Research Interests:
Research Interests: Genetics, Biology, Medicine, Epigenomics, Euchromatin, and 4 moreGenome, Gene, Chromatin, and Enhancer
Shared systems in leaf development The long, narrow leaves of grasses look rather different from the often shorter, flatter leaves of eudicot plants. Richardson et al . combined developmental genetics and computational modeling to reveal... more
Shared systems in leaf development The long, narrow leaves of grasses look rather different from the often shorter, flatter leaves of eudicot plants. Richardson et al . combined developmental genetics and computational modeling to reveal that these two types of leaves, which are widely separated by evolution, have more in common than expected. Expression of similar patterning genes in the primordial zone is confined to a wedge for the eudicot leaf but expanded to concentric domains in the grass leaf, driving development of the cylindrical, encircling sheath characteristic of grass leaves. Addition or removal of gene expression in a marginal zone contributes to the development of the broader leaf characteristic of eudicots. Thus, grass and eudicot leaves are diversified elaborations of shared toolkits. —PJH
Research Interests:
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed. Dissecting the genetic architecture of natural variation for maize leaf cuticular... more
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed. Dissecting the genetic architecture of natural variation for maize leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we performed an integrated genome- and transcriptome-wide association study (GWAS/TWAS) to identify candidate genes putatively regulating variation in leafgc. Of the 22 plausible candidate genes identified, five were predicted to be involved in cuticle precursor biosynthesis and export, two in cell wall modification, nine in intracellular membrane trafficking, and seven in the regulation of cuticle development. A gene encoding an INCREASED SALT TOLERANCE1-LIKE1 (ISTL1) protein putatively involved in intracellular protein and membrane trafficking was identified in GWAS and TWAS as the strongest candidate causal gene. A set...
Research Interests:
Research Interests:
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological... more
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SA...
Research Interests:
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of... more
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study ofgcof adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA in 2016 and 2017). Five genomic regions significantly associated withgcwere resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA...
Research Interests: Genetics, Biology, Medicine, Plant, Cutin, and 9 moreGene, Droughts, Cuticle, Plant Cuticle, Zea mays, RNA Sequencing, Waxes, Gene Expression Regulation, and Plant Leaves
Background and AimsPrior work has examined cuticle function, composition and ultrastructure in many plant species, but much remains to be learned about how these features are related. This study aims to elucidate relationships between... more
Background and AimsPrior work has examined cuticle function, composition and ultrastructure in many plant species, but much remains to be learned about how these features are related. This study aims to elucidate relationships between these features via analysis of cuticle development in adult maize (Zea mays L.) leaves, while also providing the most comprehensive investigation to date of the composition and ultrastructure of adult leaf cuticles in this important crop plant.MethodsWe examined water permeability, wax and cutin composition via gas chromatography, and ultrastructure via transmission electron microscopy, along the developmental gradient of partially expanded adult maize leaves, and analysed the relationships between these features.Key ResultsThe water barrier property of the adult maize leaf cuticle is acquired at the cessation of cell expansion. Wax types and chain lengths accumulate asynchronously over the course of development, while overall wax load does not vary. C...
Research Interests: Botany, Plant Biology, Biology, Ecology, Medicine, and 4 moreCutin, Ultrastructure, Plant Cuticle, and Wax
Research Interests:
The phloem of the Cucurbitaceae has long been a subject of interest due to its complex nature and the economic importance of the family. As in a limited number of other families, cucurbit phloem is bicollateral, i.e., with sieve tubes on... more
The phloem of the Cucurbitaceae has long been a subject of interest due to its complex nature and the economic importance of the family. As in a limited number of other families, cucurbit phloem is bicollateral, i.e., with sieve tubes on both sides of the xylem. To date little is known about the specialized functions of the internal (IP) and external phloem (EP). Here, a combination of microscopy, fluorescent dye transport analysis, micro-computed tomography, laser capture microdissection and RNA sequencing is used to study the functions of IP and EP in the vascular bundles (VBs) of cucumber fruit. There is one type of VB in the peduncle but four in the fruit: peripheral (PeVB), main (MVB), carpel (CVB) and placental (PlVB). The VBs are bicollateral except for the CVB and PlVB. Phloem mobile tracers and C applied to leaves are transported primarily in the EP and to a lesser extent in the IP. RNA-Seq data indicate preferential gene transcription in the IP related to differentation/de...
