent biochemical (reactive oxygen species, ROS) and metabolic clues to transmit the signals. This results in the increased expression of heat-shock response genes and of the transcription factor LONG HYPOCOTYL 5 (HY5, mediated by the cryptochrome photoreceptor 1, CRY1). Here, we show the existence of another response pathway in Arabidopsis. This pathway evokes the SPX1-mediated expression activation of the transcription factor PHR1 and leads to the expression of several galactolipid biosynthesis genes. Gene expression analysis of accessions Col-0, Ga-0, and Ts-1, showed activated expression of the SPX1/PHR1-mediated gene expression activation pathway acting on galactolipids biosynthesis genes in both Ga-0 and Col-0, but not in Ts-1. The activation of the SPX1/PHR1-mediated response pathway can be associated with lower photosynthesis efficiency in Ts-1, compared to Col-0 and Ga-0. Besides the accession-associated activation of the SPX1/PHR1-mediated response pathway, comparing gene expression in the accessions showed stronger activation of several heat responsive genes in Ga-0, and the opposite in Ts-1, when compared to Col-0, in line with the differences in their efficiency of photosynthesis. We conclude that natural variation in activation of both heat responsive genes and of galactolipids biosynthesis genes contribute to the variation in photosynthesis efficiency in response to irradiance increase.
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http://dx.doi.org/10.1002/pld3.69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508758PMC
July 2018

Overexpression of the MYB29 transcription factor affects aliphatic glucosinolate synthesis in Brassica oleracea.

Plant Mol Biol 2019 Sep 12;101(1-2):65-79. Epub 2019 Jun 12.

Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.

Key Message: Overexpression of BoMYB29 gene up-regulates the aliphatic glucosinolate pathway in Brassica oleracea plants increasing the production of the anti-cancer metabolite glucoraphanin, and the toxic and pungent sinigrin. Isothiocyanates, the bio-active hydrolysis products of glucosinolates, naturally produced by several Brassicaceae species, play an important role in human health and agriculture. This study aims at correlating the content of aliphatic glucosinolates to the expression of genes involved in their synthesis in Brassica oleracea, and perform functional analysis of BoMYB29 gene. To this purpose, three genotypes were used: a sprouting broccoli, a cabbage, and a wild genotype (Winspit), a high glucosinolate containing accession. Winspit showed the highest transcript level of BoMYB28, BoMYB29 and BoAOP2 genes, and BoAOP2 expression was positively correlated with that of the two MYB genes. Further analyses of the aliphatic glucosinolates also showed a positive correlation between the expression of BoAOP2 and the production of sinigrin and gluconapin in Winspit. The Winspit BoMYB29 CDS was cloned and overexpressed in Winspit and in the DH AG1012 line. Overexpressing Winspit plants produced higher quantities of alkenyl glucosinolates, such as sinigrin. Conversely, the DH AG1012 transformants showed a higher production of methylsulphinylalkyl glucosinolates, including glucoraphanin, and, despite an up-regulation of the aliphatic glucosinolate genes, no increase in alkenyl glucosinolates. The latter may be explained by the absence of a functional AOP2 gene in DH AG1012. Nevertheless, an extract of DH AG1012 lines overexpressing BoMYB29 provided a chemoprotective effect on human colon cells. This work exemplifies how the genetic diversity of B. oleracea may be used by breeders to select for higher expression of transcription factors for glucosinolate biosynthesis to improve its natural, health-promoting properties.
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http://dx.doi.org/10.1007/s11103-019-00890-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695347PMC
September 2019

Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency.

Plant J 2019 01;97(1):112-133

Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.

In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High-throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis-related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio-engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype-to-gene identification pipeline.
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http://dx.doi.org/10.1111/tpj.14190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850172PMC
January 2019

Transcriptional effects of cadmium on iron homeostasis differ in calamine accessions of Noccaea caerulescens.

Plant J 2019 01 15;97(2):306-320. Epub 2018 Nov 15.

Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland.

