scholarly journals Morphometrics reveals complex and heritable apple leaf shapes

2017 ◽  
Author(s):  
Zoë Migicovsky ◽  
Mao Li ◽  
Daniel H. Chitwood ◽  
Sean Myles
Keyword(s):  
Aspect Ratio ◽  
Leaf Shape ◽  
Persistent Homology ◽  
Primary Source ◽  
Shape Variation ◽  
Linear Measurements ◽  
Narrow Sense Heritability ◽  
Morphometric Variation ◽  
Genome Wide ◽  
Highly Correlated

AbstractApple (Malus spp.) is a widely grown and valuable fruit crop. Leaf shape and size are important for flowering in apple and may also be early indicators for other agriculturally valuable traits. We examined 9,000 leaves from 869 unique apple accessions using linear measurements and comprehensive morphometric techniques. We identified allometric variation in the length-to-width aspect ratio between accessions and species of apple. The allometric variation was due to variation in the width of the leaf blade, not length. Aspect ratio was highly correlated with the primary axis of morphometric variation (PC1) quantified using elliptical Fourier descriptors (EFDs) and persistent homology (PH). While the primary source of variation was aspect ratio, subsequent PCs corresponded to complex shape variation not captured by linear measurements. After linking the morphometric information with over 122,000 genome-wide SNPs, we found high narrow-sense heritability values even at later PCs, indicating that comprehensive morphometrics can capture complex, heritable phenotypes. Thus, techniques such as EFDs and PH are capturing heritable biological variation that would be missed using linear measurements alone, and which could potentially be used to select for a hidden phenotype only detectable using comprehensive morphometrics.

scholarly journals Geometric and topological approaches to shape variation in Ginkgo leaves

2021 ◽  
Vol 8 (11) ◽  
Author(s):  
Haibin Hang ◽  
Martin Bauer ◽  
Washington Mio ◽  
Luke Mander
Keyword(s):  
Leaf Shape ◽  
Persistent Homology ◽  
Leaf Size ◽  
Geometric Method ◽  
Topological Method ◽  
Shape Variation ◽  
Short Shoot ◽  
Plant Trait ◽  
Elastic Curves ◽  
Fossil Leaves

Leaf shape is a key plant trait that varies enormously. The range of applications for data on this trait requires frequent methodological development so that researchers have an up-to-date toolkit with which to quantify leaf shape. We generated a dataset of 468 leaves produced by Ginkgo biloba , and 24 fossil leaves produced by evolutionary relatives of extant Ginkgo . We quantified the shape of each leaf by developing a geometric method based on elastic curves and a topological method based on persistent homology. Our geometric method indicates that shape variation in modern leaves is dominated by leaf size, furrow depth and the angle of the two lobes at the leaf base that is also related to leaf width. Our topological method indicates that shape variation in modern leaves is dominated by leaf size and furrow depth. We have applied both methods to modern and fossil material: the methods are complementary, identifying similar primary patterns of variation, but also revealing different aspects of morphological variation. Our topological approach distinguishes long-shoot leaves from short-shoot leaves, both methods indicate that leaf shape influences or is at least related to leaf area, and both could be applied in palaeoclimatic and evolutionary studies of leaf shape.

scholarly journals Geometric and Topological Approaches to Shape Variation in Ginkgo Leaves

2020 ◽  
Author(s):  
Luke Mander ◽  
Martin Bauer ◽  
Haibin Hang ◽  
Washington Mio
Keyword(s):  
Leaf Shape ◽  
Persistent Homology ◽  
Leaf Size ◽  
Geometric Method ◽  
Topological Method ◽  
Shape Variation ◽  
Plant Trait ◽  
Elastic Curves ◽  
Fossil Material ◽  
Fossil Leaves

AbstractLeaf shape is a key plant trait that varies enormously. The diversity of leaf shape, and the range of applications for data on this trait, requires frequent methodological developments so that researchers have an up-to-date toolkit with which to quantify leaf shape. We generated a dataset of 468 leaves produced by Ginkgo biloba, and 24 fossil leaves produced by evolutionary relatives of extant Ginkgo. We quantified the shape of each leaf by developing a geometric method based on elastic curves and a topological method based on persistent homology. Our geometric method indicates that shape variation in modern leaves is dominated by leaf size, furrow depth, and the angle of the two lobes at the base of the leaf that is also related to leaf width. Our topological method indicates that shape variation in modern leaves is dominated by leaf size and furrow depth. Both methods indicate that there is greater diversity in the shape of fossil leaves compared to modern leaves. The two approaches we have described can be applied to modern and fossil material, and are complementary: identifying similar primary patterns of variation, but revealing some different aspects of morphological variation.

