ORCID Profile
0000-0002-2324-5495
Current Organisations
Oklahoma State University Stillwater
,
Oklahoma State University
,
University of California, Irvine
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Publications
Floral development and molecular phylogeny support the generic status of Tasmannia (Winteraceae)
Publisher: Wiley
Date: 03-2004
DOI: 10.3732/AJB.91.3.321
Abstract: The taxonomic status of and evolutionary relationship between Tasmannia and Drimys (Winteraceae) have been subjects of controversy for many years. In this paper, a molecular phylogenetic analysis of the family with sequences of previously unpublished Tasmannia and Drimys species confirms earlier conclusions that Tasmannia and Drimys do not form a monophyletic group, despite the fact that they appear to share distinctive inflorescence and floral morphological attributes. Examination of alternative hypotheses of relationships with likelihood-ratio tests and parametric bootstrapping supports the separation of Tasmannia and Drimys. A detailed analysis of floral development in Tasmannia lanceolata and T. xerophila indicates that timing and position of sepal initiation differs between them, but that the position of subsequent organ initiation predictably follows from sepal position. This is in contrast to Drimys winteri, where a prolonged delay between sepal and petal initiation leads to the production of many phyllotactic patterns. The prolonged period of calyx tube growth leading to the formation of a calyptra in Tasmannia and Drimys probably evolved in parallel in the two lineages.
Transcriptomic analysis of seed development in Paysonia auriculata (Brassicaceae) identifies genes involved in hydroxy fatty acid biosynthesis and seed maturation
Publisher: Cold Spring Harbor Laboratory
Date: 08-09-2022
DOI: 10.1101/2022.09.06.506826
Abstract: Paysonia auriculata (Brassicaceae) produces multiple hydroxy fatty acids as major components of the seed oil. We tracked the changes in seed oil composition and gene expression during development, starting 14 days after flowers had been pollinated. Seed oil changes showed initially higher levels of saturated and unsaturated fatty acids (FAs) but little accumulation of hydroxy fatty acids (HFAs). Starting 21 days after pollination (DAP) HFA content sharply increased, and reached almost 30% at 28 DAP. Total seed oil also increased from a low of approximately 2% at 14 DAP to a high of approximately 20% by 42 DAP. We identified almost all of the fatty acid synthesis and modification genes that are known from Arabidopsis, and, in addition, a strong candidate for the hydroxylase gene that mediates the hydroxylation of fatty acids to produce valuable hydroxy fatty acids (HFAs) in this species. The gene expression network revealed is very similar to that of the emerging oil crop, Physaria fendleri , in the sister genus to Paysonia . Phylogenetic analyses indicate the hydroxylase enzyme, FAH12, evolved only once in Paysonia and Physaria , and that the enzyme is closely related to FAD2 enzymes. Phylogenetic analyses of FAD2 and FAH12 in the Brassicaceae and outgroup genera suggest that the branch leading to the hydroxylase clade of Paysonia and Physaria is under relaxed selection, compared with the strong purifying selection found across the FAD2 lineages.
PlantCV v2.0: Image analysis software for high-throughput plant phenotyping
Publisher: PeerJ
Date: 05-09-2017
DOI: 10.7287/PEERJ.PREPRINTS.3225V1
Abstract: Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the ersity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.
Inflorescence diversification in the panicoid bristle grass clade (Paniceae, Poaceae): Evidence from molecular phylogenies and developmental morphology
Publisher: Wiley
Date: 08-2002
Abstract: Grasses exhibit a great variety of inflorescence forms and these appear homoplasious when mapped onto cladograms. The overall pattern is sufficiently complex that it is difficult to analyze inflorescence evolution. We have reduced the complexity of the problem by examining one group of grasses, the panicoid "bristle clade," which exhibits a less complex pattern of variation. The clade is morphologically defined by inflorescences bearing both spikelets and sterile bristles and is monophyletic in both morphological and molecular phylogenetic analyses. We have constructed a chloroplast DNA phylogeny of the three main genera, which finds three well-supported clades, two comprising species placed in Setaria and one of Pennisetum + Cenchrus. In this tree Cenchrus is monophyletic, but both Setaria and Pennisetum are paraphyletic. Developmental morphology of these groups is very similar at early stages. Changes in axis ramification, primordial differentiation, and axis elongation account for most variation in mature inflorescence morphology. Characters derived from comparisons of developmental sequences were optimized onto one of the most parsimonious trees. Most developmental characters were congruent with the molecular phylogeny except for three reversals in the subclade containing S. barbata, S. palmifolia, and two accessions of S. poiretiana. Changes in just a handful of developmental events account for inflorescence evolution in the bristle clade, and similar changes may account for inflorescence ersity in the grasses as a whole.
Transcriptomic analysis of seed development in Paysonia auriculata (Brassicaceae) identifies genes involved in hydroxy fatty acid biosynthesis
Publisher: Frontiers Media SA
Date: 13-01-2023
DOI: 10.3389/FPLS.2022.1079146
Abstract: Paysonia auriculata (Brassicaceae) produces multiple hydroxy fatty acids as major components of the seed oil. We tracked the changes in seed oil composition and gene expression during development, starting 14 days after flowers had been pollinated. Seed oil changes showed initially higher levels of saturated and unsaturated fatty acids (FAs) but little accumulation of hydroxy fatty acids (HFAs). Starting 21 days after pollination (DAP) HFA content sharply increased, and reached almost 30% at 28 DAP. Total seed oil also increased from a low of approximately 2% at 14 DAP to a high of approximately 20% by 42 DAP. We identified almost all of the fatty acid synthesis and modification genes that are known from Arabidopsis, and, in addition, a strong candidate for the hydroxylase gene that mediates the hydroxylation of fatty acids to produce valuable hydroxy fatty acids (HFAs) in this species. The gene expression network revealed is very similar to that of the emerging oil crop, Physaria fendleri , in the sister genus to Paysonia . Phylogenetic analyses indicate the hydroxylase enzyme, FAH12, evolved only once in Paysonia and Physaria , and that the enzyme is closely related to FAD2 enzymes. Phylogenetic analyses of FAD2 and FAH12 in the Brassicaceae and outgroup genera suggest that the branch leading to the hydroxylase clade of Paysonia and Physaria is under relaxed selection, compared with the strong purifying selection found across the FAD2 lineages.
Comparative sequence analysis of the Phytochrome C gene and its upstream region in allohexaploid wheat reveals new data on the evolution of its three constituent genomes
Publisher: Springer Science and Business Media LLC
Date: 07-2005
DOI: 10.1007/S11103-005-6801-Z
Abstract: Bread wheat is an allohexaploid with genome composition AABBDD. Phytochrome C is a gene involved in photomorphogenesis that has been used extensively for phylogenetic analyses. In wheat, the PhyC genes are single copy in each of the three homoeologous genomes and map to orthologous positions on the long arms of the group 5 chromosomes. Comparative sequence analysis of the three homoeologous copies of the wheat PhyC gene and of some 5 kb of upstream region has demonstrated a high level of conservation of PhyC, but frequent interruption of the upstream regions by the insertion of retroelements and other repeats. One of the repeats in the region under investigation appeared to have inserted before the ergence of the diploid wheat genomes, but was degraded to the extent that similarity between the A and D copies could only be observed at the amino acid level. Evidence was found for the differential presence of a foldback element and a miniature inverted-repeat transposable element (MITE) 5' to PhyC in different wheat cultivars. The latter may represent the first ex le of an active MITE family in the wheat genome. Several conserved non-coding sequences were also identified that may represent functional regulatory elements. The level of sequence ergence (Ks) between the three wheat PhyC homoeologs suggests that the ergence of the diploid wheat ancestors occurred some 6.9 Mya, which is considerably earlier than the previously estimated 2.5-4.5 Mya. Ka/Ks ratios were <0.15 indicating that all three homoeologs are under purifying selection and presumably represent functional PhyC genes. RT-PCR confirmed expression of the A, B and D copies. The discrepancy in evolutionary age of the wheat genomes estimated using sequences from different parts of the genome may reflect a mosaic origin of some of the Triticeae genomes.
Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria
Publisher: Public Library of Science (PLoS)
Date: 17-03-2016
Haplotype Analysis and Linkage Disequilibrium at Five Loci inEragrostis tef
Publisher: Oxford University Press (OUP)
Date: 03-2012
Abstract: Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia. Lodging is the most important production problem in tef. The rht1 and sd1 dwarfing genes have been useful for improving lodging resistance in wheat and rice, respectively, in what has been known as the “Green Revolution.” All homologs of rht1 and sd1 were cloned and sequenced from 31 tef accessions collected from across Ethiopia. The allotetraploid tef genome was found to carry two rht1 homologs. From sequence variation between these two putative homologs, an approximate ancestral ergence date of 6.4 million years ago was calculated for the two genomes within tef. Three sd1 homologs were identified in tef, with unknown orthologous aralogous relationships. The genetic ersity in the 31 studied accessions was organized into a relatively small number of haplotypes (2−4) for four of these genes, whereas one rht1 homeologue exhibited 10 haplotypes. A low level of nucleotide ersity was observed at all loci. Linkage disequilibrium analysis demonstrated strong linkage disequilibrium, extending the length of the five genes investigated (2−4 kb), with no significant decline. There was no significant correlation between haplotypes of any of these genes and their recorded site of origin.