Research Interests:
Research Interests:
Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern... more
Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic mark...
Research Interests:
SummaryAll above‐ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were... more
SummaryAll above‐ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14‐day‐old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM‐collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up‐ and down‐regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT‐PCR and/or in situ hybridization. The up‐regulated ESTs included many regulatory genes including tra...
Research Interests: Genetics, Biology, Hybridization, Development, Medicine, and 15 moreGene expression, Gene Silencing, In Situ Hybridization, Laser Capture Microdissection, Maize, Chromatin remodeling, Gene, Apical Meristem, Gen, Gramineae, cDNA, Global Gene Expression, Meristem, Gene expression profiling, and Differential expression
Research Interests:
Research Interests: Evolutionary Biology, Genetics, Algorithms, Molecular Biology, Molecular Evolution, and 15 moreBiology, Genome Size, Medicine, Humans, Computer Simulation, Animals, Molecular Phylogenetics and Evolution, Genome, Research Articles, Chromosome, Statistical models, Chromosomes, Diploidy, Ploidy, and Biochemistry and cell biology
The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic... more
The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene–targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shapi...
Research Interests:
Grass leaves develop from a ring of primordial initial cells within the periphery of the shoot apical meristem, a pool of organogenic stem cells that generates all of the organs of the plant shoot. At maturity, the grass leaf is a... more
Grass leaves develop from a ring of primordial initial cells within the periphery of the shoot apical meristem, a pool of organogenic stem cells that generates all of the organs of the plant shoot. At maturity, the grass leaf is a flattened, strap-like organ comprising a proximal supportive sheath surrounding the stem and a distal photosynthetic blade. The sheath and blade are partitioned by a hinge-like auricle and the ligule, a fringe of epidermally derived tissue that grows from the adaxial (top) leaf surface. Together, the ligule and auricle comprise morphological novelties that are specific to grass leaves. Understanding how the planar outgrowth of grass leaves and their adjoining ligules is genetically controlled can yield insight into their evolutionary origins. Here we use single-cell RNA-sequencing analyses to identify a ‘rim’ cell type present at the margins of maize leaf primordia. Cells in the leaf rim have a distinctive identity and share transcriptional signatures with...
Research Interests:
Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling, genetic and... more
Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling, genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and inhibit branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in non-grasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a non-autonomous signaling center that promotes inflorescence branching, an important compone...
Research Interests:
Plant cuticles are composed of wax and cutin and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle... more
Plant cuticles are composed of wax and cutin and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Laser microdissection RNA Sequencing (LM-RNAseq) was performed along this proximodistal gradient, and complementary network analyses identified potential regulators of cuticle biosynthesis and deposition. A weighted gene coexpression network (WGCN) analysis suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during the regulation of cuticular wax deposition. Genetic analyses reveal that phyB1 phyB2 double mutants of maize exhibit abnormal cuticle composition, supporting the predictions of our coexpression analysis. Reverse genetic analyses also show that phy mutants of the moss Physcomitrella patens exhibit abnormal cuticle composition, suggesting an ancestral role for PHYTO...
Research Interests:
Although extensive prior work has characterized cuticle composition, function, ultrastructure and development in many plant species, much remains to be learned about how these features are interrelated. Moreover, very little is known... more
Although extensive prior work has characterized cuticle composition, function, ultrastructure and development in many plant species, much remains to be learned about how these features are interrelated. Moreover, very little is known about the adult maize leaf cuticle in spite of its significance for agronomically important traits in this major crop. We analyzed cuticle composition, ultrastructure, and permeability along the developmental gradient of partially expanded adult maize leaves to probe the relationships between these features. The water barrier property is acquired at the cessation of cell expansion. Wax types and chain lengths accumulate asynchronously along the developmental gradient, while overall wax load does not vary. Cutin begins to accumulate prior to establishment of the water barrier and continues thereafter. Ultrastructurally, pavement cell cuticles consist of an epicuticular layer, a thin cuticle proper that acquires an inner, osmiophilic layer during developm...
