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Pramanik D, Vaskimo L, Batenburg KJ, Kostenko A, Droppert K, Smets E, Gravendeel B. Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11567. [PMID: 38369982 PMCID: PMC10873816 DOI: 10.1002/aps3.11567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 02/20/2024]
Abstract
Premise Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research. Methods We utilized three-dimensional (3D) micro-computed tomography (CT) scans to capture the movement of fast-growing Erycina pusilla roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing E. pusilla and Phalaenopsis equestris fruits, two-dimensional (2D) photographs were used. Results The E. pusilla roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77-84 days after germination [DAG]) and the subsequent period occurred later in development (140-154 DAG). While E. pusilla fruits twisted 45° from 56-63 days after pollination (DAP), the fruits of P. equestris only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP). Discussion Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.
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Affiliation(s)
- Dewi Pramanik
- Evolutionary EcologyNaturalis Biodiversity CenterDarwinweg 22333 CRLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
- Research Center for Horticulture, Research Organization for Agriculture and FoodNational Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN)Cibinong Science Center, Jl. Raya Jakarta‐Bogor, Pakansari, CibinongWest Java16915Indonesia
| | - Lotta Vaskimo
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 112333 CKLeidenThe Netherlands
| | - K. Joost Batenburg
- Leiden Institute of Advanced Computer Science, Faculty of ScienceLeiden University, SnelliusNiels Bohrweg 12333 CALeidenThe Netherlands
- Computational ImagingCentrum Wiskunde en InformaticaScience Park 1231090 GBAmsterdamThe Netherlands
| | - Alexander Kostenko
- Computational ImagingCentrum Wiskunde en InformaticaScience Park 1231090 GBAmsterdamThe Netherlands
| | - Kevin Droppert
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 112333 CKLeidenThe Netherlands
| | - Erik Smets
- Evolutionary EcologyNaturalis Biodiversity CenterDarwinweg 22333 CRLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
- Ecology, Evolution and Biodiversity Conservation, KU LeuvenKasteelpark Arenberg 31, BOX 24353001LeuvenBelgium
| | - Barbara Gravendeel
- Evolutionary EcologyNaturalis Biodiversity CenterDarwinweg 22333 CRLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
- Radboud Institute for Biological and Environmental SciencesRadboud UniversityHeyendaalseweg 1356500 GLNijmegenThe Netherlands
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2
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Shape asymmetry - what's new? Emerg Top Life Sci 2022; 6:285-294. [PMID: 35758318 DOI: 10.1042/etls20210273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
Studies of shape asymmetry have become increasingly abundant as the methods of geometric morphometrics have gained widespread use. Most of these studies have focussed on fluctuating asymmetry and have largely obtained similar results as more traditional analyses of asymmetry in distance measurements, but several notable differences have also emerged. A key difference is that shape analyses provide information on the patterns, not just the amount of variation, and therefore tend to be more sensitive. Such analyses have shown that apparently symmetric structures in animals consistently show directional asymmetry for shape, but not for size. Furthermore, the long-standing prediction that phenotypic plasticity in response to environmental heterogeneity can contribute to fluctuating asymmetry has been confirmed for the first time for the shape of flower parts (but not for size). Finally, shape analyses in structures with complex symmetry, such as many flowers, can distinguish multiple types of directional asymmetry, generated by distinct direction-giving factors, which combine to the single component observable in bilaterally symmetric structures. While analyses of shape asymmetry are broadly compatible with traditional analyses of asymmetry, they incorporate more detailed morphological information, particularly for structures with complex symmetry, and therefore can reveal subtle biological effects that would otherwise not be apparent. This makes them a promising tool for a wide range of studies in the basic and applied life sciences.
