@article{kaur_best_hartwig_budka_khangura_mckenzie_aragon-raygoza_strable_schulz_dilkes_2024, title={A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling}, ISSN={["1532-2548"]}, DOI={10.1093/plphys/kiae147}, abstractNote={Abstract Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.}, journal={PLANT PHYSIOLOGY}, author={Kaur, Amanpreet and Best, Norman B. and Hartwig, Thomas and Budka, Josh and Khangura, Rajdeep S. and McKenzie, Steven and Aragon-Raygoza, Alejandro and Strable, Josh and Schulz, Burkhard and Dilkes, Brian P.}, year={2024}, month={May} }
 @article{strable_aragon-raygoza_2024, title={Development and maintenance of the ligular region of maize leaves}, volume={17}, ISSN={["1752-9867"]}, DOI={10.1016/j.molp.2024.07.004}, number={8}, journal={MOLECULAR PLANT}, author={Strable, Josh and Aragon-Raygoza, Alejandro}, year={2024}, month={Aug}, pages={1175–1177} }
 @article{dewey_selote_griffin_dickey_jantz_smith_matthiadis_strable_kestell_smith_2023, title={Cytoplasmic male sterility and abortive seed traits generated through mitochondrial genome editing coupled with allotopic expression of atp1 in tobacco}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1253640}, abstractNote={Allotopic expression is the term given for the deliberate relocation of gene function from an organellar genome to the nuclear genome. We hypothesized that the allotopic expression of an essential mitochondrial gene using a promoter that expressed efficiently in all cell types except those responsible for male reproduction would yield a cytoplasmic male sterility (CMS) phenotype once the endogenous mitochondrial gene was inactivated via genome editing. To test this, we repurposed the mitochondrially encoded atp1 gene of tobacco to function in the nucleus under the transcriptional control of a CaMV 35S promoter (construct 35S:nATP1), a promoter that has been shown to be minimally expressed in early stages of anther development. The endogenous atp1 gene was eliminated (Δatp1) from 35S:nATP1 tobacco plants using custom-designed meganucleases directed to the mitochondria. Vegetative growth of most 35S:nATP1/Δatp1 plants appeared normal, but upon flowering produced malformed anthers that failed to shed pollen. When 35S:nATP1/Δatp1 plants were cross-pollinated, ovary/capsule development appeared normal, but the vast majority of the resultant seeds were small, largely hollow and failed to germinate, a phenotype akin to the seedless trait known as stenospermocarpy. Characterization of the mitochondrial genomes from three independent Δatp1 events suggested that spontaneous recombination over regions of microhomology and substoichiometric shifting were the mechanisms responsible for atp1 elimination and genome rearrangement in response to exposure to the atp1-targeting meganucleases. Should the results reported here in tobacco prove to be translatable to other crop species, then multiple applications of allotopic expression of an essential mitochondrial gene followed by its elimination through genome editing can be envisaged. Depending on the promoter(s) used to drive the allotopic gene, this technology may have potential application in the areas of: (1) CMS trait development for use in hybrid seed production; (2) seedless fruit production; and (3) transgene containment.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Dewey, Ralph E. and Selote, Devarshi and Griffin, H. Carol and Dickey, Allison N. and Jantz, Derek and Smith, J. Jeff and Matthiadis, Anna and Strable, Josh and Kestell, Caitlin and Smith, William A.}, year={2023}, month={Sep} }
 @article{strable_unger-wallace_raygoza_briggs_vollbrecht_2023, title={Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture}, volume={191}, ISSN={["1532-2548"]}, DOI={10.1093/plphys/kiac559}, abstractNote={AbstractGrass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.}, number={2}, journal={PLANT PHYSIOLOGY}, author={Strable, Josh and Unger-Wallace, Erica and Raygoza, Alejandro Aragon and Briggs, Sarah and Vollbrecht, Erik}, year={2023}, month={Feb}, pages={1084–1101} }
 @article{strable_2021, title={A pointillist portrait of maize leaf protoplasts points to bundle sheath polarity and a potentially new path to phloem loading}, volume={33}, ISSN={["1532-298X"]}, DOI={10.1093/plcell/koaa058}, number={3}, journal={PLANT CELL}, author={Strable, Josh}, year={2021}, month={Mar}, pages={447–448} }
 @article{laureyns_joossens_herwegh_pevernagie_pavie_demuynck_debray_coussens_pauwels_van hautegem_et al._2022, title={An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells}, volume={188}, ISSN={["1532-2548"]}, DOI={10.1093/plphys/kiab533}, abstractNote={Abstract
               The plant shoot apex houses the shoot apical meristem, a highly organized and active stem-cell tissue where molecular signaling in discrete cells determines when and where leaves are initiated. We optimized a spatial transcriptomics approach, in situ sequencing (ISS), to colocalize the transcripts of 90 genes simultaneously on the same section of tissue from the maize (Zea mays) shoot apex. The RNA ISS technology reported expression profiles that were highly comparable with those obtained by in situ hybridizations (ISHs) and allowed the discrimination between tissue domains. Furthermore, the application of spatial transcriptomics to the shoot apex, which inherently comprised phytomers that are in gradual developmental stages, provided a spatiotemporal sequence of transcriptional events. We illustrate the power of the technology through PLASTOCHRON1 (PLA1), which was specifically expressed at the boundary between indeterminate and determinate cells and partially overlapped with ROUGH SHEATH1 and OUTER CELL LAYER4 transcripts. Also, in the inflorescence, PLA1 transcripts localized in cells subtending the lateral primordia or bordering the newly established meristematic region, suggesting a more general role of PLA1 in signaling between indeterminate and determinate cells during the formation of lateral organs. Spatial transcriptomics builds on RNA ISH, which assays relatively few transcripts at a time and provides a powerful complement to single-cell transcriptomics that inherently removes cells from their native spatial context. Further improvements in resolution and sensitivity will greatly advance research in plant developmental biology.}, number={2}, journal={PLANT PHYSIOLOGY}, author={Laureyns, Reinout and Joossens, Jessica and Herwegh, Denia and Pevernagie, Julie and Pavie, Benjamin and Demuynck, Kirin and Debray, Kevin and Coussens, Griet and Pauwels, Laurens and Van Hautegem, Tom and et al.}, year={2022}, month={Feb}, pages={782–794} }
 @article{strable_2021, title={Developmental genetics of maize vegetative shoot architecture}, volume={41}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-021-01208-1}, abstractNote={More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.The online version contains supplementary material available at 10.1007/s11032-021-01208-1.}, number={3}, journal={MOLECULAR BREEDING}, author={Strable, Josh}, year={2021}, month={Mar} }
 @article{washburn_strable_dickinson_kothapalli_brose_covshoff_conant_hibberd_pires_2021, title={Distinct C-4 sub-types and C-3 bundle sheath isolation in the Paniceae grasses}, volume={5}, ISSN={["2475-4455"]}, DOI={10.1002/pld3.373}, abstractNote={AbstractIn C4 plants, the enzymatic machinery underpinning photosynthesis can vary, with, for example, three distinct C4 acid decarboxylases being used to release CO2 in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C4 species into three biochemical sub‐types. However, more recently, the notion that C4 species mix and match C4 acid decarboxylases has increased in popularity, and as a consequence, the validity of specific biochemical sub‐types has been questioned. Using five species from the grass tribe Paniceae, we show that, although in some species transcripts and enzymes involved in multiple C4 acid decarboxylases accumulate, in others, transcript abundance and enzyme activity is almost entirely from one decarboxylase. In addition, the development of a bundle sheath isolation procedure for a close C3 species in the Paniceae enables the preliminary exploration of C4 sub‐type evolution.}, number={12}, journal={PLANT DIRECT}, author={Washburn, Jacob D. and Strable, Josh and Dickinson, Patrick and Kothapalli, Satya S. and Brose, Julia M. and Covshoff, Sarah and Conant, Gavin C. and Hibberd, Julian M. and Pires, Joseph Chris}, year={2021}, month={Dec} }
 @misc{abraham-juarez_barnes_aragon-raygoza_tyson_kur_strable_rellan-alvarez_2021, title={The arches and spandrels of maize domestication, adaptation, and improvement}, volume={64}, ISSN={["1879-0356"]}, url={https://doi.org/10.1016/j.pbi.2021.102124}, DOI={10.1016/j.pbi.2021.102124}, abstractNote={People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland — a member of the Pueblo of Laguna tribe of New Mexico — wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, publisher={Elsevier BV}, author={Abraham-Juarez, Maria Jazmin and Barnes, Allison C. and Aragon-Raygoza, Alejandro and Tyson, Destiny and Kur, Andi and Strable, Josh and Rellan-Alvarez, Ruben}, year={2021}, month={Dec} }
 @misc{strable_nelissen_2021, title={The dynamics of maize leaf development: Patterned to grow while growing a pattern}, volume={63}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2021.102038}, abstractNote={Leaves are a significant component of the shoot system in grasses, functioning in light capture and photosynthesis. Leaf width, length, and angle are expressions of development that collectively define canopy architecture. Thus, the distinctive morphology of grass leaves is an interdependent readout of developmental patterning and growth along the proximal-distal, medial-lateral, and adaxial-abaxial axes. Here, we review the chronology of patterning and growth, namely along the proximal-distal axis, during maize leaf development. We underscore that patterning and growth occur simultaneously, making use of shared developmental gradients and molecular pathways.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Strable, Josh and Nelissen, Hilde}, year={2021}, month={Oct} }