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Iwata, Hiroyoshi; Niikura, Satoshi; Matsuura, Seiji; Takano, Yasushi; Ukai, Yasuo

doi:10.1023/a:1018392531226

Cited by 133 publications

(23 citation statements)

References 11 publications

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“…Disparities may also result from differences in 326 measurement technique and in the range of root shapes represented in each study. Interestingly, our 327 results are also similar to findings in Japanese radish (Iwata et al, 1998), which identified principal 328 components for aspect ratio (73.9 PVE), bluntness at the distal end of the root (14.2 PVE), and 329 swelling in the middle of the root (3.9 PVE). 330…”

Section: Principal Components Analysis Of Shoot Biomass and Root Shapsupporting

confidence: 81%

An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.)

Turner

et al. 2018

Preprint

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12Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most 13 important agronomic traits are lacking. To address this problem, we developed an automated analysis 14 platform that extracts components of size and shape for carrot shoots and roots, which are necessary 15 to advance carrot breeding and genetics. This method reliably measured variation in shoot size and 16 shape, leaf number, petiole length, and petiole width as evidenced by high correlations with hundreds 17 of manual measurements. Similarly, root length and biomass were accurately measured from the 18 images. This platform quantified shoot and root shapes in terms of principal components, which do 19 not have traditional, manually-measurable equivalents. We applied the pipeline in a study of a six-20 parent diallel population and an F 2 mapping population consisting of 316 individuals. We found high 21 levels of repeatability within a growing environment, with low to moderate repeatability across 22 environments. We also observed co-localization of quantitative trait loci for shoot and root 23 characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage 24 and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably 25 quantified, the development of a high-throughput image analysis pipeline to measure carrot shoot and 26 root morphology will expand the scope and scale of breeding and genetic studies. 27All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

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Section: Principal Components Analysis Of Shoot Biomass and Root Shapsupporting

confidence: 81%

An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.)

Turner

et al. 2018

Preprint

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“…To not only quantify the asymmetries we observe, but to determine which factors modulate them, we conducted an Elliptical Fourier Descriptor (EFD) analysis of leaf outlines (Iwata et al, 1998; Iwata and Ukai, 2002). A powerful feature of EFD is the ability to separate asymmetric sources of shape variance from symmetric, which is important for the question of hand.…”

Section: Resultsmentioning

confidence: 99%

“…Principal component analysis was performed on the EFDs resulting from the first 20 harmonics of Fourier coefficients. For the analysis of symmetrical shape, a and d coefficients were analyzed, while for analysis of asymmetrical shape, b and c coefficients were analyzed (Iwata et al, 1998). Coefficients of EFDs were calculated at −2 and +2 standard deviations for each principal component and the respective contour shapes reconstructed from an inverse Fourier transformation.…”

Section: Methodsmentioning

confidence: 99%

Conflict between Intrinsic Leaf Asymmetry and Phyllotaxis in the Resupinate Leaves of Alstroemeria psittacina

Chitwood¹,

Naylor²,

Thammapichai³

et al. 2012

Front. Plant Sci.

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Spiral phyllotactic patterning is the result of intricate auxin transport relationships in the shoot apical meristem (SAM) that act to place auxin maxima at the future sites of leaf initiation. Inherent to this process is a bias in auxin distribution in leaf primordia, such that increased auxin is found on the descending side of the leaf (toward the older neighbor) compared to the ascending side (toward the younger neighbor), creating phyllotactically dependent leaf asymmetry. Separate from phyllotactic-dependent asymmetry is handedness in plants – that is, genetically encoded, fixed chirality, such as the twining of certain vines and the torsions induced by microtubule mutations. Here, we perform a morphometric analysis on the resupinate leaves of Alstroemeria psittacina. Interestingly, the twist in leaves always occurs in a single direction, regardless of the phyllotactic direction of the plant. Because of the resupination, leaves in this species possess an inherent handedness. However, this asymmetry is modulated in a phyllotactic-dependent manner, consistent with the known developmental constraints of phyllotaxis upon leaf morphology. This creates the interesting circumstance in A. psittacina that leaves arising from plants with a counter-clockwise phyllotactic direction are (1) more asymmetric, (2) larger, and (3) possess symmetrical shape differences relative to leaves from plants with clockwise phyllotaxis. The mechanism underlying these differences likely involves a developmental delay in clockwise leaves caused by the conflict between the phyllotaxis-dependent asymmetry and asymmetry resulting from resupination. The evolutionary implications of a dimorphic population without a genetic basis for selection to act upon are discussed.

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“…PC analysis was performed on the EFDs resulting from the first 20 harmonics of Fourier coefficients. Only asymmetric sources of shape variance were analysed using the b and c coefficients [28]. Coefficients of EFD were calculated at 22 and þ2 s.d.…”

Section: Methodsmentioning

confidence: 99%

Left–right leaf asymmetry in decussate and distichous phyllotactic systems

Martinez

Chitwood

Smith

et al. 2016

Phil. Trans. R. Soc. B

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One contribution of 17 to a theme issue 'Provocative questions in left -right asymmetry'. Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of a particular chirality are similarly asymmetric relative to each other. Models of auxin flux capable of recapitulating spiral phyllotaxis predict handed auxin asymmetries in initiating leaf primordia with empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend a similar analysis of leaf asymmetry to decussate and distichous phyllotaxy. We found that our simulation models of these two patterns predicted mirrored asymmetries in auxin distribution in leaf primordia pairs. To empirically verify the morphological consequences of asymmetric auxin distribution, we analysed the morphology of a tomato sister-of-pin-formed1a (sopin1a) mutant, entire-2, in which spiral phyllotaxy consistently transitions to a decussate state. Shifts in the displacement of leaflets on the left and right sides of entire-2 leaf pairs mirror each other, corroborating predicted model results. We then analyse the shape of more than 800 common ivy (Hedera helix) and more than 3000 grapevine (Vitis and Ampelopsis spp.) leaf pairs and find statistical enrichment of predicted mirrored asymmetries. Our results demonstrate that left-right auxin asymmetries in models of decussate and distichous phyllotaxy successfully predict mirrored asymmetric leaf morphologies in superficially symmetric leaves.This article is part of the themed issue 'Provocative questions in leftright asymmetry'.

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Cited by 133 publications

References 11 publications

An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.)

An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.)

Conflict between Intrinsic Leaf Asymmetry and Phyllotaxis in the Resupinate Leaves of Alstroemeria psittacina

Left–right leaf asymmetry in decussate and distichous phyllotactic systems

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