Research Interests:
Plant cuticles are composed of wax and cutin, and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle... more
Plant cuticles are composed of wax and cutin, and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Laser microdissection RNA Sequencing (LM-RNAseq) was performed along this proximodistal gradient, and complementary network analyses identified potential regulators of cuticle biosynthesis and deposition. Correlations between cuticle development and cell wall biosynthesis processes were identified, as well as evidence of roles for auxin and brassinosteroids. In addition, our network analyses suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during cuticular wax deposition. Genetic analyses reveal that the phyB1 phyB2 double mutant of maize exhibits abnormal cuticle composition, supporting predictions of our coexpression analyses. Reverse genetic analyses also show that ph...
Research Interests:
Research Interests:
Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize (Zea mays) leaf is an ideal system to... more
Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize (Zea mays) leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialized ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally derived fringe. Recessive liguleless1 mutants lack ligules and auricles and have upright leaves. We used laser microdissection and RNA sequencing to identify genes that are differentially expressed in discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation and compared transcript accumulation in wild-type and liguleless1-R mutant leaf primordi...
Research Interests:
Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional... more
Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional networks that are hidden within large microarray datasets. Microarray analyses in which mutant organisms are compared to nonmutant siblings can be especially problematic when the gene of interest is expressed in relatively few cells. Here, we describe the use of laser microdissection microarray to perform transcriptional profiling of the maize shoot apical meristem (SAM), a;100-lm pillar of organogenic cells that is required for leaf initiation. Microarray analyses compared differential gene expression within the SAM and incipient leaf primordium of nonmutant and narrow sheath mutant plants, which harbored mutations in the duplicate genes narrow sheath1 (ns1) and narrow sheath2 (ns2). Expressed in eight to ten cells within the SAM, ns1 and ns2 encode pa...
Research Interests: Genetics, Biology, Medicine, Gene expression, Mutation, and 14 moreLasers, Laser Capture Microdissection, Microdissection, Maize, Transcription Factor, Zea mays, Gene Function, LEAF DEVELOPMENT, PLoS Genetics, Meristem, Differential Gene Expression, Differential expression, Molecular Sequence Data, and Signaling pathway
The narrow sheath mutant of maize displays a leaf and plant stature phenotype controlled by the duplicate factor mutations narrow sheath1 and narrow sheath2. Mutant leaves fail to develop a lateral domain that includes the leaf margins.... more
The narrow sheath mutant of maize displays a leaf and plant stature phenotype controlled by the duplicate factor mutations narrow sheath1 and narrow sheath2. Mutant leaves fail to develop a lateral domain that includes the leaf margins. Genetic data are presented to show that the narrow sheath mutations map to duplicated chromosomal regions, reflecting an ancestral duplication of the maize genome. Genetic and cytogenetic evidence indicates that the original mutation at narrow sheath2 is associated with a chromosomal inversion on the long arm of chromosome 4. Meristematic sectors of dual aneuploidy were generated, producing plants genetically mosaic for NARROW SHEATH function. These mosaic plants exhibited characteristic half-plant phenotypes, in which leaves from one side of the plant were of nonmutant morphology and leaves from the opposite side were of narrow sheath mutant phenotype. The data suggest that the narrow sheath duplicate genes may perform ancestrally conserved, redunda...
Research Interests:
The expression of class 1 knotted1-like homeobox (knox) genes affects numerous plant developmental processes, including cell-fate acquisition, lateral organ initiation, and maintenance of shoot apical meristems. The SEMAPHORE1 gene... more
The expression of class 1 knotted1-like homeobox (knox) genes affects numerous plant developmental processes, including cell-fate acquisition, lateral organ initiation, and maintenance of shoot apical meristems. The SEMAPHORE1 gene product is required for the negative regulation of a subset of maize knox genes, the duplicated loci rough sheath 1 and gnarley1 (knox4). Recessive mutations in semaphore1 result in the ectopic expression of knox genes in leaf and endosperm tissue. Genetic analyses suggest that SEMAPHORE1 may regulate knox gene expression in a different developmental pathway than ROUGH SHEATH2, the first-identified regulator of knox gene expression in maize. Mutations at semaphore1 are pleiotropic, disrupting specific domains of the shoot. However, unlike previously described mutations that cause ectopic knox gene expression, semaphore1 mutations affect development of the embryo, endosperm, lateral roots, and pollen. Moreover, polar transport of the phytohormone auxin is ...
