A plant-based chemical genomics screen for the identification of flowering inducers

Background: Floral timing is a carefully regulated process, in which the plant determines the optimal moment to switch from the vegetative to reproductive phase. While there are numerous genes known that control flowering time, little information is available on chemical compounds that are able to influence this process. We aimed to discover novel compounds that are able to induce flowering in the model plant Arabidopsis. For this purpose we developed a plant-based screening platform that can be used in a chemical genomics study. Results: Here we describe the set-up of the screening platform and various issues and pitfalls that need to be addressed in order to perform a chemical genomics screening on Arabidopsis plantlets. We describe the choice for a molecular marker, in combination with a sensitive reporter that's active in plants and is sufficiently sensitive for detection. In this particular screen, the firefly Luciferase marker was used, fused to the regulatory sequences of the floral meristem identity gene APETALA1 (AP1), which is an early marker for flowering. Using this screening platform almost 9000 compounds were screened, in triplicate, in 96-well plates at a concentration of 25μM. One of the identified potential flowering inducing compounds was studied in more detail and named Flowering1 (F1). F1 turned out to be an analogue of the plant hormone Salicylic acid (SA) and appeared to be more potent than SA in the induction of flowering. The effect could be confirmed by watering Arabidopsis plants with SA or F1, in which F1 gave a significant reduction in time to flowering in comparison to SA treatment or the control. Conclusions: In this study a chemical genomics screening platform was developed to discover compounds that can induce flowering in Arabidopsis. This platform was used successfully, to identify a compound that can speed-up flowering in Arabidopsis.</p

Development of improved pink tomato (Solanum lycopersicum L.) lines for the creation of remarkable hybrids supported by gene expression analysis

The "pink" color fruit trait in tomato is associated with a recessive monogenic y locus on chromosome 1. The pink skin phenotype is due to the lack of naringenin chalcone (NarCh), the predominant yellow pigment that accumulates during ripening. SlMYB12 is the transcription factor involved in the regulation of the NarCh biosynthesis, and its suppression causes the pink phenotype. This project aims to improve the ISI Sementi pink germplasm by generating new tomato fixed lines. During 2020, different heterozygous F1 generations with red phenotype were obtained by crossing a pink-fruited line (ISI 1) with three different red-fruited lines (ISI 2, ISI 3, ISI 4). These hybrids were then used to make a first backcross with ISI 1 and other 12 parental lines with similar characteristics. More than 20 BC1F1 lines were obtained. Expression analysis of the MYB12 gene was carried out by quantitative Real-Time PCR on 3 BC1F1lines, also considering a hybrid and a control red-fruited line. In the pink-fruited lines, MYB12 expression was almost completely abolished. Since various sequence modifications localized in MYB12 of different commercial pink lines have been reported in literature, a 591 bp portion of MYB12 cDNA was amplified and sequenced. The results showed no differences in the sequence between all the germplasm tested and the accessions of the MYB12 genes deposited in the database; therefore, the reduction in gene expression in the lines generated by ISI Sementi could be attributable to modifications present in other points of the gene. Currently the project is still in progress: we are developing BC2F1 generations and will continue with the stabilization of future parental lines useful for the development of new commercial hybrid

Molecular Diversity and Landscape Genomics of the Crop Wild Relative Triticum urartu Across the Fertile Crescent

Modern plant breeding can benefit from the allelic variation existing in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next-generation sequencing was used to generate 1.3 million genome-wide SNPs on ex situ collections of Triticum urartu L., the wild donor of the Ausub-genome of modern wheat. A set of 75,511 high quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from West to East. The incorporation of geographic information of sampling points showed that genetic diversity did correlate to geographic distance (R2= 0.19), separating samples from Jordan and Lebanon, to samples from Syria and Southern Turkey, to samples from Eastern Turkey, Iran, and Iraq. The wild emmer genome was used to derive SNPs physical positions on the 7 chromosomes of the Ausub-genome, allowing to describe a relatively slow linkage disequilibrium decay in the collection. Outlier loci were described on the basis of geographical distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and put in relation to allelic variation with a genome-wide association approach, identifying several marker-environment associations (MEAs). Fifty-seven MEAs were associated with altitude and temperature measures, while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential, some already reported in wheat, including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials to be incorporated in modern crop breeding. This article is protected by copyright. All rights reserved

