Rhonda C. Meyer

Leibniz Institute of Plant Genetics and Crop Plant Research

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Thomas Altmann

Leibniz Institute of Plant Genetics and Crop Plant Research

Jan Lisec

Federal Institute For Materials Research and Testing

Joachim Selbig

Max Planck Institute of Molecular Plant Physiology

Lothar Willmitzer

Max Planck Institute of Molecular Plant Physiology

Ottó Törjék

Hungarian Academy of Sciences

Dominic Knoch

Leibniz Institute of Plant Genetics and Crop Plant Research

Matthias Steinfath

Federal Institute for Risk Assessment

Robbie Waugh

James Hutton Institute

Marc C. Heuermann

Leibniz Institute of Plant Genetics and Crop Plant Research

Martina Becher

University of Potsdam

Cooperative Institutions

Leibniz Institute of Plant Genetics and Crop Plant Research

Max Planck Institute of Molecular Plant Physiology

Max Planck Society

University of Potsdam

Leibniz Association

James Hutton Institute

Ghent University

Vlaams Instituut voor Biotechnologie

Wageningen University & Research

Crop Research Institute

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Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

Theoretical and Applied Genetics (2006)

Karl Schmid Ottó Törjék Rhonda C. Meyer Heike Schmuths Matthias H. Hoffmann

Linkage Disequilibrium

10.1007/s00122-006-0212-7

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Citations (129)

Natural variation of BSK3 tunes brassinosteroid signaling to regulate root foraging under low nitrogen

Nature Communications (2019)

Zhongtao Jia Ricardo Fabiano Hettwer Giehl Rhonda C. Meyer Thomas Altmann Nicolaus von Wirén

Abstract Developmental plasticity of root system architecture is crucial for plant performance in nutrient-poor soils. Roots of plants grown under mild nitrogen (N) deficiency show a foraging response characterized by increased root length but mechanisms underlying this developmental plasticity are still elusive. By employing natural variation in Arabidopsis accessions, we show that the brassinosteroid (BR) signaling kinase BSK3 modulates root elongation under mild N deficiency. In particular, a proline to leucine substitution in the predicted kinase domain of BSK3 enhances BR sensitivity and signaling to increase the extent of root elongation. We further show that low N specifically upregulates transcript levels of the BR co-receptor BAK1 to activate BR signaling and stimulate root elongation. Altogether, our results uncover a role of BR signaling in root elongation under low N. The BSK3 alleles identified here provide targets for improving root growth of crops growing under limited N conditions.

Brassinosteroid

Elongation

Lateral root

10.1038/s41467-019-10331-9

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Citations (150)

Establishment of a high‐efficiency SNP‐based framework marker set for Arabidopsis

The Plant Journal (2003)

Ottó Törjék Dave K. Berger Rhonda C. Meyer Carsten Müssig Karl Schmid

Summary The major goal of this project was the establishment of a tool for rapid mapping of new mutations and genotyping in Arabidopsis consisting of at least 100 evenly spaced framework markers. We assembled a single nucleotide polymorphism (SNP)‐based marker set consisting of 112 polymorphic sites with average spacing of 1.15 Mbp derived from an SNP database that we recently developed. This information was used to set up efficient SNP detection reactions based on multiplexed primer extension assays. The 112 Columbia ( Col‐0 )/ C24 framework markers were used to assemble 18 multiplexed SNaPshot assays with which up to eight separate loci can be genotyped in a single‐tube/single‐capillary format. In addition, for 110 framework markers matrix‐assisted laser desorption/ionization time of flight (MALDI‐ToF) assays have been established for high throughput analyses. We demonstrated the usefulness and the robustness of both procedures of this tool by genotyping 48 BC 3 F 1 individuals created between the accessions Col‐0 and C24 . Subsets of 10–62 of the established markers discriminate between various combinations of the accessions Col‐0 , C24 , Landsberg erecta ( Ler ), Cape Verdi Islands ( Cvi ) and Niederzenz ( Nd ). Using a subset of 17 evenly distributed and established SNP markers that are also polymorphic between Ler and Col‐0 , we were able to rapidly map a mutant gene ( tbr1 ) to an interval of 2.3 Mbp in an Ler ( tbr1 ) × Col‐0 cross.

SNP

SNP genotyping

SNP array

Molecular Inversion Probe

10.1046/j.1365-313x.2003.01861.x

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Citations (94)

Integrating a molecular network hypothesis and QTL results for heterosis in Arabidopsis thaliana

Sandra Andorf Joachim Selbig Rhonda C. Meyer Thomas Altmann Dirk Repsilber

Integrating a molecular network hypothesis and QTL results for heterosis in Arabidopsis thaliana

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Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

PLoS Genetics (2015)

Jörg Hagmann Claude Becker Jonas Müller Oliver Stegle Rhonda C. Meyer

There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. Methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates mostly in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.