Research Interests:
The narrow sheath duplicate genes (ns1 and ns2) perform redundant functions during maize leaf development. Plants homozygous for mutations in both ns genes fail to develop wild-type leaf tissue in a lateral domain that includes the leaf... more
The narrow sheath duplicate genes (ns1 and ns2) perform redundant functions during maize leaf development. Plants homozygous for mutations in both ns genes fail to develop wild-type leaf tissue in a lateral domain that includes the leaf margin. Previous studies indicated that the NS gene product(s) functions during recruitment of leaf founder-cells in a lateral, meristematic domain that contributes to leaf margin development. A mosaic analysis was performed in which the ns1-O mutation was exposed in hemizygous, clonal sectors in a genetic background already homozygous for ns2-O. Analyses of mutant, sectored plants demonstrate that NS1 function is required in L2-derived tissue layers for development of the narrow sheath leaf domain. NS1 function is not required for development of the central region of maize leaves. Furthermore, the presence of the non-mutant ns1 gene outside the narrow sheath domain cannot compensate for the absence of the non-mutant gene within the narrow sheath dom...
Research Interests:
The formation of developmental boundaries is a common feature of multicellular plants and animals, and impacts the initiation, structure, and function of all organs. Maize leaves comprise a proximal sheath that encloses the stem, and a... more
The formation of developmental boundaries is a common feature of multicellular plants and animals, and impacts the initiation, structure, and function of all organs. Maize leaves comprise a proximal sheath that encloses the stem, and a distal photosynthetic blade that projects away from the plant axis. An epidermally-derived ligule and a joint-like auricle develop at the blade/sheath boundary of maize leaves. Mutations disturbing the ligule/auricle region disrupt leaf patterning and impact plant architecture, yet it is unclear how this developmental boundary is established. Targeted microdissection followed by transcriptomic analyses of young leaf primordia were utilized to construct a co-expression network associated with development of the blade/sheath boundary. Evidence is presented for proximodistal gradients of gene expression that establish a pre-patterned transcriptomic boundary in young leaf primordia, before the morphological initiation of the blade/sheath boundary in older leaves. This work presents a conceptual model for spatiotemporal patterning of proximodistal leaf domains, and provides a rich resource of candidate gene interactions for future investigations of the mechanisms of blade/sheath boundary formation in maize.
Research Interests:
The mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf... more
The mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf primordia, and is required for mediolateral outgrowth. To investigate the mechanisms of NS1 function, we used chromatin immunoprecipitation and laser-microdissection RNAseq of leaf primordial margins to identify gene targets bound and modulated by NS1. Microscopic analyses of cell division and gene expression in expanding leaves, and reverse genetic analyses of homologous NS1 target genes in Arabidopsis, reveal that NS1 controls mediolateral outgrowth by repression of a growth inhibitor and promotion of cell division at primordial leaf margins. Intriguingly, homologous WOX gene products are expressed in stem-cell organizing centers and traffic to adjoining cells to activate stem-cell identity non-autonomously. In contrast, WOX3/NS1 does not traffic, and s...
Research Interests:
Plant shoots grow from stem cells within Shoot Apical Meristems (SAMs), which produce lateral organs while maintaining the stem cell pool. In the model flowering plant Arabidopsis, the CLAVATA (CLV) pathway functions antagonistically with... more
Plant shoots grow from stem cells within Shoot Apical Meristems (SAMs), which produce lateral organs while maintaining the stem cell pool. In the model flowering plant Arabidopsis, the CLAVATA (CLV) pathway functions antagonistically with cytokinin signaling to control the size of the multicellular SAM via negative regulation of the stem cell organizer WUSCHEL (WUS). Although comprising just a single cell, the SAM of the model moss Physcomitrium patens (formerly Physcomitrella) performs equivalent functions during stem cell maintenance and organogenesis, despite the absence of WUS-mediated stem cell organization. Our previous work showed that the stem cell-delimiting function of the CLV pathway receptors CLAVATA1 (CLV1) and RECEPTOR-LIKE PROTEIN KINASE2 (RPK2) is conserved in the moss P. patens. Here, we use P. patens to assess whether CLV-cytokinin crosstalk is also an evolutionarily conserved feature of stem cell regulation. Genetic analyses reveal that CLV1 and RPK2 regulate SAM ...