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3
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Hamilton CA, Winiger N, Rubin JJ, Breinholt J, Rougerie R, Kitching IJ, Barber JR, Kawahara AY. Hidden phylogenomic signal helps elucidate arsenurine silkmoth phylogeny and the evolution of body size and wing shape trade-offs. Syst Biol 2021; 71:859-874. [PMID: 34791485 DOI: 10.1093/sysbio/syab090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
One of the key objectives in biological research is understanding how evolutionary processes have produced Earth's diversity. A critical step towards revealing these processes is an investigation of evolutionary tradeoffs - that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are poorly understood. In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference - a region of a tree that possesses short branches and no "support" for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks) to better illuminate the most probable generic relationships within the subfamily. We found there are putative evolutionary trade-offs between wing shape, body size, and the interaction of fore- and hindwing shape. Namely, body size tends to decrease with increasing hindwing length but increases as forewing shape becomes more complex. Additionally, the type of hindwing (i.e., tail or no tail) a lineage possesses has a significant effect on the complexity of forewing shape. We outline possible selective forces driving the complex hindwing shapes that make Arsenurinae, and silkmoths as a whole, so charismatic.
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Affiliation(s)
- Chris A Hamilton
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844 USA
| | - Nathalie Winiger
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Wildlife Ecology and Management, Albert-Ludwigs-Universität Freiburg, 79106 Freiburg, Germany
| | - Juliette J Rubin
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA
| | - Jesse Breinholt
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Division of Bioinformatics, Intermountain Healthcare, Precision Genomics, St. George, UT 84790 USA
| | - Rodolphe Rougerie
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Ian J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jesse R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725 USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA
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4
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Durrington B, Chong F, Chitwood DH. Directional phyllotactic bias in calatheas ( Goeppertia, Marantaceae): A citizen science approach. QUANTITATIVE PLANT BIOLOGY 2021; 2:e6. [PMID: 37077213 PMCID: PMC10095900 DOI: 10.1017/qpb.2021.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/16/2021] [Accepted: 02/16/2021] [Indexed: 05/03/2023]
Abstract
Lateral organs arranged in spiral phyllotaxy are separated by the golden angle, ≈137.5°, leading to chirality: either clockwise or counter-clockwise. In some species, leaves are asymmetric such that they are smaller and curved towards the side ascending the phyllotactic spiral. As such, these asymmetries lead to mirroring of leaf shapes in plants of opposite phyllotactic handedness. Previous reports had suggested that the pin-stripe calathea (Goeppertia ornata) may be exclusively of one phyllotactic direction, counter-clockwise, but had limited sampling to a single population. Here, we use a citizen science approach leveraging a social media poll, internet image searches, in-person verification at nurseries in four countries and digitally-curated, research-grade observations to demonstrate that calatheas (Goeppertia spp.) around the world are biased towards counter-clockwise phyllotaxy. The possibility that this bias is genetic and its implications for models of phyllotaxy that assume handedness is stochastically specified in equal proportions is discussed.
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Affiliation(s)
- Benjamin Durrington
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Fiona Chong
- Department of Biological & Marine Sciences, University of Hull, Hull, United Kingdom
- Energy and Environment Institute, University of Hull, Hull, United Kingdom
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, USA
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5
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A WOX/Auxin Biosynthesis Module Controls Growth to Shape Leaf Form. Curr Biol 2020; 30:4857-4868.e6. [DOI: 10.1016/j.cub.2020.09.037] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/17/2020] [Accepted: 09/11/2020] [Indexed: 12/28/2022]
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6
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Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue MJ, Edwards E, Fajardo D, Fang H, Frank MH, Gallaher T, Gebken S, Hill T, Jansky S, Kaur B, Klahs PC, Klein LL, Kuraparthy V, Londo J, Migicovsky Z, Miller A, Mohn R, Myles S, Otoni WC, Pires JC, Rieffer E, Schmerler S, Spriggs E, Topp CN, Van Deynze A, Zhang K, Zhu L, Zink BM, Chitwood DH. Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace. FRONTIERS IN PLANT SCIENCE 2018; 9:553. [PMID: 29922307 PMCID: PMC5996898 DOI: 10.3389/fpls.2018.00553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/09/2018] [Indexed: 05/18/2023]
Abstract
Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Clement Bagaza
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Albert Batushansky
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Lynn Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Viktoriya Coneva
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Erika Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Diego Fajardo
- National Center for Genome Resources (NCGR), Santa Fe, NM, United States
| | - Hui Fang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | | | - Timothy Gallaher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Sarah Gebken
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Shelley Jansky
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, United States
| | - Baljinder Kaur
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Phillip C. Klahs
