Biology subjects

Daniel H Chitwood

Publications and source records attributed to Daniel H Chitwood.

10 recordsLinked to original sources

bioRxiv2016

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

BACKGROUNDLeaf 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.\n\nRESULTSHere, we morphometrically analyze >3,300 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.\n\nCONCLUSIONSLandmarks, 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.

Plant Biology↗

bioRxiv2016

Morphometric analysis of Passiflora leaves II: divergent heteroblastic trajectories underlie the disparate leaf shapes among Passiflora species

PREMISE OF THE STUDYNot only does leaf shape vary between Passiflora species, but between sequential nodes of the vine. The profound changes in leaf shape within Passiflora vines reflect the temporal development of the shoot apical meristem from which leaves are derived and patterned, a phenomenon known as heteroblasty.\n\nMETHODSWe perform a morphometric analysis of more than 3,300 leaves from 40 different Passiflora species using two different methods: homologous landmarks and Elliptical Fourier Descriptors (EFDs).\n\nKEY RESULTSChanges in leaf shape across the vine are first quantified in allometric terms; that is, changes in the relative area of leaf sub-regions expressed in terms of overall leaf area. Shape is constrained to strict linear relationships as a function of size that vary between species. Statistical analysis of leaf shape, using landmarks and EFDs, reveals that species effects are the strongest, followed by interaction effects, and negligible heteroblasty effects. The ability of different nodes to predictively discriminate species and the variability of landmark and EFD traits at each node is then analyzed. Heteroblastic trajectories, the changes in leaf shape between the first and last measured leaves in a vine, are then compared between species in a multivariate space.\n\nCONCLUSIONLeaf shape diversity among Passiflora species is expressed in a heteroblastic-dependent manner. Leaf shape is constrained by linear, allometric relationships related to leaf size that vary between species. There is a strong species x heteroblasty interaction effect for leaf shape, suggesting that different leaf shapes between species arise through changes in shape across nodes. The first leaves in the series are not only more like each other, but are also less variable across species. From this similar, shared leaf shape, subsequent leaves in the heteroblastic series follow divergent morphological trajectories. The disparate leaf shapes characteristic of Passiflora species arise from a shared, juvenile morphology.

Plant Biology↗

bioRxiv2016

Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)

Leaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus, okra (L-D1). The okra locus is not only of agricultural importance in cotton (Gossypium hirsutum L.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at the L-D1 locus are controlled by a HD-Zip transcription factor most similar to Late Meristem Identity1 (LMI1) gene. The classical okra leaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-type normal leaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of this LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. An intermediate leaf shape allele, sub-okra, lacks both the promoter duplication and the exonic deletion. Our results indicate that sub-okra is the ancestral leaf shape of tetraploid cotton and normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton.

Plant Biology↗

bioRxiv2016

Plant Chimeras: the good, the bad, and the Bizzaria

Chimeras - organisms that are composed of cells of more than one genotype - captured the human imagination long before they were formally described and used in the laboratory. These organisms owe their namesake to a fire-breathing monster from Greek mythology that has the head of a lion, the body of a goat, and the tail of a serpent. The first description of a non-fictional chimera dates back to the middle of the seventeenth century when the Florentine gardener Pietro Nati discovered an adventitious shoot growing from the graft junction between sour orange (Citrus aurantium) and citron (C. medica). This perplexing chimera that grows with sectors phenotypically resembling each of the citrus progenitors inspired discussion and wonder from the scientific community and was fittingly named the Bizzaria. Initially, the Bizzaria was believed to be an asexual hybrid that formed from a cellular fusion between the grafted parents; however, in-depth cellular analyses carried out centuries later demonstrated that the Bizzaria, along with other chimeras, owe their unique sectored appearance to a conglomeration of cells from the two donors. Since this pivotal discovery at the turn of the twentieth century, chimeras have served both as tools and as unique biological phenomena that have contributed to our understanding of plant development at the cellular, tissue, and organismal level. Rapid advancements in genome sequencing technologies have enabled the establishment of new model species with novel morphological and developmental features that enable the generation of chimeric organisms. In this review, we show that genetic mosaic and chimera studies provide a technologically simple way to delve into the organismal, genetic, and genomic inner workings underlying the development of diverse model organisms. Moreover, we discuss the unique opportunity that chimeras present to explore universal principles governing intercellular communication and the coordination of organismal biology in a heterogenomic landscape.

Plant Biology↗

bioRxiv2016

Left-right leaf asymmetry in decussate and distichous phyllotactic systems

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 analyzed the morphology of a tomato sister-of-pinformed1a (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 analyze the shape of >800 commonivy (Hedera helix) and >3,000 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.