<I>Zuloagaea</I>, a New Genus of Neotropical Grass Within the Bristle Clade (Poaceae: Paniceae)
Publisher: American Society of Plant Taxonomists
Date: 10-2006
Effect of genotype and environment on branching in weedy green millet (Setaria viridis) and domesticated foxtail millet (Setaria italica) (Poaceae)
Publisher: Wiley
Date: 29-11-2006
Genetic control of branching in foxtail millet
Publisher: Proceedings of the National Academy of Sciences
Date: 07-06-2004
Abstract: Reduction in vegetative branching is commonplace when crops are domesticated from their wild progenitors. We have identified genetic loci responsible for these changes in foxtail millet ( Setaria italica ), a crop closely related to maize but whose genetics are little known. Quantitative trait locus (QTL) analysis and comparative genomics reveal that basal branching (tillering) and axillary branching are partially controlled by separate loci, and that the orthologue of teosinte branched1 , the major gene controlling branching phenotype in maize, has only a minor and variable effect. We identify other candidate genes for control of branching, including a number of hormone biosynthesis pathway genes. These results suggest that similar phenotypic effects may not be produced by orthologous loci, even in closely related species, and that results from well characterized model systems such as maize must be reviewed critically before being applied to other species.
Xyris l. Section xyris (xyridaceae) in australia
Publisher: CSIRO Publishing
Date: 1994
DOI: 10.1071/SB9940455
Abstract: A systematic study of the Australian species of Xyris section Xyris is presented. Seven species are recognised, of which Xyris cheumatophila A.N. Doust & B.J. Conn is described for the first time. All recognised taxa are provided with descriptions (including illustrations), distribution information (including maps), habitat descriptions, nomenclatural and other relevant notes. Lectotypes are here designated for all previously described Australian species of section Xyris which are accepted by us. An iconotype of the name of X. indica (the type of the genus) is here chosen.
Comparative floral ontogeny in Winteraceae
Publisher: JSTOR
Date: 2000
DOI: 10.2307/2666195
Grass architecture: genetic and environmental control of branching
Publisher: Elsevier BV
Date: 02-2007
DOI: 10.1016/J.PBI.2006.11.015
Abstract: Variation in grass architecture profoundly affects light capture, competition, and reproductive success, and is responsive to environmental factors such as crowding and nutrient limitation. Recent work in both model and crop systems has uncovered many aspects of the genetic control of branching, including conservation of the MONOCULM1 and MORE AXILLARY BRANCHING/DECREASED APICAL DOMINANCE/RAMOSUS (MAX/DAD/RMS) genetic pathways among the grasses and the model dicot systems of tomato, Arabidopsis, Petunia and pea. Parallel studies on the effect of environment on branching have also begun to uncover links between environmental sensing through phytochrome pathways, and resultant changes in TEOSINTE BRANCHED1 expression, and meristem inhibition. Future work promises to integrate knowledge of phenotypic responses to environment with our understanding of the genetic and hormonal changes that underlie phenotypic change.
Morphological diversity and genetic regulation of inflorescence abscission zones in grasses
Publisher: Wiley
Date: 10-2014
DOI: 10.3732/AJB.1400186
Abstract: • Variation in how seeds are dispersed in grasses is ecologically important, and selection for dispersal mechanisms has produced a great variety of dispersal structures (diaspores). Abscission ("shattering") is necessary in wild grasses, but its elimination by selection on nonshattering mutants was a key component of the domestication syndrome in cereal grasses. A key question is whether a common genetic pathway controls abscission in wild grasses, and, if so, what genes in that pathway may have been selected upon during domestication. We summarize morphological and genetic information on abscission zones and disarticulation patterns in grasses and identify hypotheses to test the likelihood of a common genetic pathway.• Morphological data on abscission zones for over 10000 species of grasses were tabulated and analyzed using a tribal phylogeny of the grasses. The genomic location of quantitative trait loci (QTLs) and orthologs of genes controlling shattering were compared across species to ascertain whether the same loci might control shattering in different grass lineages.• The simple trait of nonshattering is derived from a great ersity of shattering phenotypes. Several sets of QTLs from multiple species are syntenic yet many are not. Genes known to be involved in shattering in several species were found to have orthologs that sometimes colocalized with QTLs in different species, adding support to the hypothesis of retention of a common genetic pathway. These results are used to suggest a research plan that could test the common genetic pathway model more thoroughly.