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Laura L. Klein
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Vasu Kuraparthy
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Jason Londo
- Grape Genetics Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Geneva, NY, United States
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Allison Miller
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Rebekah Mohn
- Department of Plant and Microbial Biology, University of Minnesota – Twin Cities, St. Paul, MN, United States
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Wagner C. Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - J. C. Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Edmond Rieffer
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Sam Schmerler
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
- American Museum of Natural History, New York, NY, United States
| | - Elizabeth Spriggs
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | | | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Kuang Zhang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Linglong Zhu
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Braden M. Zink
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Daniel H. Chitwood
- Independent Researcher, Santa Rosa, CA, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
- Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
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7
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Martinez CC, Chitwood DH, Smith RS, Sinha NR. Left-right leaf asymmetry in decussate and distichous phyllotactic systems. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0412. [PMID: 27821524 DOI: 10.1098/rstb.2015.0412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2016] [Indexed: 11/12/2022] Open
Abstract
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 left-right asymmetry'.
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Affiliation(s)
- Ciera C Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany.,Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, CA 95616, USA
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8
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Abstract
Many plants show some form of helical growth, such as the circular searching movements of growing stems and other organs (circumnutation), tendril coiling, leaf and bud reversal (resupination), petal arrangement (contortion) and leaf blade twisting. Recent genetic findings have revealed that such helical growth may be associated with helical arrays of cortical microtubules and of overlying cellulose microfibrils. An alternative mechanism of coiling that is based on differential contraction within a bilayer has also recently been identified and underlies at least some of these growth patterns. Here, I provide an overview of the genes and cellular processes that underlie helical patterning. I also discuss the diversity of helical growth patterns in plants, highlighting their potential adaptive significance and comparing them with helical growth patterns in animals.
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Affiliation(s)
- David R Smyth
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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9
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Chitwood DH, Otoni WC. Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade. Gigascience 2017; 6:1-13. [PMID: 28369351 PMCID: PMC5437945 DOI: 10.1093/gigascience/giw008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/23/2016] [Indexed: 01/15/2023] Open
Abstract
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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Affiliation(s)
| | - Wagner C Otoni
- Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brasil
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10
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Chitwood DH, Otoni WC. Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade. Gigascience 2017. [PMID: 28369351 DOI: 10.5524/100251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
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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Affiliation(s)
| | - Wagner C Otoni
- Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brasil
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11
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Martinez CC, Chitwood DH, Smith RS, Sinha NR. Left-right leaf asymmetry in decussate and distichous phyllotactic systems. Philos Trans R Soc Lond B Biol Sci 2016; 371:rstb.2015.0412. [PMID: 27821524 DOI: 10.1101/043869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2016] [Indexed: 05/22/2023] Open
Abstract
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 left-right asymmetry'.
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Affiliation(s)
- Ciera C Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, CA 95616, USA
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12
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Chitwood DH, Klein LL, O'Hanlon R, Chacko S, Greg M, Kitchen C, Miller AJ, Londo JP. Latent developmental and evolutionary shapes embedded within the grapevine leaf. THE NEW PHYTOLOGIST 2016; 210:343-55. [PMID: 26580864 PMCID: PMC5063178 DOI: 10.1111/nph.13754] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/13/2015] [Indexed: 05/02/2023]
Abstract
Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a single leaf. Here, we measured the shapes of > 3200 leaves representing > 270 vines from wild relatives of domesticated grape (Vitis spp.) to determine whether leaf shapes attributable to genetics and development are separable from each other. We isolated latent shapes (multivariate signatures that vary independently from each other) embedded within the overall shape of leaves. These latent shapes can predict developmental stages independent from species identity and vice versa. Shapes predictive of development were then used to stage leaves from 1200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity. Our results indicate that distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.
