• An in situ and morphometric study of maize (Zea mays L.) cob rondel phytoliths from Southwestern North American landraces

      Yost, Chad L.; Michas, McCaela; Adams, Karen R.; Swarts, Kelly; Puseman, Kathryn; Ball, Terry; Department of Geosciences, University of Arizona (Elsevier BV, 2021-02)
      We present the first comprehensive computer-assisted morphometric analysis of microscopic rondel1 phytoliths (plant opal microfossils) produced in the cobs of 24 historic Southwestern North American landraces of maize (Zea mays L.) after all were grown in a well-documented agronomic field study. We also present an in situ study of the location of rondel phytolith production within the maize cob and provide a detailed review of previous maize phytolith studies. We found that glumes contained abundant rondel phytoliths throughout the tissue; however, lemma/palea tissue contained no phytoliths. In contrast, cupule tissue had some areas with abundant phytoliths, some with fewer scattered phytoliths, and vast areas that contained no rondel phytoliths. The rondel-rich areas appear to be where the glumes had once attached to the cupule and may be remnants of glume tissue adhering to the cupule. From the morphometric study, we found there were significant differences in the size morphometries of glume rondels depending on their cob location (top, middle, base) but no significant differences in shape morphometries. Using shape morphometries, we could not discriminate reliably among maize cob rondel phytoliths produced by the diverse landraces considered. The inclusion of morphometrics from areas in addition to or in combination with the outer periclinal surface may allow for some discrimination of maize landraces and is an avenue that should be explored further. Although our approach was not successful at identifying differences between essentially modern landraces, there may be significant rondel phytolith morphometric differences between wild, progenitor, and domesticated Zea.
    • The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

      Walls, Ramona L; Cooper, Laurel; Elser, Justin; Gandolfo, Maria Alejandra; Mungall, Christopher J; Smith, Barry; Stevenson, Dennis W; Jaiswal, Pankaj; Univ Arizona, Inst Bio5 (FRONTIERS MEDIA SA, 2019-06-04)
      The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
    • Rearrangement with the nkd2 promoter contributed to allelic diversity of the r1 gene in maize (Zea mays)

      Wu, H.; Li, G.; Zhan, J.; Zhang, S.; Beall, B.D.; Yadegari, R.; Becraft, P.W.; School of Plant Sciences, University of Arizona (John Wiley and Sons Inc, 2022)
      The maize red1 (r1) locus regulates anthocyanin accumulation and is a classic model for allelic diversity; changes in regulatory regions are responsible for most of the variation in gene expression patterns. Here, an intrachromosomal rearrangement between