scholarly journals Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Todd R. Robeck ◽  
Zhe Fei ◽  
Ake T. Lu ◽  
Amin Haghani ◽  
Eve Jourdain ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Age Estimation ◽  
Species Conservation ◽  
Genome Wide ◽  
Epigenetic Aging ◽  
Highly Correlated ◽  
Methylation Patterns ◽  
Cg Dinucleotides ◽  
Free Ranging ◽  
Unique Species

AbstractThe development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples.

scholarly journals MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yanping Zhang ◽  
Jing Peng ◽  
Xiaohui Yuan ◽  
Lisi Zhang ◽  
Dongzi Zhu ◽  
...  
Keyword(s):  
Prunus Avium ◽  
Cultivar Identification ◽  
Leaf Shape ◽  
Persistent Homology ◽  
Growth Period ◽  
Image Features ◽  
Crop Species ◽  
Score Level Fusion ◽  
Level Fusion ◽  
Leaf Image

AbstractRecognizing plant cultivars reliably and efficiently can benefit plant breeders in terms of property rights protection and innovation of germplasm resources. Although leaf image-based methods have been widely adopted in plant species identification, they seldom have been applied in cultivar identification due to the high similarity of leaves among cultivars. Here, we propose an automatic leaf image-based cultivar identification pipeline called MFCIS (Multi-feature Combined Cultivar Identification System), which combines multiple leaf morphological features collected by persistent homology and a convolutional neural network (CNN). Persistent homology, a multiscale and robust method, was employed to extract the topological signatures of leaf shape, texture, and venation details. A CNN-based algorithm, the Xception network, was fine-tuned for extracting high-level leaf image features. For fruit species, we benchmarked the MFCIS pipeline on a sweet cherry (Prunus avium L.) leaf dataset with >5000 leaf images from 88 varieties or unreleased selections and achieved a mean accuracy of 83.52%. For annual crop species, we applied the MFCIS pipeline to a soybean (Glycine max L. Merr.) leaf dataset with 5000 leaf images of 100 cultivars or elite breeding lines collected at five growth periods. The identification models for each growth period were trained independently, and their results were combined using a score-level fusion strategy. The classification accuracy after score-level fusion was 91.4%, which is much higher than the accuracy when utilizing each growth period independently or mixing all growth periods. To facilitate the adoption of the proposed pipelines, we constructed a user-friendly web service, which is freely available at http://www.mfcis.online.

Developmental comparison of leaf shape variation in three Chamaedorea species

Botany ◽  
2009 ◽  
Vol 87 (2) ◽  
pp. 210-221 ◽  
Author(s):  
Julia Nowak ◽  
Adam Nowak ◽  
Usher Posluszny
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Light Microscopy ◽  
Leaf Development ◽  
Leaf Shape ◽  
Shape Variation ◽  
Differential Growth ◽  
Scanning Electron ◽  
Palm Leaf ◽  
The Ideal

Compound palm leaf development is unique and consists of two processes. First, the primordial tissue folds through differential growth, forming plications. Second, these plications separate through an abscission-like process, forming leaflets. The second process of leaflet separation allows for the development of compound leaves. The question that this study addresses concerns the development of bifid leaves, as they do not form leaflets but only develop a cleft through an apical incision. The ideal genus to use for this study is Chamaedorea as it includes species with both pinnate and bifid leaves. Chamaedorea fragrans (Ruiz & Pav.) Mart. and Chamaedorea stolonifera H. Wendl. ex Hook. f. were chosen as the species with adult bifid leaves. Although Chamaedorea seifrizii Burret is a pinnate-leaved palm, its juvenile leaves are bifid. Scanning electron microscopy and light microscopy were used to study the development of bifid leaves. Our results indicate that neither of these bifid palms develop separation sites within the lamina, but rather the apical cleft develops through “late leaflet separation” or by an abscission-like process. In contrast, C. seifrizii juvenile leaves exhibit “early leaflet separation” when developing the apical cleft.

scholarly journals Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.)

2018 ◽  
Vol 19 (9) ◽  
pp. 2794 ◽  
Author(s):  
Rong Zhou ◽  
Komivi Dossa ◽  
Donghua Li ◽  
Jingyin Yu ◽  
Jun You ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Yield ◽  
Association Studies ◽  
Oil Quality ◽  
Genome Wide Association ◽  
Oilseed Crop ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Highly Correlated ◽  
Capsule Size

Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10−7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame.

scholarly journals Positional variation rather than salt stress dominates changes in three-dimensional leaf shape patterns in cucumber canopies

2019 ◽  
Author(s):  
Dominik Schmidt ◽  
Katrin Kahlen
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Leaf Shape ◽  
Three Dimensional ◽  
Size Variation ◽  
Canopy Architecture ◽  
Shape Variation ◽  
Stress Study ◽  
Salinity Levels ◽  
Adaptation Processes