Research Interests:
Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing to achieve an unbiased characterization of the transcriptional... more
Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem cell organizing center subtending these cells. In addition, we use trajectory inference to trace the gene expression changes that accompany cell differentiation. These data provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis.
Research Interests:
ABSTRACT Plant epidermal cuticles are composed of hydrophobic lipids that provide a barrier to non-stomatal water loss, and arose in land plants as an adaptation to the dry terrestrial environment. The expanding maize adult leaf displays... more
ABSTRACT Plant epidermal cuticles are composed of hydrophobic lipids that provide a barrier to non-stomatal water loss, and arose in land plants as an adaptation to the dry terrestrial environment. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Recently, our gene co-expression network analyses together with reverse genetic analyses suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during cuticular wax deposition. The present work extends these findings by identifying a role for a specific LIPID TRANSFER PROTEIN (LTP) in cuticle development, and validating it via transgenic experiments in Arabidopsis. Given that LTPs and cuticles both evolved in land plants and are absent from aquatic green algae, we propose that during plant evolution, LTPs arose as one of the innovations of land plants that enabled development of the cuticle.
Research Interests:
Research Interests:
Bulliform cells comprise specialized cell types that develop on the adaxial (upper) surface of grass leaves, and are patterned to form linear rows along the proximodistal axis of the adult leaf blade. Bulliform cell patterning affects... more
Bulliform cells comprise specialized cell types that develop on the adaxial (upper) surface of grass leaves, and are patterned to form linear rows along the proximodistal axis of the adult leaf blade. Bulliform cell patterning affects leaf angle and is presumed to function during leaf rolling, thereby reducing water loss during temperature extremes and drought. In this study, epidermal leaf impressions were collected from a genetically and anatomically diverse population of maize inbred lines. Subsequently, convolutional neural networks were employed to measure microscopic, bulliform cell-patterning phenotypes in high-throughput. A genome-wide association study, combined with RNAseq analyses of the bulliform cell ontogenic zone, identified candidate regulatory genes affecting bulliform cell column number and cell width. This study is the first to combine machine learning approaches, transcriptomics, and genomics to study bulliform cell patterning, and the first to utilize natural va...
Leaves are initiated as lateral outgrowths from shoot apical meristems throughout the vegetative life of the plant. To achieve proper developmental patterning, cell-type specification and growth must occur in an organized fashion along... more
Leaves are initiated as lateral outgrowths from shoot apical meristems throughout the vegetative life of the plant. To achieve proper developmental patterning, cell-type specification and growth must occur in an organized fashion along the proximodistal (base-to-tip), mediolateral (central-to-edge), and adaxial–abaxial (top-bottom) axes of the developing leaf. Early studies of mutants with defects in patterning along multiple leaf axes suggested that patterning must be coordinated across developmental axes. Decades later, we now recognize that a highly complex and interconnected transcriptional network of patterning genes and hormones underlies leaf development. Here, we review the molecular genetic mechanisms by which leaf development is coordinated across leaf axes. Such coordination likely plays an important role in ensuring the reproducible phenotypic outcomes of leaf morphogenesis.
Research Interests:
Research Interests:
Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously... more
Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify as an enhancer of , and to identify a new allele of Our method provides a quick, simple way to clone genes in maize.
Research Interests:
The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effects should have been B73,... more
The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effects should have been B73, rather than Mo17, due to the original coding of biallele SNPs as "0s" and "1s". Going through the entire analysis procedure, it was determined that the mistake was made while tabulating the eQTL results from QTL Cartographer.
Research Interests:
How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine... more
How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine overall body form. The emergence of plants on land coincided with a new capacity to rotate stem cell divisions through multiple planes, and this enabled three-dimensional (3D) forms to arise from ancestral forms constrained to 2D growth. The genes involved in this evolutionary innovation are largely unknown. The evolution of 3D growth is recapitulated during the development of modern mosses when leafy shoots arise from a filamentous (2D) precursor tissue. Here, we show that a conserved, CLAVATA peptide and receptor-like kinase pathway originated with land plants and orients stem cell division planes during the transition from 2D to 3D growth in a moss, Physcomitrella. We find that this newly identified role for CLAVATA in regulating cell division plane or...