MOESM1 of A plant-based chemical genomics screen for the identification of flowering inducers

Additional file 1: Fig. S1. Effect of DMSO on flowering time of Arabidopsis in 96 well plates. Effect of DMSO on pAP1::AP1-LUC. Plants were grown for 12 days in 96-well plates with different concentrations of DMSO, after which the luciferase activity was measured. Fig. S2. Distribution of initial hits from the Chembridge library. A Distribution of the average luciferase activity from 56 96-well plates of the initial screen from the Chembridge library. B Distribution of the number of initial hits from all screened 96-well plates from the Chembridge library. Columns 1 and 12 are controls containing DMSO. Note that hits were more often found at the borders of the plate pointing towards a position effect due to the screening conditions and set-up. The wells are colour coded based on the average luciferase activity (A), or number of hits (B). Fig. S3. Structure clustering of the SA-analogues with SA. Positive SA-analogues (F1, A, and B) from the screen were clustered together with SA in Pubchem (pubchem.ncbi.nlm.nih.gov). Fig. S4. Results from a selection of initial screening plates that contained F1 and its derivatives. The screen was performed in triplicate with the DMSO controls in the first and last column of each plate. The Fluc values for F1 and its analogues are colour coded. Fig. S5. Result of a Structure Activity Relationship (SAR) analysis for F1. Two positive compounds from the initial screen similar in structure to F1 (Compound A and B), and one analogue of F1 (Compound F1-4F) were retested for the induction of AP1 expression. Compounds were tested at 25 µM against pAP1::AP1-LUC plants in 96-well plates with water as a control (compounds were dissolved in water). Plants were grown for 12 days before luciferase measurement. Error bars represent SE of six replicates with 16 plants/replicate

Green plants in the red : a baseline global assessment for the IUCN Sampled Red List Index for Plants

Plants provide fundamental support systems for life on Earth and are the basis for all terrestrial ecosystems; a decline in plant diversity will be detrimental to all other groups of organisms including humans. Decline in plant diversity has been hard to quantify, due to the huge numbers of known and yet to be discovered species and the lack of an adequate baseline assessment of extinction risk against which to track changes. The biodiversity of many remote parts of the world remains poorly known, and the rate of new assessments of extinction risk for individual plant species approximates the rate at which new plant species are described. Thus the question 'How threatened are plants?' is still very difficult to answer accurately. While completing assessments for each species of plant remains a distant prospect, by assessing a randomly selected sample of species the Sampled Red List Index for Plants gives, for the first time, an accurate view of how threatened plants are across the world. It represents the first key phase of ongoing efforts to monitor the status of the world's plants. More than 20% of plant species assessed are threatened with extinction, and the habitat with the most threatened species is overwhelmingly tropical rain forest, where the greatest threat to plants is anthropogenic habitat conversion, for arable and livestock agriculture, and harvesting of natural resources. Gymnosperms (e.g. conifers and cycads) are the most threatened group, while a third of plant species included in this study have yet to receive an assessment or are so poorly known that we cannot yet ascertain whether they are threatened or not. This study provides a baseline assessment from which trends in the status of plant biodiversity can be measured and periodically reassessed.Publisher PDFPeer reviewe

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<p>Numbers of species from the combined SRLI for Plants sample of gymnosperms, monocots, legumes and pteridophytes by IUCN Red List Category for each group of plants.</p

Global map of average extinction risk of species per country from the combined SRLI for Plants sample of gymnosperms, monocots, legumes and pteridophytes.

<p>A. Number of species assessed per country. B. Percentage of assessed species that are threatened per country. C. Percentage of assessed species that are Data Deficient per country.</p

Numbers of species from the combined SRLI for Plants sample of gymnosperms, monocots, legumes and pteridophytes in each IUCN Red List Category by realm.

<p>Numbers of species from the combined SRLI for Plants sample of gymnosperms, monocots, legumes and pteridophytes in each IUCN Red List Category by realm.</p

Red List Indices for birds, mammals, amphibians and corals (source: IUCN), with baseline values for crayfish [13], freshwater crabs [16], dragonflies & damselflies [17], reptiles [19] and plants (this study).

<p>Values for crayfish, freshwater crabs, dragonflies and damselflies, reptiles and plants are based on a sampled approach.</p