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Affiliation(s)
| | - Laura L. Klein
- Department of BiologySaint Louis UniversitySt LouisMO63103USA
| | - Regan O'Hanlon
- Department of BiologySaint Louis UniversitySt LouisMO63103USA
| | - Steven Chacko
- Department of BiologySaint Louis UniversitySt LouisMO63103USA
| | - Matthew Greg
- Department of BiologySaint Louis UniversitySt LouisMO63103USA
| | | | | | - Jason P. Londo
- United States Department of AgricultureAgriculture Research ServiceGrape Genetics Research UnitGenevaNY14456USA
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13
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Chitwood DH, Klein LL, O'Hanlon R, Chacko S, Greg M, Kitchen C, Miller AJ, Londo JP. Latent developmental and evolutionary shapes embedded within the grapevine leaf. THE NEW PHYTOLOGIST 2016. [PMID: 26580864 DOI: 10.5061/dryad.zkh189377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a single leaf. Here, we measured the shapes of > 3200 leaves representing > 270 vines from wild relatives of domesticated grape (Vitis spp.) to determine whether leaf shapes attributable to genetics and development are separable from each other. We isolated latent shapes (multivariate signatures that vary independently from each other) embedded within the overall shape of leaves. These latent shapes can predict developmental stages independent from species identity and vice versa. Shapes predictive of development were then used to stage leaves from 1200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity. Our results indicate that distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.
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Affiliation(s)
| | - Laura L Klein
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Regan O'Hanlon
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Steven Chacko
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Matthew Greg
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Cassandra Kitchen
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Jason P Londo
- United States Department of Agriculture, Agriculture Research Service, Grape Genetics Research Unit, Geneva, NY, 14456, USA
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Analyzing Fluctuating Asymmetry with Geometric Morphometrics: Concepts, Methods, and Applications. Symmetry (Basel) 2015. [DOI: 10.3390/sym7020843] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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15
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Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland LR, Ostria-Gallardo E, Aguilar-Martínez JA, Bush S, Carriedo L, Fulop D, Martinez CC, Peng J, Maloof JN, Sinha NR. Resolving distinct genetic regulators of tomato leaf shape within a heteroblastic and ontogenetic context. THE PLANT CELL 2014; 26:3616-29. [PMID: 25271240 PMCID: PMC4213164 DOI: 10.1105/tpc.114.130112] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 05/18/2023]
Abstract
Leaf shape is mutable, changing in ways modulated by both development and environment within genotypes. A complete model of leaf phenotype would incorporate the changes in leaf shape during juvenile-to-adult phase transitions and the ontogeny of each leaf. Here, we provide a morphometric description of >33,000 leaflets from a set of tomato (Solanum spp) introgression lines grown under controlled environment conditions. We first compare the shape of these leaves, arising during vegetative development, with >11,000 previously published leaflets from a field setting and >11,000 leaflets from wild tomato relatives. We then quantify the changes in shape, across ontogeny, for successive leaves in the heteroblastic series. Using principal component analysis, we then separate genetic effects modulating (1) the overall shape of all leaves versus (2) the shape of specific leaves in the series, finding the former more heritable than the latter and comparing quantitative trait loci regulating each. Our results demonstrate that phenotype is highly contextual and that unbiased assessments of phenotype, for quantitative genetic or other purposes, would ideally sample the many developmental and environmental factors that modulate it.