Architectural Evolution and its Implications for Domestication in Grasses
Publisher: Oxford University Press (OUP)
Date: 28-07-2007
DOI: 10.1093/AOB/MCM040
Detection of members of the Secoviridae in the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA
Publisher: Elsevier BV
Date: 07-2012
DOI: 10.1016/J.VIRUSRES.2012.03.016
Abstract: Viruses are most frequently discovered because they cause disease. To expand knowledge of plant-associated viruses beyond these narrow constraints, non-cultivated plants of the Tallgrass Prairie of the United States were systematically surveyed for evidence of viruses. This report discusses putative viruses of the family Secoviridae identified by the survey. Sequence analysis suggests the presence of at least six viruses in the study site, including Bean pod mottle virus, Maize chlorotic dwarf virus, three previously undescribed viruses within the subfamily Comovirinae and one unclassifiable virus.
The C4 Model Grass Setaria Is a Short Day Plant with Secondary Long Day Genetic Regulation
Publisher: Frontiers Media SA
Date: 06-07-2017
Wheels within wheels, Nested Function-value Traits as a Tool for Modeling Ontogeny
Publisher: Cold Spring Harbor Laboratory
Date: 17-03-2021
DOI: 10.1101/2021.03.16.435729
Abstract: Plant morphologies exhibit a wide array of outcomes that have evolved as a consequence adapting to a wide array of ecological pressures. These disparate morphologies have provided a rich field for comparative morphologists, developmental biologists, and geneticists to explore. Ultimately the array of variation observed in nature across different plant species is built on the same functional unit, the phytomer, which is composed of a leaf, a node, and an internode. Sequentially produced phytomers exhibit heteroblasty, that is, a gradual or abrupt change in shape, either due to size changes or changes due to reproductive phase. The progression of shape change over time is often indirectly measured by s ling several stages of plant growth and comparing allometric relationships between shape variables. However, a more precise method is to use an absolute time scale and measure shape change of sequential organs directly. In this study we use such time-dependent measurements to build a general model of organ growth for several Setaria genotypes, for both leaves and internodes. We term this the second-order function-value trait (2FVT) model, because it generalizes in idual function-value trait models generated for each organ. This model reduces phenotypic noise by averaging the general trend of ontogeny and provides a quantitative tool to describe where and when phenotypic shifts occur during the ontogenies of different genotypes. The ability to recognize how ontogenetic variation is distributed within equivalent positions of the body plan at the interspecific level can be used as a tool to explore various questions related to growth and form in plants both for comparative morphology and developmental genetics.
Morphological Development of Setaria viridis from Germination to Flowering
Publisher: Springer International Publishing
Date: 20-12-2016
The Effect of Photoperiod on Flowering Time, Plant Architecture, and Biomass in Setaria
Publisher: Springer International Publishing
Date: 20-12-2016
Pearl millet response to drought: A review
Publisher: Frontiers Media SA
Date: 10-02-2023
DOI: 10.3389/FPLS.2023.1059574
Abstract: The C4 grass pearl millet is one of the most drought tolerant cereals and is primarily grown in marginal areas where annual rainfall is low and intermittent. It was domesticated in sub-Saharan Africa, and several studies have found that it uses a combination of morphological and physiological traits to successfully resist drought. This review explores the short term and long-term responses of pearl millet that enables it to either tolerate, avoid, escape, or recover from drought stress. The response to short term drought reveals fine tuning of osmotic adjustment, stomatal conductance, and ROS scavenging ability, along with ABA and ethylene transduction. Equally important are longer term developmental plasticity in tillering, root development, leaf adaptations and flowering time that can both help avoid the worst water stress and recover some of the yield losses via asynchronous tiller production. We examine genes related to drought resistance that were identified through in idual transcriptomic studies and through our combined analysis of previous studies. From the combined analysis, we found 94 genes that were differentially expressed in both vegetative and reproductive stages under drought stress. Among them is a tight cluster of genes that are directly related to biotic and abiotic stress, as well as carbon metabolism, and hormonal pathways. We suggest that knowledge of gene expression patterns in tiller buds, inflorescences and rooting tips will be important for understanding the growth responses of pearl millet and the trade-offs at play in the response of this crop to drought. Much remains to be learnt about how pearl millet’s unique combination of genetic and physiological mechanisms allow it to achieve such high drought tolerance, and the answers to be found may well be useful for crops other than just pearl millet.
