Potent Induction of Arabidopsis thaliana Flowering by Elevated Growth Temperature

The transition to flowering is an important event in the plant life cycle and is modulated by several environmental factors including photoperiod, light quality, vernalization, and growth temperature, as well as biotic and abiotic stresses. In contrast to light and vernalization, little is known about the pathways that mediate the responses to other environmental variables. A mild increase in growth temperature, from 23 °C to 27 °C, is equally efficient in inducing flowering of Arabidopsis plants grown in 8-h short days as is transfer to 16-h long days. There is extensive natural variation in this response, and we identify strains with contrasting thermal reaction norms. Exploiting this natural variation, we show that FLOWERING LOCUS C potently suppresses thermal induction, and that the closely related floral repressor FLOWERING LOCUS M is a major-effect quantitative trait locus modulating thermosensitivity. Thermal induction does not require the photoperiod effector CONSTANS, acts upstream of the floral integrator FLOWERING LOCUS T, and depends on the hormone gibberellin. Analysis of mutants defective in salicylic acid biosynthesis suggests that thermal induction is independent of previously identified stress-signaling pathways. Microarray analyses confirm that the genomic responses to floral induction by photoperiod and temperature differ. Furthermore, we report that gene products that participate in RNA splicing are specifically affected by thermal induction. Above a critical threshold, even small changes in temperature can act as cues for the induction of flowering. This response has a genetic basis that is distinct from the known genetic pathways of floral transition, and appears to correlate with changes in RNA processing

The impact of Mendelian genetics on the breeding of apple and sweet cherry

Mendels Einfluss auf die moderne Obstzüchtung ist unverkennbar. Die von ihm aufgestellten Vererbungsregeln haben es Züchtern ermöglicht, Kreuzungsprogramme gezielt zu designen, Vorhersagen über den möglichen Erfolg zu treffen und die Selektion von Nachkommen mit verbesserten Merkmalskombinationen mithilfe molekulargenetischer Marker kostengünstig und effizient zu gestalten. Am Beispiel des Apfels und der Süßkirsche als Vertreter für Kern- und Steinobst werden ausgewählte mendelnde Merkmale vorgestellt, die von besonderer Bedeutung für die Züchtung sind. Darüber hinaus wird der derzeitige Stand an molekularen Markern und genetischen Karten bei diesen Kulturen präsentiert. Sie beeinflussen die Effizienz in der Obstzüchtung enorm. Ihre Entwicklung wäre jedoch ohne Mendels Erkenntnisse nicht möglich gewesen. Beim Apfel, der bedeutendsten einheimischen Obstart, gibt es eine Vielzahl von wirtschaftlich inte­ressanten mendelnden Merkmalen. Einige von ihnen, wie der Säulenwuchs, die rote Fruchtfleischfarbe, das Kältebedürfnis zum Brechen der Winterknospenruhe, die Samenlosigkeit der Früchte sowie gefüllte Blüten für den Anbau als Ziergehölz und die Resistenz gegenüber Schorf und Mehltau sind phänotypisch einfach zu erfassen. Eine Selektion auf der Basis des Phänotyps ist bei diesen Merkmalen meist problemlos möglich, wenngleich sie mithilfe molekularer Marker noch effektiver gestaltet werden kann. Andere Merkmale, wie die Resistenz gegenüber Insekten, verschiedenen Lagerkrankheiten oder der bakteriellen Feuerbrandkrankheit sind nicht so einfach anhand des Phänotyps zu bestimmen. Hier sind für eine erfolgreiche Züchtung molekulare Marker unabdingbar. Das gilt auch für die rote Färbung der Fruchtschale. Bei Süßkirschen ist die Situation sehr ähnlich. Zu den mendelnden Merkmalen mit ökonomischer Bedeutung gehören hier neben der Selbstfertilität auch die Mehltauresistenz und die ­Farbe der Fruchtschale.The influence of Mendel on modern fruit breeding is undeniable. The inheritance rules he established have enabled breeders to design breeding programmes in a targeted manner to make predictions about possible success and to select offspring with improved trait combinations using molecular genetic markers in a cost-effective and efficient way. Using the example of the apple and the sweet cherry as representatives of pome and stone fruit, we highlight selected Mendelian traits that are of particular importance for breeding. In addition, the current status of molecular markers and genetic maps and their enormous influence in efficient fruit breeding are presented. However, molecular marker progress would not have been possible without Mendel's insights. In apples, the most important native fruit species, there is a large number of economically interesting Mendelian traits some of which are easy to phenotype. For example, columnar growth, red flesh colour, cold requirement for breaking winter bud dormancy, seedlessness of the fruits and double flowers for cultivation as an ornamental tree and resistance to scab and powdery mildew. Other traits, such as resistance to insects, and the bacterial disease fire blight and various storage diseases are not as straightforward to phenotype. This also applies to red colouration of the fruit skin. Nevertheless, in both situations, molecular markers are indispensable for successful breeding. This also applies to sweet cherries. In addition to self-fertility, powdery mildew resistance and fruit skin colour are among the Mendelian traits with economic significance in sweet cherry breeding

Diversity of Flowering Responses in Wild Arabidopsis thaliana Strains

Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species

Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis when grown under conditions typical of their natural habitats. We show that several independent cases result from epistatic interactions that trigger autoimmune-like responses. In at least one case, an allele of an NB-LRR disease resistance gene homolog is both necessary and sufficient for the induction of hybrid necrosis, when combined with a specific allele at a second locus. The A. thaliana cases provide insights into the molecular causes of hybrid necrosis, and serve as a model for further investigation of intra- and interspecific incompatibilities caused by a simple epistatic interaction. Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host–pathogen conflict might cause the evolution of gene flow barriers in plants