Research Interests:
There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply... more
There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a Bayesian-based method for genome-wide association studies (GWAS) in which RNA-seq-based measures of transcript accumulation are used as explanatory variables (eRD-GWAS). The ability of eRD-GWAS to identify true associations between gene expression variation and phenotypic diversity is supported by ...
Research Interests:
One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major... more
One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affecting normal plant growth and causing agricultural losses worldwide. The advent of state-of-the-art technologies such as high throughput mRNA sequencing (RNA-seq) has revolutionized whole-transcriptome analysis by allowing, with high precision, to measure changes in gene expression. In this work, we used tissue-specific RNA-seq to gain insight into the Petunia hybrida transcriptional responses under NaCl stress using a controlled hydroponic system. Roots and leaves samples were taken from a continuum of 48 h of acute 150 mM NaCl. This analysis revealed a set of tissue and time point specific differentially expressed genes, such as genes related to transport, signal tran...
Research Interests:
The maize (Zea mays subsp. mays L.) shoot apical meristem (SAM) is a self-replenishing pool of stem cells that produces all above-ground plant tissues. Improvements in image acquisition and processing techniques have allowed... more
The maize (Zea mays subsp. mays L.) shoot apical meristem (SAM) is a self-replenishing pool of stem cells that produces all above-ground plant tissues. Improvements in image acquisition and processing techniques have allowed high-throughput, quantitative genetic analyses of SAM morphology. As with other large-scale phenotyping efforts, meaningful descriptions of genetic architecture depend on the collection of relevant measures. In this study, we tested two quantitative image processing methods to describe SAM morphology within the genus Zea, represented by 33 wild relatives of maize and 841 lines from a domesticated maize by wild teosinte progenitor (MxT) backcross population, along with previously reported data from several hundred diverse maize inbred lines. Approximating the MxT SAM as a paraboloid derived eight parabolic estimators of SAM morphology that identified highly overlapping quantitative trait loci (QTL) on eight chromosomes, which implicated previously identified SAM ...
Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not detected or are not identified as differentially expressed (DE) in transcriptomic... more
Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not detected or are not identified as differentially expressed (DE) in transcriptomic analyses of whole plant organs. Laser Microdissection RNA-Seq (LM RNA-Seq) is a powerful tool to identify genes that are DE in specific developmental domains. However, the choice of cellular domains to microdissect and compare, and the accuracy of the microdissections are crucial to the success of the experiments. Here, two examples illustrate design considerations for transcriptomics experiments; a LM RNA-seq analysis to identify genes that are DE along the maize leaf proximal-distal axis, and a second experiment to identify genes that are DE in liguleless1-R (lg1-R) mutants compared to wild-type. Key elements that contributed to the success of these experiments were detailed histological and in situ hybridization analyses of the region to be analyz...
Stem cell regulation is critical to the development of all multicellular organisms; in plants, stem cell niches reside in meristems. Two newly identified plant genes establish a novel signaling feedback from the incipient leaf primordia... more
Stem cell regulation is critical to the development of all multicellular organisms; in plants, stem cell niches reside in meristems. Two newly identified plant genes establish a novel signaling feedback from the incipient leaf primordia back to the meristem that is required to regulate stem cell proliferation.
Research Interests:
The 4942 bp DNA sequence of Zea mays transposon MuA2 was determined. Previous evidence indicated MuA2 controls activity of the Mu1 transposon located in the mutable allele a1-mum2. MuA2 contains two large, ATG-initiated open reading... more
The 4942 bp DNA sequence of Zea mays transposon MuA2 was determined. Previous evidence indicated MuA2 controls activity of the Mu1 transposon located in the mutable allele a1-mum2. MuA2 contains two large, ATG-initiated open reading frames (ORFs) of 612 and 232 codons, respectively, located on opposite strands. MuA2 produces two transcripts, each containing one of these ORFs. Four different tandem direct repeat sequences are located downstream of the 612 codon ORF. The restriction map of MuA2 is identical to that of transposon MuR1, which also is known to regulate mutability of a1-mum2. Furthermore, except for a single nucleotide, MuA2 is identical to the Mutator element Mu9.