A naked grass in the bristle clade: A phylogenetlc and developmental study of Panicum section bulbosa (Paniceae: Poaceae)
Publisher: University of Chicago Press
Date: 05-2005
DOI: 10.1086/428701
New Ways to Gather Grains
Publisher: Elsevier BV
Date: 04-2013
DOI: 10.1016/J.DEVCEL.2013.04.010
Abstract: A crucial step in cereal grass domestication is acquisition of seed retention in the inflorescence/seed head for efficient harvesting. Reporting in Nature Genetics, Ishii and colleagues (2013) show that a change in inflorescence architecture is sufficient to increase seed retention, providing an alternative pathway toward cereal grass domestication.
Divergent gene expression networks underlie morphological diversity of abscission zones in grasses
Publisher: Wiley
Date: 28-08-2019
DOI: 10.1111/NPH.16087
Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria
Publisher: Springer Science and Business Media LLC
Date: 11-04-2013
Abstract: The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica , are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis , S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca , S. plicata , and S. arenaria , with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca , S. plicata , and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii . Chromosomes of Qing 9, an accession formerly considered as S. viridis , hybridized strong signal only to B genome of S. adherans . Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the s les in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D ( S. glauca ), E ( S. plicata ) and F (S . arenaria ) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC’C’. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.
Grain shattering by cell death and fracture in Eragrostis tef
Publisher: Oxford University Press (OUP)
Date: 09-02-2023
Abstract: Abscission, known as shattering in crop species, is a highly regulated process by which plants shed parts. Although shattering has been studied extensively in cereals and a number of regulatory genes have been identified, much ersity in the process remains to be discovered. Teff (Eragrostis tef) is a crop native to Ethiopia that is potentially highly valuable worldwide for its nutritious grain and drought tolerance. Previous work has suggested that grain shattering in Eragrostis might have little in common with other cereals. In this study, we characterize the anatomy, cellular structure, and gene regulatory control of the abscission zone (AZ) in E. tef. We show that the AZ of E. tef is a narrow stalk below the caryopsis, which is common in Eragrostis species. X-ray microscopy, scanning electron microscopy, transmission electron microscopy, and immunolocalization of cell wall components showed that the AZ cells are thin walled and break open along with programmed cell death (PCD) at seed maturity, rather than separating between cells as in other studied species. Knockout of YABBY2/SHATTERING1, documented to control abscission in several cereals, had no effect on abscission or AZ structure in E. tef. RNA sequencing analysis showed that genes related to PCD and cell wall modification are enriched in the AZ at the early seed maturity stage. These data show that E. tef drops its seeds using a unique mechanism. Our results provide the groundwork for understanding grain shattering in Eragrostis and further improvement of shattering in E. tef.
The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis
Publisher: Wiley
Date: 02-08-2023
DOI: 10.1111/NPH.19157
Abstract: Abscission is predetermined in specialized cell layers called the abscission zone (AZ) and activated by developmental or environmental signals. In the grass family, most identified AZ genes regulate AZ anatomy, which differs among lineages. A YABBY transcription factor, SHATTERING1 ( SH1 ), is a domestication gene regulating abscission in multiple cereals, including rice and Setaria . In rice, SH1 inhibits lignification specifically in the AZ. However, the AZ of Setaria is nonlignified throughout, raising the question of how SH1 functions in species without lignification. Crispr‐Cas9 knockout mutants of SH1 were generated in Setaria viridis and characterized with histology, cell wall and auxin immunofluorescence, transmission electron microscopy, hormonal treatment and RNA‐Seq analysis. The sh1 mutant lacks shattering, as expected. No differences in cell anatomy or cell wall components including lignin were observed between sh1 and the wild‐type (WT) until abscission occurs. Chloroplasts degenerated in the AZ of WT before abscission, but degeneration was suppressed by auxin treatment. Auxin distribution and expression of auxin‐related genes differed between WT and sh1 , with the signal of an antibody to auxin detected in the sh1 chloroplast. SH1 in Setaria is required for activation of abscission through auxin signaling, which is not reported in other grass species.
