Geometric morphometrics reveals shifts in flower shape symmetry and size following gene knockdown of CYCLOIDEA and ANTHOCYANIDIN SYNTHASE

Berger, Brent A.; Ricigliano, Vincent A.; Savriama, Yoland; Lim, Aedric; Thompson, Veronica; Howarth, Dianella G.

doi:10.1186/s12870-017-1152-x

Cited by 20 publications

(27 citation statements)

References 97 publications

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“…In fact, the use of GM tools to analyze plant shape have already started, from a botanical, systematic, archaeological [32, 33, 35], and even experimental [58] point of view.…”

Section: Discussionmentioning

confidence: 99%

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Arabidopsis phenotyping through geometric morphometrics

Manacorda¹,

Asurmendi

2018

GigaScience

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BackgroundRecently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units.ResultsHere, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed.ConclusionsCombined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.

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“…In fact, the use of GM tools to analyze plant shape have already started, from a botanical, systematic, archaeological [32, 33, 35], and even experimental [58] point of view.…”

Section: Discussionmentioning

confidence: 99%

“…In a few recent studies that focused on flowers [58–60] or leaves [61], asymmetry in plants was examined by comparing GM with those in animals [51]. Although we did not study the asymmetry issue, it must be briefly considered.…”

Section: Methodsmentioning

confidence: 99%

Arabidopsis phenotyping through geometric morphometrics

Manacorda¹,

Asurmendi

2018

GigaScience

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“…We argue that anthesis is the most relevant ontogenetic stage for reproduction as well as pollinator attraction and thus is the most meaningful stage to include in our study. Following other plant studies (Berger et al, 2017;Gómez, Perfectti & Camacho, 2006;Gomez, Perfectti & Klingenberg, 2014;Savriama et al, 2012), we decided to include all floral parts at their own, separate, anthesis. This results in the separate datasets of the TUBE (containing the nectar tube and stamens) and the PETAL (containing the corolla).…”

Section: Virtual3d Connexion Of 2d Data Setsmentioning

confidence: 99%

Capturing variation in floral shape: a virtual3D based morphospace for Pelargonium

Kerke

Engelenhoven

et al. 2020

PeerJ

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Background Variation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a virtual3D model reconstructed from 2D photographical data and demonstrate its performance in capturing shape variation. Methods This approach offers unique benefits to complement established imaging techniques (i) by enabling adequate coverage of the potential morphospace of large and diverse flowering-plant clades; (ii) by circumventing asynchronicity in anthesis of different floral parts; and (iii) by incorporating variation in copy number of floral organs within structures. We demonstrate our approach by analysing 90 florally-diverse species of the Southern African genus Pelargonium (Geraniaceae). We quantify Pelargonium floral shapes using 117 landmarks and show similarities in reconstructed morphospaces for nectar tube, corolla (2D datasets), and a combined virtual3D dataset. Results Our results indicate that Pelargonium species differ in floral shape, which can also vary extensively within a species. PCA results of the reconstructed virtual3D floral models are highly congruent with the separate 2D morphospaces, indicating it is an accurate, virtual, representation of floral shape. Through our approach, we find that adding the third dimension to the data is crucial to accurately interpret the manner of, as well as levels of, shape variation in flowers.

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“…We argue that anthesis is the most relevant ontogenetic stage for reproduction as well as pollinator attraction and thus is the most meaningful stage to include in our study. Following other plant studies (Berger et al, 2017;Gómez et al, 2006;Gomez, Perfectti, & Klingenberg, 2014;Savriama, Gomez, Perfectti, & Klingenberg, 2012), we decided to include all floral parts at their own, separate, anthesis. This results in the separate datasets of the TUBE (containing the nectar tube and stamens) and the PETAL (containing the corolla).…”

Section: Virtual3d Connection Of 2d Data Setsmentioning

confidence: 99%

Peer Review #1 of "Capturing variation in floral shape: a virtual3D based morphospace for Pelargonium (v0.1)"

Jones¹

2020

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Background. Variation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a virtual3D model reconstructed based on 2D photographical data and demonstrate its performance in capturing shape variation. Methods. This approach offers unique benefits to complement established imaging techniques i) by enabling adequate coverage of the potential morphospace of large and diverse flowering-plant clades; (ii) by circumventing asynchronicity in anthesis of different floral parts; and (iii) by incorporating variation in copy number of floral organs within structures. We demonstrate our approach by analysing 90 florallydiverse species of the Southern African genus Pelargonium (Geraniaceae). We quantify Pelargonium floral shapes using 117 landmarks and show similarities in reconstructed morphospaces for nectar tube, corolla (2D datasets), and a combined virtual3D dataset. Results. Our results indicate that Pelargonium species differ in floral shape, which can also vary extensively within a species. PCA results of the reconstructed virtual3D floral models are highly congruent with the separate 2D morphospaces, indicating it is an accurate, virtual, representation of floral shape. Through our approach, we find that adding the third dimension to the data is crucial to accurately interpret the manner of, as well as levels of, shape variation in flowers.

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Geometric morphometrics reveals shifts in flower shape symmetry and size following gene knockdown of CYCLOIDEA and ANTHOCYANIDIN SYNTHASE

Cited by 20 publications

References 97 publications

Arabidopsis phenotyping through geometric morphometrics

Arabidopsis phenotyping through geometric morphometrics

Capturing variation in floral shape: a virtual3D based morphospace for Pelargonium

Peer Review #1 of "Capturing variation in floral shape: a virtual3D based morphospace for Pelargonium (v0.1)"

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