Calamine accessions of the zinc/cadmium/nickel hyperaccumulator, Noccaea caerulescens, exhibit striking variation in foliar cadmium accumulation in nature. The Ganges accession (GA) from Southern France displays foliar cadmium hyperaccumulation (>1000 μg g DW), whereas the accession La Calamine (LC) from Belgium, with similar local soil metal composition, does not (<100 μg g DW). All calamine accessions are cadmium hypertolerant. To find out the differences between LC and GA in their basic adaptation mechanisms, we bypassed the cadmium excluding phenotype of LC by exposing the plants to 50 μm cadmium in hydroponics, achieving equal cadmium accumulation in the shoots. The iron content increased in the roots of both accessions. GA exhibited significant decreases in manganese and zinc contents in the roots and shoots, approaching those in LC. Altogether 702 genes responded differently to cadmium exposure between the accessions, 157 and 545 in the roots and shoots, respectively. Cadmium-exposed LC showed a stress response and had decreased levels of a wide range of photosynthesis-related transcripts. GA showed less changes, mainly exhibiting an iron deficiency-like response. This included increased expression of genes encoding five iron deficiency-regulated bHLH transcription factors, ferric reduction oxidase FRO2, iron transporters IRT1 and OPT3, and nicotianamine synthase NAS1, and decreased expression of genes encoding ferritins and NEET (a NEET family iron-sulfur protein), which is possibly involved in iron transfer, distribution and/or management. The function of the IRT1 gene in the accessions was compared. We conclude that the major difference between the two accessions is in the way they cope with iron under cadmium exposure.
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http://dx.doi.org/10.1111/tpj.14121DOI Listing
January 2019

Cadmium associates with oxalate in calcium oxalate crystals and competes with calcium for translocation to stems in the cadmium bioindicator Gomphrena claussenii.

Metallomics 2018 11;10(11):1576-1584

Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.

Cadmium (Cd) was shown to co-localise with calcium (Ca) in oxalate crystals in the stems and leaves of Cd tolerant Gomphrena claussenii, but Cd binding remained unresolved. Using synchrotron radiation X-ray absorption near edge spectroscopy we demonstrate that in oxalate crystals of hydroponically grown G. claussenii the vast majority of Cd is bound to oxygen ligands in oxalate crystals (>88%; Cd-O-C coordination) and the remaining Cd is bound to sulphur ligands (Cd-S-C coordination). Cadmium binding to oxalate does not depend on the amount of Ca supplied or from which organs the crystals originate (stems and mature leaves). By contrast, roots contain no oxalate crystals and therein Cd is bound predominantly by S ligands. The potential to remove Cd by extraction of Cd-rich oxalate crystals from plant material should be tested in phytoextraction or phytomining strategies.
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http://dx.doi.org/10.1039/c8mt00149aDOI Listing
November 2018

Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

Genetics 2018 Jan 15;208(1):307-322. Epub 2017 Nov 15.

Laboratory of Genetics, Wageningen University, 6708PB, The Netherlands.

The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change.
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http://dx.doi.org/10.1534/genetics.117.300519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753865PMC
January 2018

Natural variation of YELLOW SEEDLING1 affects photosynthetic acclimation of Arabidopsis thaliana.

Nat Commun 2017 11 10;8(1):1421. Epub 2017 Nov 10.

Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.

Exploiting genetic variation for more efficient photosynthesis is an underexplored route towards new crop varieties. This study demonstrates the genetic dissection of higher plant photosynthesis efficiency down to the genomic DNA level, by confirming that allelic sequence variation at the Arabidopsis thaliana YELLOW SEEDLING1 (YS1) gene explains natural diversity in photosynthesis acclimation to high irradiance. We use a genome-wide association study to identify quantitative trait loci (QTLs) involved in the Arabidopsis photosynthetic acclimation response. Candidate genes underlying the QTLs are prioritized according to functional clues regarding gene ontology, expression and function. Reverse genetics and quantitative complementation confirm the candidacy of YS1, which encodes a pentatrico-peptide-repeat (PPR) protein involved in RNA editing of plastid-encoded genes (anterograde signalling). Gene expression analysis and allele sequence comparisons reveal polymorphisms in a light-responsive element in the YS1 promoter that affect its expression, and that of its downstream targets, resulting in the variation in photosynthetic acclimation.
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http://dx.doi.org/10.1038/s41467-017-01576-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680337PMC
November 2017

Genomics of Adaptation Depends on the Rate of Environmental Change in Experimental Yeast Populations.

