SAS-ARABIDOPSIS-GWA

Exploring natural variation of Shade Avoidance Syndrome in Arabidopsis using high-throughput phenotyping and Genome-wide association studies

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 Obiettivo del progetto (Objective)

'Higher plants respond to a change in light quality -indicative of competition from other plants- by eliciting a range of adaptations summarized under the term Shade Avoidance Syndrome (SAS). These action responses include e.g. increased elongation of organs (e.g. hypocotyls, stems), a decrease in leaf surface, a more erect leaf position, rapid changes in gene expression and an accelerated transition to flowering. Our molecular understanding of SAS mostly comes from studies in Arabidopsis thaliana but numerous questions remain unanswered. Most SAS studies were performed in young seedlings but the role of many SAS regulators in more adult plants remains poorly characterized. In order to extent our understanding of SAS the following issues are addressed in the proposed project: (i) SAS traits will be measured (phenotyped) on rosette stage plants using a custom built high-throughput phenotyping device (Scanalyzer HTS) as well as in young seedlings. (ii) The SAS includes a number of physiological adaptations in different organs and different growth stages. To determine the extent to which regulators of the SAS are involved in shade avoidance we will phenotype selected mutants with a defective response to shade such as pif4, pif5, and sav3. (iii) It has been proposed that PIF4/PIF5 and SAV3 act in different pathways. To test this hypothesis we will phenotype pif4, pif5, sav3 and associated double/triple mutants. (iv) Natural variation in shade avoidance will be assessed by phenotyping a collection of field-collected Arabidopsis accessions (v) SAS traits measured in those accessions will further be exploited by a Genome-wide association (GWA) study to identify genetic loci that control SAS and may underlie adaptation to their local environment. In consequence, the GWA could lead to unravel the function of known and novel regulators of SAS, which in turn should contribute to a better understanding of the SAS regulatory network in different organs and developmental stages.'

Introduzione (Teaser)

Scientists have developed a sophisticated high-throughput method to study the responses of plants to changes in light.

Descrizione progetto (Article)

It is well known that plants change their growth habits in response to altered light conditions in a phenomenon known as shade avoidance syndrome (SAS). However, SAS has not been well studied in adult plants, and many questions about the genetic and molecular control of this process remain unanswered.

The EU-funded SAS-ARABIDOPSIS-GWA project aimed to address this by developing a complex high-throughput imaging and data collection system to study SAS in Arabidopsis thaliana. Coupled with genetic analyses, this would provide new data on the physical and genetic changes in adult plants in response to poor light conditions.

Early work focused on establishing the imaging system and data pipeline. This required standardised growth protocols, software to convert 2D images to 3D data points, and storing the data in a database.Nearly 200 plants were grown and characterised using this system. At the same time, genetic data was collected from each plant for a genome-wide association (GWA) study to link physical and genetic traits.

Preliminary results showed that genes involved in SAS in young plants played different roles in adult plants. Several new genes that play a role in SAS were identified and will be studied further.

The imaging system developed during this project is very precise, lending itself to a wide range of plant physiology research questions. Taken with the other research findings, SAS-ARABIDOPSIS-GWA will have a major impact on our understanding of plant development.