Activation of apoplastic sugar at the transition stage may be essential for axillary bud outgrowth in the grasses
Publisher: Frontiers Media SA
Date: 26-10-2022
DOI: 10.3389/FPLS.2022.1023581
Abstract: Shoot branches develop from buds in leaf axils. Once formed from axillary meristems, the buds enter a transition stage before growing into branches. The buds may transition into dormancy if internal and environmental factors limit sucrose supply to the buds. A fundamental question is why sucrose can be limiting at the transition stage for bud outgrowth, whereas new buds continue to be formed. Sucrose is transported to sink tissues through symplastic or apoplastic pathways and a shift from symplastic to apoplastic pathway is common during seed and fruit development. In addition, symplastic connected tissues are stronger sinks than symplastically isolated tissues that rely on sugars effluxed to the apoplast. Recent studies in sorghum, sugarcane, and maize indicate activation of apoplastic sugar in buds that transition to outgrowth but not to dormancy, although the mode of sugar transport during bud formation is still unclear. Since the apoplastic pathway in sorghum buds was specifically activated during bud outgrowth, we posit that sugar for axillary bud formation is most likely supplied through the symplastic pathway. This suggests a key developmental change at the transition stage, which alters the sugar transport pathway of newly-formed buds from symplastic to apoplastic, making the buds a less strong sink for sugars. We suggest therefore that bud outgrowth that relies on overflow of excess sucrose to the apoplast will be more sensitive to internal and environmental factors that enhance the growth of sink tissues and sucrose demand in the parent shoot whereas bud formation that relies on symplastic sucrose will be less affected by these factors.
Early inflorescence development in the grasses (Poaceae)
Publisher: Frontiers Media SA
Date: 2013
Pleiotropic and Non-redundant Effects of an Auxin Importer in Setaria and Maize1
Publisher: Cold Spring Harbor Laboratory
Date: 14-10-2021
DOI: 10.1101/2021.10.14.464408
Abstract: Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis . SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis . Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins. Mutations in a single auxin importer gene Spp1/SvAUX1 uncover broad and unexpected effects in nearly all aspects of the development of shoots, inflorescences, and flowers.
Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum
Publisher: Oxford University Press (OUP)
Date: 02-2021
DOI: 10.1093/G3JOURNAL/JKAB024
Abstract: Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.
Sensitivity to Gibberellin of Dwarf Foxtail Millet Varieties
Publisher: Wiley
Date: 05-2012
The genetic basis for inflorescence variation between foxtail and green millet (Poaceae)
Publisher: Oxford University Press (OUP)
Date: 03-2005
DOI: 10.1534/GENETICS.104.035543
Abstract: Grass species differ in many aspects of inflorescence architecture, but in most cases the genetic basis of the morphological difference is unknown. To investigate the genes underlying the morphology in one such instance, we undertook a developmental and QTL analysis of inflorescence differences between the cereal grain foxtail millet and its presumed progenitor green millet. Inflorescence differences between these two species are the result of changes in primary branch number and density, spikelet number, and bristle (sterile branchlet) number these differences also account for inflorescence variation within the clade of 300+ species that share the presence of bristles in the inflorescence. Fourteen replicated QTL were detected for the four inflorescence traits, and these are suggested to represent genes that control differences between the species. Comparative mapping using common markers from rice and maize allowed a number of candidate genes from maize to be localized to QTL regions in the millet genome. Searches of regions of the sequenced rice genome orthologous to QTL regions on foxtail millet identified a number of transcription factors and hormone pathway genes that may be involved in control of inflorescence branching.
Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 60 Years after Ownbey's discovery
Publisher: Wiley
Date: 05-2009
DOI: 10.3732/AJB.0800299
Abstract: In plants, polyploidy has been a significant evolutionary force on both recent and ancient time scales. In 1950, Ownbey reported two newly formed Tragopogon allopolyploids in the northwestern United States. We have made the first synthetic lines of T. mirus and T. miscellus using T. dubius, T. porrifolius, and T. pratensis as parents and colchicine treatment of F(1) hybrids. We also produced allotetraploids between T. porrifolius and T. pratensis, which are not known from nature. We report on the crossability between the diploids, as well as the inflorescence morphology, pollen size, meiotic behavior, and fertility of the synthetic polyploids. Morphologically, the synthetics resemble the natural polyploids with short- and long-liguled forms of T. miscellus resulting when T. pratensis and T. dubius are reciprocally crossed. Synthetic T. mirus was also formed reciprocally, but without any obvious morphological differences resulting from the direction of the cross. Of the 27 original crosses that yielded 171 hybrid in iduals, 18 of these lineages have persisted to produce 386 S(1) progeny each of these lineages has produced S(2) seed that are viable. The successful generation of these synthetic polyploids offers the opportunity for detailed comparative studies of natural and synthetic polyploids within a nonmodel system.
