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Genome-wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk.
Nagle, Michael F; Yuan, Jialin; Kaur, Damanpreet; Ma, Cathleen; Peremyslova, Ekaterina; Jiang, Yuan; Goralogia, Greg S; Magnuson, Anna; Li, Jia Yi; Muchero, Wellington; Fuxin, Li; Strauss, Steven H.
Afiliação
  • Nagle MF; Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.
  • Yuan J; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.
  • Kaur D; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.
  • Ma C; Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.
  • Peremyslova E; Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.
  • Jiang Y; Statistics Department, Oregon State University, Corvallis, OR, 97331, USA.
  • Goralogia GS; Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.
  • Magnuson A; Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.
  • Li JY; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.
  • Muchero W; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
  • Fuxin L; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
  • Strauss SH; Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA.
New Phytol ; 242(5): 2059-2076, 2024 Jun.
Article em En | MEDLINE | ID: mdl-38650352
ABSTRACT
Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high-throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross-referenced complementary red, green, and blue (RGB) and fluorescent-hyperspectral images. We performed association mapping using single-marker and combined variant methods, followed by statistical tests for epistasis and integration of published multi-omic datasets to identify likely regulatory hubs. We report 409 candidate genes implicated by associations within 5 kb of coding sequences, and epistasis tests implicated 81 of these candidate genes as regulators of one another. Gene ontology terms related to protein-protein interactions and transcriptional regulation are overrepresented, among others. In addition to auxin and cytokinin pathways long established as critical to TR, our results highlight the importance of stress and wounding pathways. Potential regulatory hubs of signaling within and across these pathways include GROWTH REGULATORY FACTOR 1 (GRF1), PHOSPHATIDYLINOSITOL 4-KINASE ß1 (PI-4Kß1), and OBF-BINDING PROTEIN 1 (OBP1).
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Reguladores de Crescimento de Plantas / Populus / Estudo de Associação Genômica Ampla Idioma: En Revista: New Phytol Assunto da revista: BOTANICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Reguladores de Crescimento de Plantas / Populus / Estudo de Associação Genômica Ampla Idioma: En Revista: New Phytol Assunto da revista: BOTANICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos