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Yamamoto E, Yabe S, Inari-Ikeda M, Yoshida H, Morinaka Y, Matsuoka M, Kitano H. Independent control of organ number and distribution pattern in rice panicle. FRONTIERS IN PLANT SCIENCE 2023; 14:1119770. [PMID: 36824199 PMCID: PMC9941638 DOI: 10.3389/fpls.2023.1119770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
As the determinants of yield products, rice panicle traits are important targets for breeding. Despite their importance in grain filling and subsequent yield productivity, knowledge on the organ distribution pattern in rice panicles is limited owing to the lack of objective evaluation methods. In this study, we developed a method for quantifying rice panicle organ distribution patterns. To validate our method for practical application in biology, we integrated this method into a quantitative trait locus (QTL) analysis and identified QTLs for panicle organ distribution patterns in rice. Interestingly, Grain number 1 (Gn1), a major QTL of organ number, was not identified as a QTL for distribution pattern, indicating that the number and distribution of panicle organs are independently controlled. This study provides insight into rice panicle organ distribution patterns that will help improve breeding targeting rice panicle architecture.
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Affiliation(s)
- Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Shiori Yabe
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Mayuko Inari-Ikeda
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
| | - Hideki Yoshida
- Institute of Fermentation Sciences, Fukushima University, Fukushima, Fukushima, Japan
| | - Yoichi Morinaka
- Department of Sustainable Agri-Culture, Fukui Prefectural University, Awara, Fukui, Japan
| | - Makoto Matsuoka
- Institute of Fermentation Sciences, Fukushima University, Fukushima, Fukushima, Japan
| | - Hidemi Kitano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
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Abstract
A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.
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Affiliation(s)
- Hao Xu
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
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Kirie S, Iwasaki H, Noshita K, Iwata H. A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea). PLoS One 2020; 15:e0239781. [PMID: 33045021 PMCID: PMC7549838 DOI: 10.1371/journal.pone.0239781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/13/2020] [Indexed: 12/01/2022] Open
Abstract
Water lilies (Nymphaea spp.) have diverse floral morphologies. Water lilies are not only commonly used as ornamental plants, but they are also important for understanding the diversification of basal angiosperms. Although the diversity in floral morphology of water lily provides useful information for evolutionary biology, horticulture, and horticultural science, it is difficult to describe and analyze the three-dimensional morphology of flowers. In this study, we propose a method to describe the floral morphology of water lily using a three-dimensional theoretical morphological model. The theoretical model was constructed based on three components, i.e., (1) the gradual change in size of floral organs, (2) spiral phyllotaxis, and (3) the interpolation of elevation angles, which were integrated into the model. We generated three-dimensional representation of water lily flowers and visualized theoretical morphospaces by varying each morphological parameter. The theoretical morphospace is a mathematical space of morphological spectrum generated by a theoretical morphological model. These morphospaces seems to display the large part of morphological variations of water lily. We measured morphological parameters of real flowers based on our theoretical model and display the occupation pattern of morphological parameters. We also surveyed the relation between morphological parameters and flower shape descriptions found in a catalog. In some parameters, we found breeders’ description can link to our morphological model. In addition, the relationship between the global features of floral morphology and the parameters of the theoretical model was calculated with flower silhouettes simulated with a range of parameter values and the global features of the silhouette. We used two simple indices to assess the global morphological features, which were calculated with the convex hull. The results indicated that our method can effectively provide an objective and quantitative overview of the diversity in the floral morphology of water lily.
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Affiliation(s)
- Shiryu Kirie
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hideo Iwasaki
- metaPhorest, Department of Electrical Engineering and Bioscience, Waseda University, TWIns, Shinjuku, Tokyo, Japan
| | - Koji Noshita
- Department of Biology, Faculty of Science of Science, Kyushu University, Fukuoka, Fukuoka, Japan
- Plant Frontier Research Center, Kyushu University, Fukuoka, Fukuoka, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail:
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Wang CN, Hsu HC, Wang CC, Lee TK, Kuo YF. Quantifying floral shape variation in 3D using microcomputed tomography: a case study of a hybrid line between actinomorphic and zygomorphic flowers. FRONTIERS IN PLANT SCIENCE 2015; 6:724. [PMID: 26442038 PMCID: PMC4564768 DOI: 10.3389/fpls.2015.00724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/28/2015] [Indexed: 05/20/2023]
Abstract
The quantification of floral shape variations is difficult because flower structures are both diverse and complex. Traditionally, floral shape variations are quantified using the qualitative and linear measurements of two-dimensional (2D) images. The 2D images cannot adequately describe flower structures, and thus lead to unsatisfactory discrimination of the flower shape. This study aimed to acquire three-dimensional (3D) images by using microcomputed tomography (μCT) and to examine the floral shape variations by using geometric morphometrics (GM). To demonstrate the advantages of the 3D-μCT-GM approach, we applied the approach to a second-generation population of florist's gloxinia (Sinningia speciosa) crossed from parents of zygomorphic and actinomorphic flowers. The flowers in the population considerably vary in size and shape, thereby served as good materials to test the applicability of the proposed phenotyping approach. Procedures were developed to acquire 3D volumetric flower images using a μCT scanner, to segment the flower regions from the background, and to select homologous characteristic points (i.e., landmarks) from the flower images for the subsequent GM analysis. The procedures identified 95 landmarks for each flower and thus improved the capability of describing and illustrating the flower shapes, compared with typically lower number of landmarks in 2D analyses. The GM analysis demonstrated that flower opening and dorsoventral symmetry were the principal shape variations of the flowers. The degrees of flower opening and corolla asymmetry were then subsequently quantified directly from the 3D flower images. The 3D-μCT-GM approach revealed shape variations that could not be identified using typical 2D approaches and accurately quantified the flower traits that presented a challenge in 2D images. The approach opens new avenues to investigate floral shape variations.
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Affiliation(s)
- Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipei, Taiwan
- Department of Life Science, National Taiwan UniversityTaipei, Taiwan
| | - Hao-Chun Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipei, Taiwan
| | - Cheng-Chun Wang
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan UniversityTaipei, Taiwan
| | - Tzu-Kuei Lee
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan UniversityTaipei, Taiwan
| | - Yan-Fu Kuo
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan UniversityTaipei, Taiwan
- *Correspondence: Yan-Fu Kuo, Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan
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Guo W, Fukatsu T, Ninomiya S. Automated characterization of flowering dynamics in rice using field-acquired time-series RGB images. PLANT METHODS 2015; 11:7. [PMID: 25705245 PMCID: PMC4336727 DOI: 10.1186/s13007-015-0047-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/19/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Flowering (spikelet anthesis) is one of the most important phenotypic characteristics of paddy rice, and researchers expend efforts to observe flowering timing. Observing flowering is very time-consuming and labor-intensive, because it is still visually performed by humans. An image-based method that automatically detects the flowering of paddy rice is highly desirable. However, varying illumination, diversity of appearance of the flowering parts of the panicles, shape deformation, partial occlusion, and complex background make the development of such a method challenging. RESULTS We developed a method for detecting flowering panicles of rice in RGB images using scale-invariant feature transform descriptors, bag of visual words, and a machine learning method, support vector machine. Applying the method to time-series images, we estimated the number of flowering panicles and the diurnal peak of flowering on each day. The method accurately detected the flowering parts of panicles during the flowering period and quantified the daily and diurnal flowering pattern. CONCLUSIONS A powerful method for automatically detecting flowering panicles of paddy rice in time-series RGB images taken under natural field conditions is described. The method can automatically count flowering panicles. In application to time-series images, the proposed method can well quantify the daily amount and the diurnal changes of flowering during the flowering period and identify daily peaks of flowering.
