A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

Abstract

Large-scale phenotyping of multicellular organisms is one of the current challenges in biology. We present a comprehensive and scalable pipeline that allows for the efficient phenotyping of root growth traits on a large scale. This includes a highresolution, low-cost acquisition setup as well as the automated image processing software BRAT. We assess the performance of this pipeline in Arabidopsis thaliana under multiple growth conditions and show its utility by performing genome-wide association studies on 16 root growth traits quantified by BRAT each day during a 5-d time-course experiment. The most significantly associated genome region for root growth rate is a locus encoding a calcium sensing receptor. We find that loss of function and overexpression of this gene can significantly alter root growth in a growth condition dependent manner and that the minor natural allele of the Calcium Sensor Receptor locus is highly significantly enriched in populations in coastal areas, demonstrating the power of our approach to identify regulators of root growth that might have adaptive relevance.

Natural Variation of Root Traits: From Development to Nutrient Uptake

“…However, for root phenotyping, many solutions are available (http://www. plant-image-analysis.org), and root phenotyping pipelines have recently been developed that specifically aim at the quantification of a large number of root traits at a high throughput Slovak et al, 2014).…”

“…The most significant association led to the identification of a condition-dependent regulator of root growth. Interestingly, the minor allele of this Calcium Sensor Receptor (CaS) gene was found to be enriched in populations in coastal regions, suggesting that variation in CaS could have adaptive significance for growth in coastal environments (Slovak et al, 2014). A chemical genetics approach combined with mapping using an RIL population that used different sensitivity to a small molecule ([5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione) that inhibits abscisic acid (ABA) -induced gene expression and signaling and eventually leads to a reduction of PR growth identified a Toll-Interleukin1 Receptor nucleotide binding-leucine-rich repeat coding gene and its natural variants underlying these responses (Kim et al, 2012).…”

Quantitative Variation in Responses to Root Spatial Constraint within Arabidopsis thaliana

“…However, given that the root constraint is 5 mm deep 3 5 mm in diameter, this would require a root angle of 26.6 to hit the very bottom of the physical barrier. In agar, the Bay accession has been found to have a root growth angle of only 2 degrees off of vertical and only 1 of 163 accessions had an angle of greater than 19 degrees off of vertical (Slovak et al, 2014). Thus, this is likely not a source of difference between the Bay and Sha parents for the 5-mm-deep root constraint.…”

“…Thus, this is likely not a source of difference between the Bay and Sha parents for the 5-mm-deep root constraint. The angle required to hit the barrier at least once decreases to only 9 degrees off of vertical for the 15-mm root constraint, suggesting that thigmotropic aspects may become an issue with the deeper root constraints (Slovak et al, 2014).…”

“…The root's primary gravitropism and associated set point growth angle establish the initial vector for a young root's growth (Slovak et al, 2014). The root tip then perceives any ensuing obstruction to growth and alters its growth to avoid this obstruction.…”