Lineage (genetic)

Epigenome

10.1371/journal.pgen.1004920

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Citations (151)

Expression of tandem invertase genes associated with sexual and vegetative growth cycles in potato.

Plant Molecular Biology (1999)

Anne L. Maddison Pete E. Hedley Rhonda C. Meyer Naveed Aziz Diane Davidson

GUS reporter system

Beta-glucuronidase

10.1023/a:1006389013179

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Citations (51)

Epigenetic Variation at a Genomic Locus Affecting Biomass Accumulation under Low Nitrogen in Arabidopsis thaliana

Agronomy (2020)

Markus Kuhlmann Rhonda C. Meyer Zhongtao Jia Doreen Klose Lisa-Marie Krieg

Nitrogen (N) is a macronutrient determining crop yield. The application of N fertilisers can substantially increase the yield, but excess use also causes the nitrate pollution of water resources and increases production costs. Increasing N use efficiency (NUE) in crop plants is an important step to implement low-input agricultural systems. We used Arabidopsis thaliana as model system to investigate the natural genetic diversity in traits related to NUE. Natural variation was used to study adaptive growth patterns and changes in gene expression associated with limited nitrate availability. A genome-wide association study revealed an association of eight SNP markers on Chromosome 1 with shoot growth under limited N. The identified linkage disequilibrium (LD) interval includes the DNA sequences of three cysteine/histidine-rich C1 domain proteins in tandem orientation. These genes differ in promoter structure, methylation pattern and expression level among accessions, correlating with growth performance under N deficiency. Our results suggest the involvement of epigenetic regulation in the expression of NUE-related traits.

Linkage Disequilibrium

10.3390/agronomy10050636

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Citations (9)

Strong temporal dynamics of QTL action on plant growth progression revealed through high‐throughput phenotyping in canola

Plant Biotechnology Journal (2019)

Dominic Knoch Amine Abbadi Fabian Grandke Rhonda C. Meyer Birgit Samans

A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height and colour uniformity, were established and complemented by fresh and dry weight biomass. Genome-wide SNP array data provided the framework for genome-wide association analyses. Using time point data and relative growth rates, multiple robust main effect marker-trait associations for biomass and related traits were detected. Candidate genes involved in meristem development, cell wall modification and transcriptional regulation were detected. Our results demonstrate that early plant growth is a highly complex trait governed by several medium and many small effect loci, most of which act only during short phases. These observations highlight the importance of taking the temporal patterns of QTL/allele actions into account and emphasize the need for detailed time-resolved analyses to effectively unravel the complex and stage-specific contributions of genes affecting growth processes that operate at different developmental phases.

Genome-wide Association Study

Trait

Genetic Association

10.1111/pbi.13171

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Citations (59)

Hybrid Incompatibility in Arabidopsis Is Determined by a Multiple-Locus Genetic Network

PLANT PHYSIOLOGY (2011)

Diana Burkart‐Waco Caroline Josefsson Brian P. Dilkes Nora Kozloff Ottó Törjék

Abstract The cross between Arabidopsis thaliana and the closely related species Arabidopsis arenosa results in postzygotic hybrid incompatibility, manifested as seed death. Ecotypes of A. thaliana were tested for their ability to produce live seed when crossed to A. arenosa. The identified genetic variation was used to map quantitative trait loci (QTLs) encoded by the A. thaliana genome that affect the frequency of postzygotic lethality and the phenotypes of surviving seeds. Seven QTLs affecting the A. thaliana component of this hybrid incompatibility were identified by crossing a Columbia × C24 recombinant inbred line population to diploid A. arenosa pollen donors. Additional epistatic loci were identified based on their pairwise interaction with one or several of these QTLs. Epistatic interactions were detected for all seven QTLs. The two largest additive QTLs were subjected to fine-mapping, indicating the action of at least two genes in each. The topology of this network reveals a large set of minor-effect loci from the maternal genome controlling hybrid growth and viability at different developmental stages. Our study establishes a framework that will enable the identification and characterization of genes and pathways in A. thaliana responsible for hybrid lethality in the A. thaliana × A. arenosa interspecific cross.

Epistasis

10.1104/pp.111.188706

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Citations (49)

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Plant Cell & Environment (2019)

John N. Ferguson Rhonda C. Meyer Kieron D. Edwards Matt Humphry Oliver Brendel

Abstract Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf‐level water‐use efficiency ( WUE ). In Arabidopsis, little is known about the variation of whole‐plant water use (PWU) and whole‐plant WUE ( transpiration efficiency ). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large‐scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water‐use strategies, namely, C24 (low PWU) and Col‐0 (high PWU). Subsequent quantitative trait loci mapping and validation through near‐isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ 13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ 13 C. and rosette water use were independent of allelic variation at FRI and FLC , suggesting that flowering is critical in determining lifetime PWU but not always leaf‐level traits.

10.1111/pce.13527

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Citations (13)