Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach

Cantó, Carla de la Fuente; Kalogiros, Dimitris I.; Ptashnyk, Mariya; George, Timothy S.; Waugh, Robbie; Bengough, A. Glyn; Russell, Joanne; Dupuy, Lionel

doi:10.1016/j.jtbi.2018.03.020

Cited by 5 publications

(3 citation statements)

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“…Prompted by the current large sets of genetic data from genome-wide association studies (GWAS) and advancements in imaging and data processing, high throughput digital root phenotyping techniques have become attractive. Hund et al (2009) used a pouch system to phenotype root traits in maize and, this system has subsequently been applied in other crops such as wheat (Atkinson et al, 2015), Brassica (Thomas et al, 2016), and barley (Canto et al, 2018) for examples.…”

Section: Introductionmentioning

confidence: 99%

The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses

et al. 2019

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Roots are fundamental organs for water and nutrient uptake as well as for signal transduction in response to biotic and abiotic stresses. Flax has a shallow tap root system that relies mostly on top soil nutrient and moisture resources. The crop can easily be outcompeted by weeds or other crops in intercropping systems, especially in moisture deficit conditions. However, there is a wide range of variation among genotypes in terms of performance under scarce resources such as moisture limitation. Here we phenotyped 15 root, two shoot traits and shoot to root dry weight ratio on 115 flax accessions grown in a hydroponic pouch system and performed a genome-wide association study (GWAS) based on seven different models to identify quantitative trait loci underlying these traits. Significant variation among genotypes was observed for the two shoot and 12 of the 14 root traits. Shoot dry weight was correlated with root network volume, length, surface area, and root dry weight (r > 0.5, P < 0.001) but not significantly correlated with root depth (r = 0.033, P > 0.05). The seven GWAS models detected a total of 228 quantitative trait nucleotides (QTNs) for 16 traits. Most loci, defined by an interval of 100 kb up and downstream of the QTNs, harbored genes known to play role(s) in root and shoot development, suggesting them as candidates. Examples of candidate genes linked to root network QTNs included genes encoding GRAS transcription factors, mitogen-activated protein kinases, and auxin related lateral organ boundary proteins while QTN loci for shoot dry weight harbored genes involved in photomorphogenesis and plant immunity. These results provide insights into the genetic bases of early shoot and root development traits in flax that could be capitalized upon to improve its root architecture, particularly in view of better withstanding water limiting conditions during the cropping season.

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Section: Introductionmentioning

confidence: 99%

The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses

et al. 2019

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“…These differences could eventually relate to genotypic differences in root system development across the population. In fact, in a recent evaluation of few RCSLs we found important genotypic variations of root growth parameters in a 2D pouch experimental approach [ 89 ]. Hence, precise phenotyping of these traits in the subset of 28 RCSLs could lead to the identification of major loci governing phenotypic variation of new interesting traits requiring thorough and expensive analysis.…”

Section: Discussionmentioning

confidence: 99%

Genetic dissection of quantitative and qualitative traits using a minimum set of barley Recombinant Chromosome Substitution Lines

et al. 2018

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BackgroundExploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar ‘Harrington’ as the recurrent parent, and a wild barley accession from the Fertile Crescent ‘Caesarea 26–24’, as the donor parent (Matus et al. Genome 46:1010–23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool.MethodsTwenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388–92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach.ResultsWe identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly.ConclusionThis study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1527-7) contains supplementary material, which is available to authorized users.

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“…It has a low cost and is suitable to large-scale studies (Atkinson et al, 2015;Dupuy et al, 2017). The root system of plants growing on paper developed in a 2D plane facilitates stacking (Le Marié et al, 2014) and the application of high resolution and low-cost imaging systems such as cameras and flatbed scanners for data acquisition (Adu et al, 2014;Canto et al, 2018). They are generally available in a range of colours, which facilitated automated processing and analysis of image (Pound et al, 2013(Pound et al, , 2017Adu et al, 2016).…”

Section: Paper Microfluidics For Plant Science Research Applicationsmentioning

confidence: 99%

Spatial and temporal detection of root exudates with a paper-based microfluidic device

Patko,

Gunatilake,

Dupuy

et al. 2023

Preprint

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Root exudates control critical processes in the rhizosphere, retaining water, selecting for beneficial microorganisms or solubilising nutrients prior to uptake by the plant. Analysing root exudation patterns however is challenging because existing methods are often destructive and unable to resolve spatial and temporal variations in the production of root exudates. Here, we present a paper-based microfluidic device with integrated colorimetric sensors for the continuous extraction of root exudates along plant roots. The microfluidic device used standard filter paper wax printer to create channels for water to carry the exudates towards the sensors. TiO2nanotubes/alginate hydrogel-based sensors were used to analyse the glucose content of the root exudates of living plants. The study shows that the paper microfluidic substrate successfully extracts the released glucose from the root, and transfers it to the hydrogel-based sensor to be calorimetrically detected from independent sections of the root at different times, up to 7 days. The method was tested on two different wheat varietiesTriticum aestivum(rgt Tocayo and Filon varieties), where significant differences in exudation patterns were recorded. The researchdemonstrates the feasibility of low cost technological solution for high precision screening and diagnostic of the biochemical composition of root exudates.

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Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach

Cited by 5 publications

References 74 publications

The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses

The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses

Genetic dissection of quantitative and qualitative traits using a minimum set of barley Recombinant Chromosome Substitution Lines

Spatial and temporal detection of root exudates with a paper-based microfluidic device

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