Mol Biol Evol 2017 10;34(10):2613-2626

Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.

The rate of directional environmental change may have profound consequences for evolutionary dynamics and outcomes. Yet, most evolution experiments impose a sudden large change in the environment, after which the environment is kept constant. We previously cultured replicate Saccharomyces cerevisiae populations for 500 generations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium, nickel, and zinc. Here, we investigate how each of these treatments affected genomic evolution. Whole-genome sequencing of evolved clones revealed that adaptation occurred via a combination of SNPs, small indels, and whole-genome duplications and other large-scale structural changes. In contrast to some theoretical predictions, gradual and abrupt environmental change caused similar numbers of genomic changes. For cadmium, which is toxic already at comparatively low concentrations, mutations in the same genes were used for adaptation to both gradual and abrupt increase in concentration. Conversely, for nickel and zinc, which are toxic at high concentrations only, mutations in different genes were used for adaptation depending on the rate of change. Moreover, evolution was more repeatable following a sudden change in the environment, particularly for nickel and zinc. Our results show that the rate of environmental change and the nature of the selection pressure are important drivers of evolutionary dynamics and outcomes, which has implications for a better understanding of societal problems such as climate change and pollution.
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http://dx.doi.org/10.1093/molbev/msx185DOI Listing
October 2017

Natural variation in Arabidopsis thaliana reveals shoot ionome, biomass, and gene expression changes as biomarkers for zinc deficiency tolerance.

J Exp Bot 2017 06;68(13):3643-3656

Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

Zinc (Zn) is an essential nutrient for plants, with a crucial role as a cofactor for many enzymes. Approximately one-third of the global arable land area is Zn deficient, leading to reduced crop yield and quality. To improve crop tolerance to Zn deficiency, it is important to understand the mechanisms plants have adopted to tolerate suboptimal Zn supply. In this study, physiological and molecular aspects of traits related to Zn deficiency tolerance were examined in a panel of 19 Arabidopsis thaliana accessions. Accessions showed a larger variation for shoot biomass than for Zn concentration, indicating that they have different requirements for their minimal Zn concentration required for growth. Accessions with a higher tolerance to Zn deficiency showed an increased expression of the Zn deficiency-responsive genes ZIP4 and IRT3 in comparison with Zn deficiency-sensitive accessions. Changes in the shoot ionome, as a result of the Zn treatment of the plants, were used to build a multinomial logistic regression model able to distinguish plants regarding their Zn nutritional status. This set of biomarkers, reflecting the A. thaliana response to Zn deficiency and Zn deficiency tolerance, can be useful for future studies aiming to improve the performance and Zn status of crop plants grown under suboptimal Zn concentrations.
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http://dx.doi.org/10.1093/jxb/erx191DOI Listing
June 2017

Genome-Wide Identification, Cloning and Functional Analysis of the Zinc/Iron-Regulated Transporter-Like Protein () Gene Family in Trifoliate Orange ( L. Raf.).

Front Plant Sci 2017 19;8:588. Epub 2017 Apr 19.

Citrus Research Institute, Southwest UniversityChongqing, China.

Zinc (Zn) and iron (Fe) deficiency are widespread among citrus plants, but the molecular mechanisms regarding uptake and transport of these two essential metal ions in citrus are still unclear. In the present study, 12 members of the Zn/Fe-regulated transporter (ZRT/IRT)-related protein () gene family were identified and isolated from a widely used citrus rootstock, trifoliate orange ( L. Raf.), and the genes were correspondingly named as according to the sequence and functional similarity to . The 12 genes were predicted to encode proteins of 334-419 amino acids, harboring 6-9 putative transmembrane (TM) domains. All of the PtZIP proteins contained the highly conserved ZIP signature sequences in TM-IV, and nine of them showed a variable region rich in histidine residues between TM-III and TM-IV. Phylogenetic analysis subdivided the PtZIPs into four groups, similar as found for the family of , with clustered PtZIPs sharing a similar gene structure. Expression analysis showed that the genes were very differently induced in roots and leaves under conditions of Zn, Fe and Mn deficiency. Yeast complementation tests indicated that , and were able to complement the mutant, which was deficient in Zn uptake; and were able to complement the mutant, which was deficient in Fe uptake, and was able to complement the mutant, which was deficient in Mn uptake, suggesting their respective functions in Zn, Fe, and Mn transport. The present study broadens our understanding of metal ion uptake and transport and functional divergence of the various genes in citrus plants.
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http://dx.doi.org/10.3389/fpls.2017.00588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395618PMC
April 2017

De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens.

