A biomarker based on gene expression indicates plant water status in controlled and natural environments

Abstract

Plant or soil water status is required in many scientific fields to understand plant responses to drought. Because the transcriptomic response to abiotic conditions, such as water deficit, reflects plant water status, genomic tools could be used to develop a new type of molecular biomarker. Using the sunflower (Helianthus annuus L.) as a model species to study the transcriptomic response to water deficit both in greenhouse and field conditions, we specifically identified three genes that showed an expression pattern highly correlated to plant water status as estimated by the pre-dawn leaf water potential, fraction of transpirable soil water, soil water content or fraction of total soil water in controlled conditions. We developed a generalized linear model to estimate these classical water status indicators from the expression levels of the three selected genes under controlled conditions. This estimation was independent of the four tested genotypes and the stage (pre-or post-flowering) of the plant. We further validated this gene expression biomarker under field conditions for four genotypes in three different trials, over a large range of water status, and we were able to correct their expression values for a large diurnal sampling period.

Stress-Related Gene Expression Reflects Morphophysiological Responses to Water Deficit

“…Several studies searched for biomarkers (transcripts) that can be used to assess the physiological state of a plant using high-throughput and candidate-gene approaches (Yang et al, 2011;Rengel et al, 2012;Marchand et al, 2013). We observed a strong relationship between relative NCED3 expression levels during MWD and SWD and the response ratios of water content and leaf dry matter content ( Fig.…”

“…Little is also known about gene expression and its morphophysiological consequences during later phases of acclimation to WD conditions. Knowledge of these processes could generate useful applications, such as gene expression-based markers for assessing plant physiology or predictive models of plant WD responses (Yang et al, 2011;Marchand et al, 2013).…”

Promises and challenges of eco-physiological genomics in the field: tests of drought responses in switchgrass

“…Methods to emulate field-like conditions in the laboratory or greenhouse settings have been developed as an alternative to traditional soil water dry-downs (Harb et al, 2010); however, even factorial combinations of stressors (Suzuki et al, 2014) may fail to capture the complex interplay of environmental variables experienced in the field. Furthermore, while it is crucial to relate findings of field studies with those performed under controlled conditions, only a few studies have been published that compare physiological traits and gene expression data in drought treatments in both field and greenhouse conditions (but see Rengel et al, 2012;Marchand et al, 2013).…”

“…A classic solution is to increase biological replication, but this is generally not feasible with costly and time-sensitive physiological and genetic assays (Poorter et al, 2012b;Marchand et al, 2013). Despite these difficulties, understanding the effects of drought in field conditions is necessary because it is in these settings that yield is impacted and selection is acting to shape adaptive responses to stress.…”

Changes in sunflower breeding over the last fifty years

“…fr/en/project/presentation). It has already been possible to identify markers and genes active under stressed conditions (Marchand et al, 2013). In other collaborative programmes, markers have been found for good yield under dry conditions, but since this is a most competitive aspect of sunflower breeding, results remain largely confidential.…”