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Affiliation(s)
- Wei Guo
- />Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1. Midori-cho, Nishi-Tokyo, Tokyo 188-0002 Japan
| | - Tokihiro Fukatsu
- />National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666 Japan
| | - Seishi Ninomiya
- />Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1. Midori-cho, Nishi-Tokyo, Tokyo 188-0002 Japan
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Severa L. Shape and strength of Red Haven peaches at the different stages of their maturity. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2014. [DOI: 10.11118/actaun200856040161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Bubeníčková A, Simeonovová J. Contour determination and shape characteristics of different varieties of potato tubers. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2014. [DOI: 10.11118/actaun201159010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Chacón B, Ballester R, Birlanga V, Rolland-Lagan AG, Pérez-Pérez JM. A quantitative framework for flower phenotyping in cultivated carnation (Dianthus caryophyllus L.). PLoS One 2013; 8:e82165. [PMID: 24349209 PMCID: PMC3862579 DOI: 10.1371/journal.pone.0082165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/21/2013] [Indexed: 11/26/2022] Open
Abstract
Most important breeding goals in ornamental crops are plant appearance and flower characteristics where selection is visually performed on direct offspring of crossings. We developed an image analysis toolbox for the acquisition of flower and petal images from cultivated carnation (Dianthus caryophyllus L.) that was validated by a detailed analysis of flower and petal size and shape in 78 commercial cultivars of D. caryophyllus, including 55 standard, 22 spray and 1 pot carnation cultivars. Correlation analyses allowed us to reduce the number of parameters accounting for the observed variation in flower and petal morphology. Convexity was used as a descriptor for the level of serration in flowers and petals. We used a landmark-based approach that allowed us to identify eight main principal components (PCs) accounting for most of the variance observed in petal shape. The effect and the strength of these PCs in standard and spray carnation cultivars are consistent with shared underlying mechanisms involved in the morphological diversification of petals in both subpopulations. Our results also indicate that neighbor-joining trees built with morphological data might infer certain phylogenetic relationships among carnation cultivars. Based on estimated broad-sense heritability values for some flower and petal features, different genetic determinants shall modulate the responses of flower and petal morphology to environmental cues in this species. We believe our image analysis toolbox could allow capturing flower variation in other species of high ornamental value.
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Affiliation(s)
- Borja Chacón
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Roberto Ballester
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Virginia Birlanga
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
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Ivakov A, Persson S. Plant cell shape: modulators and measurements. FRONTIERS IN PLANT SCIENCE 2013; 4:439. [PMID: 24312104 PMCID: PMC3832843 DOI: 10.3389/fpls.2013.00439] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/14/2013] [Indexed: 05/19/2023]
Abstract
Plant cell shape, seen as an integrative output, is of considerable interest in various fields, such as cell wall research, cytoskeleton dynamics and biomechanics. In this review we summarize the current state of knowledge on cell shape formation in plants focusing on shape of simple cylindrical cells, as well as in complex multipolar cells such as leaf pavement cells and trichomes. We summarize established concepts as well as recent additions to the understanding of how cells construct cell walls of a given shape and the underlying processes. These processes include cell wall synthesis, activity of the actin and microtubule cytoskeletons, in particular their regulation by microtubule associated proteins, actin-related proteins, GTP'ases and their effectors, as well as the recently-elucidated roles of plant hormone signaling and vesicular membrane trafficking. We discuss some of the challenges in cell shape research with a particular emphasis on quantitative imaging and statistical analysis of shape in 2D and 3D, as well as novel developments in this area. Finally, we review recent examples of the use of novel imaging techniques and how they have contributed to our understanding of cell shape formation.
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Affiliation(s)
- Alexander Ivakov
- *Correspondence: Alexander Ivakov and Staffan Persson, Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany e-mail: ;
| | - Staffan Persson
- *Correspondence: Alexander Ivakov and Staffan Persson, Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany e-mail: ;
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Langlade NB, Feng X, Dransfield T, Copsey L, Hanna AI, Thébaud C, Bangham A, Hudson A, Coen E. Evolution through genetically controlled allometry space. Proc Natl Acad Sci U S A 2005; 102:10221-6. [PMID: 16009935 PMCID: PMC1177394 DOI: 10.1073/pnas.0504210102] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding evolutionary change requires phenotypic differences between organisms to be placed in a genetic context. However, there are few cases where it has been possible to define an appropriate genotypic space for a range of species. Here we address this problem by defining a genetically controlled space that captures variation in shape and size between closely related species of Antirrhinum. The axes of the space are based on an allometric model of leaves from an F2 of an interspecific cross between Antirrhinum majus and Antirrhinum charidemi. Three principal components were found to capture most of the genetic variation in shape and size, allowing a three-dimensional allometric space to be defined. The contribution of individual genetic loci was determined from QTL analysis, allowing each locus to be represented as a vector in the allometric space. Leaf shapes and sizes of 18 different Antirrhinum taxa, encompassing a broad range of leaf morphologies, could be accurately represented as clouds within the space. Most taxa overlapped with, or were near to, at least one other species in the space, so that together they defined a largely interconnected domain of viable forms. It is likely that the pattern of evolution within this domain reflects a combination of directional selection and evolutionary tradeoffs within a high dimensional space.
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Affiliation(s)
- Nicolas B Langlade
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, United Kingdom
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