Plant growth conditions alter phytolith carbon
Publisher: Frontiers Media SA
Date: 17-09-2015
A reinterpretation of the staminate flowers of Haptanthus
Publisher: American Society of Plant Taxonomists
Date: 10-2005
Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum
Publisher: Cold Spring Harbor Laboratory
Date: 06-07-2020
DOI: 10.1101/2020.07.06.189548
Abstract: Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ~1920 bin markers spanning ~875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.
Editorial: Setaria as a Model Genetic System to Accelerate Yield Increases in Cereals, Forage Crops, and Bioenergy Grasses
Publisher: Frontiers Media SA
Date: 10-10-2019
Foxtail Millet: A Sequence-Driven Grass Model System
Publisher: Oxford University Press (OUP)
Date: 2009
Congruence, Conflict, and Polyploidization Shown by Nuclear and Chloroplast Markers in the Monophyletic ''Bristle Clade'' (Paniceae, Panicoideae, Poaceae)
Publisher: American Society of Plant Taxonomists
Date: 07-2007
Pleiotropic and nonredundant effects of an auxin importer in Setaria and maize
Publisher: Oxford University Press (OUP)
Date: 14-03-2022
Abstract: Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
Domestication and Improvement in the Model C4 Grass, Setaria
Publisher: Frontiers Media SA
Date: 29-05-2018
Primaclade—a flexible tool to find conserved PCR primers across multiple species
Publisher: Oxford University Press (OUP)
Date: 11-11-2004
DOI: 10.1093/BIOINFORMATICS/BTI134
Abstract: Summary: Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of polymerase chain reaction (PCR) primers that will bind across the alignment. Primaclade iteratively runs the Primer3 application for each alignment sequence and collates the results. Primaclade creates an HTML results page that recaps the original alignment, provides a consensus sequence and lists primers for each alignment area, with primers color-coded to reflect the level of degeneracy in the primer. Availability: Primaclade can be accessed freely at www.umsl.edu/~biology/Kellogg rimaclade.html Contact: tkellogg@umsl.edu
Current perspectives and the future of domestication studies
Publisher: Proceedings of the National Academy of Sciences
Date: 22-04-2014
Abstract: It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae)
Publisher: Oxford University Press (OUP)
Date: 02-2013
Abstract: We report the first study on the genetic control of flowering in Setaria, a panicoid grass closely related to switchgrass, and in the same subfamily as maize and sorghum. A recombinant inbred line mapping population derived from a cross between domesticated Setaria italica (foxtail millet) and its wild relative Setaria viridis (green millet), was grown in eight trials with varying environmental conditions to identify a small number of quantitative trait loci (QTL) that control differences in flowering time. Many of the QTL across trials colocalize, suggesting that the genetic control of flowering in Setaria is robust across a range of photoperiod and other environmental factors. A detailed comparison of QTL for flowering in Setaria, sorghum, and maize indicates that several of the major QTL regions identified in maize and sorghum are syntenic orthologs with Setaria QTL, although the maize large effect QTL on chromosome 10 is not. Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci. Candidate genes from flowering time pathways identified in rice and Arabidopsis were identified in Setaria QTL intervals, including those involved in the CONSTANS photoperiod pathway. However, only three of the approximately seven genes cloned for flowering time in maize colocalized with Setaria QTL. This suggests that variation in flowering time in separate grass lineages is controlled by a combination of conserved and lineage specific genes.
PlantCV v2: Image analysis software for high-throughput plant phenotyping
Publisher: PeerJ
Date: 12-2017
DOI: 10.7717/PEERJ.4088
Abstract: Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the ersity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.
Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids
Publisher: Springer Science and Business Media LLC
Date: 11-03-2009
DOI: 10.1038/HDY.2009.24
Abstract: Whole-genome duplication (polyploidisation) is a widespread mechanism of speciation in plants. Over time, polyploid genomes tend towards a more diploid-like state, through downsizing and loss of duplicated genes (homoeologues), but relatively little is known about the timing of gene loss during polyploid formation and stabilisation. Several studies have also shown gene transcription to be affected by polyploidisation. Here, we examine patterns of gene loss in 10 sets of homoeologues in five natural populations of the allotetraploid Tragopogon miscellus that arose within the past 80 years following independent whole-genome duplication events. We also examine 44 first-generation synthetic allopolyploids of the same species. No cases of homoeologue loss arose in the first allopolyploid generation, but after 80 years, 1.6% of homoeologues were lost in natural populations. For seven homoeologue sets we also examined transcription, finding that 3.4% of retained homoeologues had been silenced in the natural populations, but none in the synthetic plants. The homoeologue losses and silencing events found were not fixed within natural populations and did not form a predictable pattern among populations. We therefore show haphazard loss and silencing of homoeologues, occurring within decades of polyploid formation in T. miscellus, but not in the initial generation.
Reference genome sequence of the model plant Setaria
Publisher: Springer Science and Business Media LLC
Date: 13-05-2012
DOI: 10.1038/NBT.2196
Abstract: We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).
Development of Genomic and Genetic Tools for Foxtail Millet, and Use of These Tools in the Improvement of Biomass Production for Bioenergy Crops
Publisher: Office of Scientific and Technical Information (OSTI)
Date: 11-11-2011
DOI: 10.2172/1029122
Setaria: A Food Crop and Translational Research Model for C4 Grasses
Publisher: Frontiers Media SA
Date: 15-12-2016
Taxonomy, phylogeny, and inflorescence development of the genus Ixophorus (Panicoideae: Poaceae)
Publisher: University of Chicago Press
Date: 11-2004
DOI: 10.1086/423880
Spatial Genetic Structure of the Tallgrass Prairie Grass Dichanthelium oligosanthes (Scribner's panicum)
Publisher: Oklahoma State University Library
Date: 12-2011
The developmental basis of floral variation in Drimys winteri (Winteraceae)
Publisher: University of Chicago Press
Date: 07-2001
DOI: 10.1086/320790
De novo homology assessment from landmark data: A workflow to identify and track segmented structures in plant time series images
Publisher: Cold Spring Harbor Laboratory
Date: 21-02-2021
DOI: 10.1101/2021.02.21.432162
Abstract: Assessing the phenotypes underlying plant growth and development is integral to exploring the development, genetics, and evolution of morphology and plays an essential role in agronomic and basic research studies. Although various automated or semi-automated phenomic approaches have recently been developed, tools assessing differential growth of plant organs remains a key topic of interest, but one which is often difficult to analyze due to the requirements of segmenting and annotating specific structures or positions in the plant body in time-series data. To address this gap, we have developed a generalized workflow linking our previously published function, acute , with a companion function, homology , in the PlantCV environment. The homology function uses a generalized strategy of dimensionality reduction via starscape followed by hierarchical clustering through constella to identify ‘constellations’ of segments in eigenspace that represent the same landmark in consecutive images of a time-series. We devised a quality control function, constellaQC , that can test the accuracy of the clustering approach, and we use it to show that the approach accurately clustered the pseudo-landmarks derived from acute , although with several sources of error. We discuss the reasons for and consequences of these errors in automated workflows, and suggest how to develop these functions so that they can easily be repurposed for other phenomics datasets that may vary in dimensional complexity.
Xyris L. Section Pomatoxyris Endl. (Xyridaceae) in Australia
Publisher: CSIRO Publishing
Date: 1997
DOI: 10.1071/SB96014
Abstract: A systematic study of the endemic Australian sectionPomatoxyris Endl. of the genusXyris is presented. Eighteen species are recognised, ofwhich Xyris atrovirida, X. exilisand X. maxima A.N.Doust & B.J.Conn are described forthe first time. Xyris bracteata R.Br. is reinstated forthe taxon more recently known as Xyris gracilis R.Br.subsp. laxa O.D.Evans.Xyris gracilis R.Br. subsp.tasmanica D.I.Morris is here raised to specific statusas X. tasmanica (D.I.Morris) A.N.Doust & B.J.Conn.All recognised taxa are provided with descriptions, distribution information(including maps), habitat descriptions, nomenclatural and other relevantnotes. Where appropriate, lectotypes are here designated for all previouslydescribed species of section Pomatoxyris Endl. which areaccepted by us. All species are illustrated.
Related Organisations
Oklahoma State University Stillwater
Location: United States of America
Related Funding Activities
No related grants have been discovered for Andrew Doust.