Research Interests:
AGRIS record. Record number, GB1997038568. Titles, The narrow sheath leaf domain deletion: a genetic tool used to reveal developmental homologies among modified maize organs. Personal Authors, Scanlon, MJ,Freeling, M ...
Research Interests:
ABSTRACT Increasing resistance of crops to abiotic stresses is one of the primary objectives of plant biotechnology. Desiccation of plant cells due to drought or salt stress can lead to protein misfolding and inactivation. Trehalose sugar... more
ABSTRACT Increasing resistance of crops to abiotic stresses is one of the primary objectives of plant biotechnology. Desiccation of plant cells due to drought or salt stress can lead to protein misfolding and inactivation. Trehalose sugar may act as an osmoprotectant to prevent physical and chemical instability in proteins when exposed to salt or drought stress. Trehalose is a non-reducing disaccharide sugar and its accumulation is thought to offer osmotic stress protection role in many bacteria and fungi. Whereas in most plants trehalose levels are low, the concentration of this sugar is high in “resurrection plants” (Selaginella lepidophylla) which recover quickly from drought stress. Both tomato and rice have been genetically modified with microbial TPS1 increasing their tolerance to salt. With an aim toward overexpressing trehalose-6-phosphate synthase 1 gene to improve salt tolerance in the model floriculture species Petunia x hybrida we cloned the TPS1 gene from Petunia ‘Mitchell Diploid’. This generated a 2784-bp open reading frame that predicts a 58kDA protein of 927 amino acids. The sequence is available in NCBI database (Accession HQ259080). In Saccharomyces cerevisiae it is thought that the TPS1 exerts an essential control on the influx of glucose into glycolysis. The deletion of ScTPS1 causes an inability to grow on glucose because of a hyperaccumulation of sugar phosphates and depletion of ATP. To prove the functionality of the petunia TPS1 we carried out yeast complementation experiments to determine whether PhTPS1 would rescue function in mutant yeast (W303-1A background) while growing on glucose as a carbon source. We truncated the first ca. 80 amino acids to increase TPS1 catalytic activity as has been reported for AtTPS1. We cloned the trimmed PhTPS1 (ΔPhTPS1) into pDB20 yeast expression vector in vivo by means of homologous recombination. Eight transformations were carried out using four yeast strains: wild type (WT), knockout for TPS1 (tps1Δ), knockout for the related gene TPS2 (tps2Δ), and a double knockout (tps1Δtps2Δ); they received the pDB20 yeast vector with the overexpressed Petunia ΔTPS1 and with only the empty pDB20 vector. We successfully restored the ability of mutant yeast (tps1Δ, tps1Δtps2Δ) to grow in glucose by the insertion of ΔPhTPS1, indicating that ΔPhTPS1 is a functional gene capable of complementing trehalose biosynthesis. The rate limiting step in trehalose biosynthesis appears to be TPS1 gene since (tps1Δtps2Δ) with the ΔPhTPS1 vector was able to grow in glucose suggesting that the T6P intermediate can be dephosphorylated by nonspecific phosphatases.
A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes.... more
A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization-the founding term of the Xfunctionalization lexicon-while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish t...
Research Interests:
The maize shoot apical meristem (SAM) comprises a small pool of stem cells that generate all above-ground organs. Although mutational studies have identified genetic networks regulating SAM function, little is known about SAM... more
The maize shoot apical meristem (SAM) comprises a small pool of stem cells that generate all above-ground organs. Although mutational studies have identified genetic networks regulating SAM function, little is known about SAM morphological variation in natural populations. Here we report the use of high-throughput image processing to capture rich SAM size variation within a diverse maize inbred panel. We demonstrate correlations between seedling SAM size and agronomically important adult traits such as flowering time, stem size and leaf node number. Combining SAM phenotypes with 1.2 million single nucleotide polymorphisms (SNPs) via genome-wide association study reveals unexpected SAM morphology candidate genes. Analyses of candidate genes implicated in hormone transport, cell division and cell size confirm correlations between SAM morphology and trait-associated SNP alleles. Our data illustrate that the microscopic seedling SAM is predictive of adult phenotypes and that SAM morphom...