Abstract Leaf shape plays a key role in the interaction of a plant with its environment, best-known in the plant’s light harvest. Effects of the environment on the interplay of canopy architecture and physiological functioning can be estimated using functional-structural plant models (FSPMs). In order to reduce the complexity of canopy simulations, leaf shape models used in FSPMs are often simple prototypes scaled to match current leaf area. L-Cucumber is such an FSPM, whose leaf prototype mimics average real leaf shape of unstressed cucumber plants well. However, adaptation processes or stress responses may lead to non-proportional changes in leaf geometries, which, for example, could affect length to width ratios or curvatures. The current leaf shape model in L-Cucumber is static and hence does not incorporate changes in leaf shape within or between plants. Thus, the aim of this study was to estimate leaf shape variation and exemplarily study its effects on FSPM simulations. Three-dimensional leaf coordinate data from a salt stress study were analysed with a robust Bayesian mixed-effects model for estimating leaf shape depending on rank, size and salinity. Results showed that positional and size variation rather than salinity levels dominated 3D leaf shape patterns of cucumber. Considering variable leaf shapes in relation to this main sources of variation in L-Cucumber simulations, only minor effects compared to a realistic, yet static average shape were found. However, with similar computational demands variation in shapes other studies highly sensitive to shape dynamics, for example, pesticide spraying might be affected more strongly.

scholarly journals Inheritance of Fruit, Foliar, and Plant Habit Attributes in Capsicum

2008 ◽  
Vol 133 (3) ◽  
pp. 396-407 ◽  
Author(s):  
John R. Stommel ◽  
Robert J. Griesbach
Keyword(s):  
Plant Height ◽  
Leaf Shape ◽  
Leaf Length ◽  
Fruit Color ◽  
Broad Sense ◽  
Leaf Width ◽  
Broad Sense Heritability ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Plant Habit

Considerable diversity exists in Capsicum L. germplasm for fruit and leaf shape, size, and color as well as plant habit. Using F1, F2, and backcross generations developed from diverse parental stocks, this report describes the inheritance patterns and relationships between unique foliar characters and diverse fruit and plant habit attributes. Our results demonstrate that pepper fruit color, shape, and fruit per cluster were simply inherited with modifying gene action. Broad-sense heritability for fruit color and shape and fruit per cluster was high, whereas narrow-sense heritability for these characters was moderate to low. Although fruit clustering was simply inherited, the number of fruit per cluster exhibited a quantitative mode of inheritance. High fruit counts per cluster were linked with red fruit color and anthocyanin pigmented foliage. Fruit shape was linked with immature fruit color and inherited independently of mature fruit color. Leaf color, length, and plant height were quantitatively inherited. Leaf shape did not vary, but leaf length varied and was positively correlated with leaf width. Broad-sense heritability for leaf characters, including leaf length, leaf width, and leaf color, was high. With the exception of leaf width, which exhibited low narrow-sense heritability, high narrow-sense heritability for leaf characters denoted additive gene action. Plant height displayed high broad-sense heritability. Moderate narrow-sense heritability suggested that additive effects also influence plant height. Analysis of segregating populations demonstrated that red and orange fruit color can be combined with all possible leaf colors from green to black. These results provide new data to clarify and extend available information on the inheritance of Capsicum fruit attributes and provide new information on the genetic control of leaf characters and plant habit.

scholarly journals Morphometric Correlates of Age and Breeding Status in American Coots

The Auk ◽  
1987 ◽  
Vol 104 (4) ◽  
pp. 640-646 ◽  
Author(s):  
Ray T. Alisauskas
Keyword(s):  
Body Size ◽  
Multivariate Techniques ◽  
Same Sex ◽  
Linear Measurements ◽  
Morphometric Variation ◽  
Size And Shape ◽  
Multivariate Dispersion ◽  
Age Related ◽  
The Social ◽  
Males And Females

Abstract I studied morphometric variation in 13 linear measurements from 228 American Coots (Fulica americana) collected in southern Manitoba. Univariate and multivariate techniques revealed differences in size and shape among adult coots that were 1, 2, and =2 yr old. In addition to the obvious differences in size between males and females, the morphometry of older birds differed from that of younger birds in two ways. First, older coots were of larger body size than younger coots of the same sex. Second, older coots had proportionately larger feet and claws relative to the size of their tarsi, and proportionately wider bills and heads relative to other head measurements, than did younger birds. Multivariate dispersion matrices within age/sex cohorts were less variable for older coots. In an analysis of 1-yr-old males, breeders did not differ from nonbreeders in overall body size, but breeders had relatively longer claws and wings than nonbreeders. Age-related differences in morphology may have relevance to the social structure of nesting coots, which involves highly aggressive territorial behavior. Part of the age-related variation in nesting phenology that has been documented elsewhere for coots may be a consequence of covariation in body size and shape.

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