Sci Data 2017 01 31;4:160131. Epub 2017 Jan 31.

University of Eastern Finland, Department of Environmental and Biological Sciences, Kuopio 70210, Finland.

Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition. Transcriptomes from root and shoot tissues of four N. caerulescens accessions with contrasting Zn, Cd and Ni hyperaccumulation and tolerance traits were sequenced with Illumina Hiseq2000. Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. The comparison against the BUSCO plant early release dataset indicated high-quality assemblies. The predicted protein sequences have been clustered into ortholog groups with closely related species. The data serve as important reference sequences in whole transcriptome studies, in analyses of genetic differences between the accessions and other species, and for primer design.
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http://dx.doi.org/10.1038/sdata.2016.131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283065PMC
January 2017

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping.

New Phytol 2017 Feb 4;213(3):1346-1362. Epub 2016 Oct 4.

Wageningen University and Research Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, the Netherlands.

Plants are exposed to combinations of various biotic and abiotic stresses, but stress responses are usually investigated for single stresses only. Here, we investigated the genetic architecture underlying plant responses to 11 single stresses and several of their combinations by phenotyping 350 Arabidopsis thaliana accessions. A set of 214 000 single nucleotide polymorphisms (SNPs) was screened for marker-trait associations in genome-wide association (GWA) analyses using tailored multi-trait mixed models. Stress responses that share phytohormonal signaling pathways also share genetic architecture underlying these responses. After removing the effects of general robustness, for the 30 most significant SNPs, average quantitative trait locus (QTL) effect sizes were larger for dual stresses than for single stresses. Plants appear to deploy broad-spectrum defensive mechanisms influencing multiple traits in response to combined stresses. Association analyses identified QTLs with contrasting and with similar responses to biotic vs abiotic stresses, and below-ground vs above-ground stresses. Our approach allowed for an unprecedented comprehensive genetic analysis of how plants deal with a wide spectrum of stress conditions.
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http://dx.doi.org/10.1111/nph.14220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5248600PMC
February 2017

Multi-Element Bioimaging of Arabidopsis thaliana Roots.

Plant Physiol 2016 10 26;172(2):835-847. Epub 2016 Aug 26.

Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.P.P., A.C., J.K.S., S.H.);Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands (M.G.M.A.); andCentre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (D.E.S.).

Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047091PMC
http://dx.doi.org/10.1104/pp.16.00770DOI Listing
October 2016

Whole-Genome Hitchhiking on an Organelle Mutation.

Curr Biol 2016 05 28;26(10):1306-11. Epub 2016 Apr 28.

Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.

Strong selection on a beneficial mutation can cause a selective sweep, which fixes the mutation in the population and reduces the genetic variation in the region flanking the mutation [1-3]. These flanking regions have increased in frequency due to their physical association with the selected loci, a phenomenon called "genetic hitchhiking" [4]. Theoretically, selection could extend the hitchhiking to unlinked parts of the genome, to the point that selection on organelles affects nuclear genome diversity. Such indirect selective sweeps have never been observed in nature. Here we show that strong selection on a chloroplast gene in the wild plant species Arabidopsis thaliana has caused widespread and lasting hitchhiking of the whole nuclear genome. The selected allele spread more than 400 km along the British railway network, reshaping the genetic composition of local populations. This demonstrates that selection on organelle genomes can significantly reduce nuclear genetic diversity in natural populations. We expect that organelle-mediated genetic draft is a more common occurrence than previously realized and needs to be considered when studying genome evolution.
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http://dx.doi.org/10.1016/j.cub.2016.03.027DOI Listing
May 2016

Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses.

Plant J 2016 05;86(3):249-67

Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands.