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Affiliation(s)
- Daniel H Chitwood
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Aashish Ranjan
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Ravi Kumar
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Lauren R Headland
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | | | | | - Susan Bush
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Leonela Carriedo
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Daniel Fulop
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Ciera C Martinez
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Jie Peng
- Department of Statistics, University of California at Davis, Davis, California 95616
| | - Julin N Maloof
- Department of Plant Biology, University of California at Davis, Davis, California 95616
| | - Neelima R Sinha
- Department of Plant Biology, University of California at Davis, Davis, California 95616
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16
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Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya M, Prins B, Li L, Myles S, Sinha NR. A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. PLANT PHYSIOLOGY 2014; 164:259-72. [PMID: 24285849 PMCID: PMC3875807 DOI: 10.1104/pp.113.229708] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/25/2013] [Indexed: 05/18/2023]
Abstract
Terroir, the unique interaction between genotype, environment, and culture, is highly refined in domesticated grape (Vitis vinifera). Toward cultivating terroir, the science of ampelography tried to distinguish thousands of grape cultivars without the aid of genetics. This led to sophisticated phenotypic analyses of natural variation in grape leaves, which within a palmate-lobed framework exhibit diverse patterns of blade outgrowth, hirsuteness, and venation patterning. Here, we provide a morphometric analysis of more than 1,200 grape accessions. Elliptical Fourier descriptors provide a global analysis of leaf outlines and lobe positioning, while a Procrustes analysis quantitatively describes venation patterning. Correlation with previous ampelography suggests an important genetic component, which we confirm with estimates of heritability. We further use RNA-Seq of mutant varieties and perform a genome-wide association study to explore the genetic basis of leaf shape. Meta-analysis reveals a relationship between leaf morphology and hirsuteness, traits known to correlate with climate in the fossil record and extant species. Together, our data demonstrate a genetic basis for the intricate diversity present in grape leaves. We discuss the possibility of using grape leaves as a breeding target to preserve terroir in the face of anticipated climate change, a major problem facing viticulture.
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17
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Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR. A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. THE PLANT CELL 2013; 25:2465-81. [PMID: 23872539 PMCID: PMC3753377 DOI: 10.1105/tpc.113.112391] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/27/2013] [Accepted: 07/05/2013] [Indexed: 05/18/2023]
Abstract
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations.
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Affiliation(s)
- Daniel H. Chitwood
- Department of Plant Biology, University of California, Davis, California 95616
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, California 95616
| | - Lauren R. Headland
- Department of Plant Biology, University of California, Davis, California 95616
| | - Aashish Ranjan
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, California 95616
| | - Daniel Fulop
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Jie Peng
- Department of Statistics, University of California, Davis, California 95616
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, California 95616
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, California 95616
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18
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Chitwood DH, Sinha NR. A census of cells in time: quantitative genetics meets developmental biology. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:92-9. [PMID: 23218243 DOI: 10.1016/j.pbi.2012.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 11/06/2012] [Accepted: 11/08/2012] [Indexed: 05/09/2023]
Abstract
Quantitative genetics has become a popular method for determining the genetic basis of natural variation. Combined with genomic methods, it provides a tool for discerning the genetic basis of gene expression. So-called genetical genomics approaches yield a wealth of genomic information, but by necessity, because of cost and time, fail to resolve the differences between organs, tissues, and/or cell types. Similarly, quantitative approaches in development that might potentially address these issues are seldom applied to quantitative genetics. We discuss recent advances in cell type-specific isolation methods, the quantitative analysis of phenotype, and developmental modeling that are compatible with quantitative genetics and, with time, promise to bridge the gap between these two powerful disciplines yielding unprecedented biological insight.
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Affiliation(s)
- Daniel H Chitwood
- Department of Plant Biology, University of California at Davis, Davis, CA 95616, United States
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19
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Benítez M. An interdisciplinary view on dynamic models for plant genetics and morphogenesis: scope, examples and emerging research avenues. FRONTIERS IN PLANT SCIENCE 2013; 4:7. [PMID: 23386856 PMCID: PMC3560346 DOI: 10.3389/fpls.2013.00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/10/2013] [Indexed: 05/08/2023]
Affiliation(s)
- Mariana Benítez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
- *Correspondence:
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