MowJoe: a method for automated-high throughput dissected leaf phenotyping

Background: Accurate and automated phenotyping of leaf images is necessary for high throughput studies of leaf form like genome-wide association analysis and other forms of quantitative trait locus mapping. Dissected leaves (also referred to as compound) that are subdivided into individual units are an attractive system to study diversification of form. However, there are only few software tools for their automated analysis. Thus, high-throughput image processing algorithms are needed that can partition these leaves in their phenotypically relevant units and calculate morphological features based on these units. Results: We have developed MowJoe, an image processing algorithm that dissects a dissected leaf into leaflets, petiolule, rachis and petioles. It employs image skeletonization to convert leaves into graphs, and thereafter applies algorithms operating on graph structures. This partitioning of a leaf allows the derivation of morphological features such as leaf size, or eccentricity of leaflets. Furthermore, MowJoe automatically places landmarks onto the terminal leaflet that can be used for further leaf shape analysis. It generates specific output files that can directly be imported into downstream shape analysis tools. We applied the algorithm to two accessions of Cardamine hirsuta and show that our features are able to robustly discriminate between these accessions. Conclusion: MowJoe is a tool for the semi-automated, quantitative high throughput shape analysis of dissected leaf images. It provides the statistical power for the detection of the genetic basis of quantitative morphological variations

Genomic Responses at the Shoot Apex to Light or Temperature Treatment

<p>For (A), (E), and (F), the day of sample collection (0, 2, 5, and 9), type of shift (light-photoperiodic shift, temp-thermal shift) and the background (Col-0 and L<i>er</i>) are given in the <i>x</i>-axis. Log-normalized expression levels are plotted along the <i>y</i>-axis. The scale is the same for all three panels.</p> <p>(A) Response of floral marker genes <i>(AP1, FUL, AP3, PI, AG, SEP1–3)</i> to light and temperature shifts.</p> <p>(B) Principal component analysis. <i>x</i>-axis: first principal component explaining 39.5% of the variation, which appears to be mostly due to genetic differences between L<i>er</i> and Col (indicated above). <i>y</i>-axis: second principal component explaining 25% of the variation. The second component mostly distinguishes light versus temperature treatment (shown to the right).</p> <p>(C, D) Most genes that show alterations in expression levels (significantly different between day 0 and day 9 based on logit-T) appear to be specific to the type of induction (thermal or photoperiodic). Red indicates expression levels above average across all experiments; blue, levels below average. The left panel shows genes that are induced by light (top) or repressed by light (bottom), but largely unchanged in response to temperature. The right panel shows genes with the opposite behavior.</p> <p>(E) Examples of light specific changes in expression profiles <i>(CCA1, GI, COL2, SUMO3, AGL6, CRC,</i> and <i>TFL1).</i></p> <p>(F) As examples of temperature specific changes in expression profiles, several genes encoding SR proteins and genes associated with the Gene Ontology term “RNA processing” are shown <i>(At2g24590, At5g46250, At1g55310, At1g09140, At1g51510</i> and <i>At2g27230).</i></p

Flowering Response of L<i>er</i> and Col under Different Temperature Regimens

<p>(A) Arabidopsis thaliana strain L<i>er</i> grown in 23 °C short days (left) and 27 °C short days (right).</p> <p>(B) Flowering time of L<i>er</i> (black bars) and Col (white bars) in different conditions. Error bars indicate standard deviation.</p

Effect of Different Genetic Pathways on Flowering Time in 27 °C Short Days

<p>Flowering time of mutants with defects in flowering time genes in 23 °C short days (black bars) and 27 °C short days (white bars). L<i>er</i> and Col controls are included both panels.</p> <p>(A) Mutants with defects in the photoperiod pathway, and <i>eds16–1. co-1</i> is in a mixed background of Col-0 and L<i>er</i>.</p> <p>(B) Mutants with defects in floral integrators. <i>ft-2</i> and <i>ft-7</i> are two independently isolated alleles with the same mutation.</p

Effect of <i>FLM</i> on Thermal Sensitivity in Short Days

<p>(A) QTL maps of NdC RILs for TLN in 27 °C short days (red lines) and 23 °C short days (black lines) and for thermal sensitivity, as expressed by the slope of the regression line mean over the environmental mean in arbitrary units (blue lines). The phenotype data for the 23 °C map are from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020106#pgen-0020106-b024" target="_blank">24</a>]. The prominent QTL corresponding to <i>FLM</i> on Chromosome 1 disappears at 27 °C, while the QTL on Chromosome 2 becomes more significant. The QTL for thermal sensitivity colocalize with <i>FLM.</i> A likelihood of odds threshold determined after 1,000 permutations is given. The same threshold was obtained for each of the phenotypes.</p> <p>(B) Thermal sensitivity of various genotypes as above. Col_F and Nd_F refers to the mean sensitivity of NdC recombinant inbred lines that are homozygous for the Col wild-type allele (Col_F) and homozygous for the Nd-1 <i>FLM</i> deletion (Nd_F). For comparison the sensitivity of <i>flc-3</i> is shown. <i>flm-3</i> is a T-DNA insertion allele at <i>FLM</i> locus in Col background. The last genotype is the accession Ei-6, which has the same <i>FLM</i> deletion as Nd-1. The effect of loss of <i>FLM</i> in different backgrounds varies considerably between backgrounds, indicating natural variation in this pathway.</p