In nature, plants have to cope with a wide range of stress conditions that often occur simultaneously or in sequence. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to six sequential double stresses inflicted by combinations of: (i) infection by the necrotrophic fungus Botrytis cinerea, (ii) herbivory by chewing larvae of Pieris rapae, and (iii) drought stress. Each of these stresses induced specific expression profiles over time, in which one-third of all differentially expressed genes was shared by at least two single stresses. Of these, 394 genes were differentially expressed during all three stress conditions, albeit often in opposite directions. When two stresses were applied in sequence, plants displayed transcriptome profiles that were very similar to the second stress, irrespective of the nature of the first stress. Nevertheless, significant first-stress signatures could be identified in the sequential stress profiles. Bioinformatic analysis of the dynamics of co-expressed gene clusters highlighted specific clusters and biological processes of which the timing of activation or repression was altered by a prior stress. The first-stress signatures in second stress transcriptional profiles were remarkably often related to responses to phytohormones, strengthening the notion that hormones are global modulators of interactions between different types of stress. Because prior stresses can affect the level of tolerance against a subsequent stress (e.g. prior herbivory strongly affected resistance to B. cinerea), the first-stress signatures can provide important leads for the identification of molecular players that are decisive in the interactions between stress response pathways.
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http://dx.doi.org/10.1111/tpj.13167DOI Listing
May 2016

Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply.

Genom Data 2016 Mar 1;7:256-8. Epub 2016 Feb 1.

CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark.

Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed methodology, bioinformatics analysis and quality controls related to the microarray gene expression profiling published by Assunção and co-workers [2]. Most significantly, the present dataset comprises new experimental variables, including analysis of shoot tissue, and zinc sufficiency and excess supply. Thus, it expands from 8 to 42 microarrays hybridizations, which have been deposited at the Gene Expression Omnibus (GEO) under the accession number GSE77286. Overall, it provides a resource for research on the molecular basis and regulatory events of the plant response to zinc supply, emphasizing the importance of Arabidopsis bZIP19 and bZIP23 transcription factors.
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http://dx.doi.org/10.1016/j.gdata.2016.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778672PMC
March 2016

Expression of the ZNT1 Zinc Transporter from the Metal Hyperaccumulator Noccaea caerulescens Confers Enhanced Zinc and Cadmium Tolerance and Accumulation to Arabidopsis thaliana.

PLoS One 2016 1;11(3):e0149750. Epub 2016 Mar 1.

Laboratory of Genetics, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.

Prompt regulation of transition metal transporters is crucial for plant zinc homeostasis. NcZNT1 is one of such transporters, found in the metal hyperaccumulator Brassicaceae species Noccaea caerulescens. It is orthologous to AtZIP4 from Arabidopsis thaliana, an important actor in Zn homeostasis. We examined if the NcZNT1 function contributes to the metal hyperaccumulation of N. caerulescens. NcZNT1 was found to be a plasma-membrane located metal transporter. Constitutive overexpression of NcZNT1 in A. thaliana conferred enhanced tolerance to exposure to excess Zn and Cd supply, as well as increased accumulation of Zn and Cd and induction of the Fe deficiency response, when compared to non-transformed wild-type plants. Promoters of both genes were induced by Zn deficiency in roots and shoots of A. thaliana. In A. thaliana, the AtZIP4 and NcZNT1 promoters were mainly active in cortex, endodermis and pericycle cells under Zn deficient conditions. In N. caerulescens, the promoters were active in the same tissues, though the activity of the NcZNT1 promoter was higher and not limited to Zn deficient conditions. Common cis elements were identified in both promoters by 5' deletion analysis. These correspond to the previously determined Zinc Deficiency Responsive Elements found in A. thaliana to interact with two redundantly acting transcription factors, bZIP19 and bZIP23, controlling the Zn deficiency response. In conclusion, these results suggest that NcZNT1 is an important factor in contributing to Zn and Cd hyperaccumulation in N. caerulescens. Differences in cis- and trans-regulators are likely to account for the differences in expression between A. thaliana and N. caerulescens. The high, constitutive NcZNT1 expression in the stele of N. caerulescens roots implicates its involvement in long distance root-to-shoot metal transport by maintaining a Zn/Cd influx into cells responsible for xylem loading.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149750PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773103PMC
July 2016

Phenomics for photosynthesis, growth and reflectance in Arabidopsis thaliana reveals circadian and long-term fluctuations in heritability.

