Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits

Chitwood, Daniel H.; Topp, Christopher N.

doi:10.1016/j.pbi.2015.01.009

Cited by 48 publications

(38 citation statements)

References 54 publications

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“…Using all traits can node be distinguished separately from species? Such a framework is consistent with developmental genetic theory that differences in leaf shape between species versus more conserved heteroblastic changes in leaf shape within individual plants are regulated by distinct genetic pathways [16] that lead to separable morphological effects within single leaves (so-called “cryptotypes” [46]). We also note that the LDAs performed use the “leave one out” approach of cross-validation, in which a separate LDA for each leaf, minus the leaf in question, is used to predict the identity of that leaf.…”

Section: Analysessupporting

confidence: 70%

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

Chitwood

Otoni²

2017

GigaScience

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Background: Leaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology—vasculature and blade—provides different insights into leaf patterning. Results: Here, we morphometrically analyze >3300 leaves from 40 different Passiflora species collected sequentially across the vine. Each leaf is measured in two different ways: using 1) 15 homologous Procrustes-adjusted landmarks of the vasculature, sinuses, and lobes; and 2) Elliptical Fourier Descriptors (EFDs), which quantify the outline of the leaf. The ability of landmarks, EFDs, and both datasets together are compared to determine their relative ability to predict species and node position within the vine. Pairwise correlation of x and y landmark coordinates and EFD harmonic coefficients reveals close associations between traits and insights into the relationship between vasculature and blade patterning. Conclusions: Landmarks, more reflective of the vasculature, and EFDs, more reflective of the blade contour, describe both similar and distinct features of leaf morphology. Landmarks and EFDs vary in ability to predict species identity and node position in the vine and exhibit a correlational structure (both within landmark or EFD traits and between the two data types) revealing constraints between vascular and blade patterning underlying natural variation in leaf morphology among Passiflora species.

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Section: Analysessupporting

confidence: 70%

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

Chitwood

Otoni²

2017

GigaScience

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“…Shade avoidance most closely aligns with genes responsible for differentiating leaf primordia from the meristem and patterning leaf complexity, in particular LeT6 (Janssen et al, 1998;Kim et al, 2003;David-Schwartz et al, 2009), and is distinct from heteroblastic changes mediated by TCPs and CUCs (Ori et al, 2007;Efroni et al, 2008;Berger et al, 2009;Rubio-Somoza et al, 2014) or evolutionary changes mediated by BOP or other KNOX-related pathways (PETROSELINUM and BIPINNATA; Kimura et al, 2008). The morphology of any tomato leaf is the result of contributions of separate developmental, genetic, and environmental effects Chitwood and Topp, 2015), modulated by distinct molecular pathways.…”

Section: Discussionmentioning

confidence: 69%

“…Not only is the shape of a single leaf highly multivariate, but the shape of leaves within and between plants is influenced by evolutionary, genetic, developmental, and environmental factors (Chitwood et al, 2012a(Chitwood et al, , 2012b(Chitwood et al, , 2013Chitwood and Topp, 2015). Over a lifetime, a plant will produce numerous leaf shapes, influenced by the development of individual leaves as their blades unequally expand (allometric expansion; Hales, 1727;Remmler and Rolland-Lagan, 2012;Rolland-Lagan et al, 2014) and the different types of leaf shapes a plant produces at successive nodes, a result of the temporal development of the shoot apical meristem (SAM; heteroblasty; Goebel, 1900;Ashby, 1948;Poethig, 1990Poethig, , 2010Kerstetter and Poethig, 1998).…”

mentioning

confidence: 99%

Light-induced indeterminacy alters shade avoiding tomato leaf morphology

et al. 2015

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Plants sense the foliar shade of competitors and alter their developmental programs through the shade-avoidance response. Internode and petiole elongation, and changes in overall leaf area and leaf mass per area, are the stereotypical architectural responses to foliar shade in the shoot. However, changes in leaf shape and complexity in response to shade remain incompletely, and qualitatively, described. Using a meta-analysis of more than 18,000 previously published leaflet outlines, we demonstrate that shade avoidance alters leaf shape in domesticated tomato (Solanum lycopersicum) and wild relatives. The effects of shade avoidance on leaf shape are subtle with respect to individual traits but are combinatorially strong. We then seek to describe the developmental origins of shade-induced changes in leaf shape by swapping plants between light treatments. Leaf size is light responsive late into development, but patterning events, such as stomatal index, are irrevocably specified earlier. Observing that shade induces increases in shoot apical meristem size, we then describe gene expression changes in early leaf primordia and the meristem using laser microdissection. We find that in leaf primordia, shade avoidance is not mediated through canonical pathways described in mature organs but rather through the expression of KNOTTED1-LIKE HOMEOBOX and other indeterminacy genes, altering known developmental pathways responsible for patterning leaf shape. We also demonstrate that shade-induced changes in leaf primordium gene expression largely do not overlap with those found in successively initiated leaf primordia, providing evidence against classic hypotheses that shaded leaf morphology results from the prolonged production of juvenile leaf types.

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“…Single images can capture data on hundreds of individuals, entire populations, and mixed communities, simultaneously aiding the linkage of genes to traits. The broader collection of gene‐to‐trait associations can be integrated in network models to form a systems biology view of the trait combinations and their correlations underlying phenotype expression and adaptation (Chitwood & Topp, ).…”

Section: Developing Resources For a Tractable Sphagnum Model System Wmentioning

confidence: 99%

The Sphagnome Project: enabling ecological and evolutionary insights through a genus‐level sequencing project

et al. 2017

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SummaryConsiderable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.

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Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits

Cited by 48 publications

References 54 publications

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

Light-induced indeterminacy alters shade avoiding tomato leaf morphology

The Sphagnome Project: enabling ecological and evolutionary insights through a genus‐level sequencing project

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