Plant Biology↗

bioRxiv2016

A Sister of PIN1 gene in tomato (Solanum lycopersicum) defines organ initiation patterns by maintaining epidermal auxin flux

The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One of the main contributors to auxin localization is the auxin efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis has revealed that PIN1 genes are split into two sister clades; PIN1 and the relatively uncharacterized Sister-Of-PIN1 (SoPIN1). In this paper we identify entire-2 as a loss-of-function SlSoPIN1a (Solyc10g078370) mutant in Solanum lycopersicum. The entire-2 plants are unable to specify proper leaf initiation leading to a frequent switch from the wild type spiral phyllotactic pattern to distichous and decussate patterns. Leaves in entire-2 are large and less complex and the leaflets display spatial deformities in lamina expansion, vascular development, and margin specification. During sympodial growth in entire-2 the specification of organ position and identity is greatly affected resulting in variable branching patterns on the main sympodial and inflorescence axes. To understand how SlSoPIN1a functions in establishing proper auxin maxima we used the auxin signaling reporter DR5::Venus to visualize differences in auxin localization between entire-2 and wild type. DR5::Venus visualization shows a widening of auxin localization which spreads to subepidermal tissue layers during early leaf and flower organogenesis, showing that SoPIN1 functions to focus auxin signaling to the epidermal layer. The striking spatial deformities observed in entire-2 help provide a mechanistic framework for explaining the function of the SoPIN1 clade in angiosperm species.\n\nAuthor SummaryThe plant hormone auxin acts as a positional signal in most plant developmental processes. The PIN-FORMED family of auxin transporters are the main contributors to auxin localization, especially PIN-FORMED1, which has been studied extensively in plant model species Arabidopsis thaliana. Members of the PIN-FORMED gene family have been found in all plant species, but there is a scarcity of mutants described outside Arabidopsis thaliana. Using Solanum lycopersicum (tomato) as a system, this study identifies a loss of function mutant from the Sister-Of-PIN1 clade in the SlSoPIN1a gene. The characterization of this mutant reveals the role of SlSoPIN1a in establishing position of organ initiation during shoot and reproductive development, including a role in establishing proper spiral phyllotaxy. We use an auxin visualization technique to conclude SlSoPIN1a functions in specifying auxin presence in proper cell layers to establish organ and tissue positioning. This work gives further evolutionary context to how PIN-FORMED genes act to establish organogenesis in the plant kingdom.

Plant Biology↗

bioRxiv2016

eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression Quantitative Trait Loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato Solanum lycopersicum to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome, and identified ~7,200 eQTL regulating the steady state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hotspots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity, and hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive expression QTL analysis details the influence of these loci on plant phenotypes, and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.

Genomics↗

bioRxiv2015

Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

Light is an essential resource for photosynthesis. Limitation of light by shade from plant neighbors can induce a light competition program known as the shade avoidance response (SAR), thereby altering plant growth and development for the sake of survival. Natural genetic variation in SAR is found in plants adapted to distinct environments, including domesticated tomato Solanum lycopersicum and its wild relative Solanum pennellii. QTL mapping was used to examine variation of the SAR between these two species. We found organ specific responses in the elongation of the stem and petiole, including developmental acceleration of growth. Through RNAseq analysis we identified a number of ILs with reduced expression of auxin-related genes in shade treatment. These same ILs display a shade tolerant phenotype in stem growth and overall height. We also identified ILs with altered SAR expression of cell wall expansion genes, although these genotypes had no accompanying alteration in phenotype. Examination of weighted gene co-expression Connectivity networks in sun- and shade-treated plants revealed Connectivity changes in auxin and light signaling genes; this result was supported by the Identification of motifs within the promoters of a subset of shade-responsive genes that were enriched in light signaling, developmental pathways, and auxin responsive transcriptional domains. The Identification ofboth systemic and organ-specific shade tolerance in the ILs, as well as associated changes in the transcriptome, has the potential to inform future studies for breeding plants able to be grown closely (while neighbor-shaded), yet still maintaining high yield.\n\nSummaryGrowth plasticity in response to shade involves expression of specific auxin signaling and cell wall expansion genes, and shade avoidance QTL affect both stem elongation and developmental rate.

Plant Biology↗

bioRxiv2015

Climate and developmental plasticity: interannual variability in grapevine leaf morphology

The shape of leaves are dynamic, changing over evolutionary time between species, within a single plant producing different shaped leaves at successive nodes, during the development of a single leaf as it allometrically expands, and in response to the environment. Notably, strong correlations between the dissection and size of leaves with temperature and precipitation exist in both the paleorecord and extant populations. Yet, a morphometric model integrating evolutionary, developmental, and environmental effects on leaf shape is lacking. Here, we continue a morphometric analysis of >5,500 leaves representing 270 grapevines of multiple Vitis species between two growing seasons. Leaves are paired one-to-one, vine-to-vine accounting for developmental context, between growing seasons. Linear Discriminant Analysis reveals shape features that specifically define growing season, regardless of species or developmental context. The shape feature, a more pronounced distal sinus, is associated with the colder, drier growing season, consistent with patterns observed in the paleorecord. We discuss the implications of such plasticity in a long-lived woody perennial, such as grapevine, with respect to the evolution and functionality of plant morphology and changes in climate.

Plant Biology↗

bioRxiv2015

Latent developmental and evolutionary shapes embedded within the grapevine leaf

O_LIAcross 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. Additionally, leaf shape varies among individuals, populations, and species due to evolutionary processes and environmental influences.\nC_LIO_LIBecause 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 measure the shapes of >3,200 leaves representing >270 vines from wild relatives of domesticated grape (Vitis spp.) to determine if leaf shapes attributable to genetics and development are separable from each other.\nC_LIO_LIWe isolate 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 are then used to stage leaves from 1,200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity.\nC_LIO_LIOur results indicate distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.\nC_LI

Plant Biology↗