Plant Methods 2016 15;12:14. Epub 2016 Feb 15.

Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.

Background: Recent advances in genome sequencing technologies have shifted the research bottleneck in plant sciences from genotyping to phenotyping. This shift has driven the development of phenomics, high-throughput non-invasive phenotyping technologies.

Results: We describe an automated high-throughput phenotyping platform, the Phenovator, capable of screening 1440 Arabidopsis plants multiple times per day for photosynthesis, growth and spectral reflectance at eight wavelengths. Using this unprecedented phenotyping capacity, we have been able to detect significant genetic differences between Arabidopsis accessions for all traits measured, across both temporal and environmental scales. The high frequency of measurement allowed us to observe that heritability was not only trait specific, but for some traits was also time specific.

Conclusions: Such continuous real-time non-destructive phenotyping will allow detailed genetic and physiological investigations of the kinetics of plant homeostasis and development. The success and ultimate outcome of a breeding program will depend greatly on the genetic variance which is sampled. Our observation of temporal fluctuations in trait heritability shows that the moment of measurement can have lasting consequences. Ultimately such phenomic level technologies will provide more dynamic insights into plant physiology, and the necessary data for the omics revolution to reach its full potential.
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http://dx.doi.org/10.1186/s13007-016-0113-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754911PMC
February 2016

Effect of prior drought and pathogen stress on Arabidopsis transcriptome changes to caterpillar herbivory.

New Phytol 2016 06 5;210(4):1344-56. Epub 2016 Feb 5.

Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA, Wageningen, the Netherlands.

In nature, plants are exposed to biotic and abiotic stresses that often occur simultaneously. Therefore, plant responses to combinations of stresses are most representative of how plants respond to stresses. We used RNAseq to assess temporal changes in the transcriptome of Arabidopsis thaliana to herbivory by Pieris rapae caterpillars, either alone or in combination with prior exposure to drought or infection with the necrotrophic fungus Botrytis cinerea. Pre-exposure to drought stress or Botrytis infection resulted in a significantly different timing of the caterpillar-induced transcriptional changes. Additionally, the combination of drought and P. rapae induced an extensive downregulation of A. thaliana genes involved in defence against pathogens. Despite a more substantial growth reduction observed for plants exposed to drought plus P. rapae feeding compared with P. rapae feeding alone, this did not affect weight increase of this specialist caterpillar. Plants respond to combined stresses with phenotypic and transcriptional changes that differ from the single stress situation. The effect of a previous exposure to drought or B. cinerea infection on transcriptional changes to caterpillars is largely overridden by the stress imposed by caterpillars, indicating that plants shift their response to the most recent stress applied.
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http://dx.doi.org/10.1111/nph.13847DOI Listing
June 2016

A transposon insertion in FLOWERING LOCUS T is associated with delayed flowering in Brassica rapa.

Plant Sci 2015 Dec 23;241:211-20. Epub 2015 Oct 23.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, 100081 Beijing, China. Electronic address:

Long days and vernalization accelerate the transition from vegetative growth to reproductive growth in Brassica rapa. Bolting before plants reach the harvesting stage is a serious problem in B. rapa vegetable crop cultivation. The genetic dissection of flowering time is important for breeding of premature bolting-resistant B. rapa crops. Using a recombinant inbred line (RIL) population, we twice detected two major quantitative trait loci (QTLs) for flowering time in two different growing seasons that were located on chromosomes A02 and A07, respectively. We hypothesized that an orthologue of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene, named as BrFT2, was the candidate gene underlying the QTL localized to A07. A transposon insertion in the second intron of BrFT2 was detected in one of the parental lines, which was predicted to generate a loss-of-function allele. Transcription analysis revealed that the BrFT2 transcript was not present in the parental line that harbored the mutated allele. RILs carrying only the mutated BrFT2 allele showed delayed flowering regardless of growing seasons when compared to RILs carrying the wild-type BrFT2 allele. These data suggest that BrFT2 is involved in flowering time regulation in controlling flowering time in B. rapa.
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http://dx.doi.org/10.1016/j.plantsci.2015.10.007DOI Listing
December 2015
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