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Title: Defining the genetic components of callus formation: A GWAS approach

Abstract

A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide–log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showedmore » homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.« less

Authors:
 [1]; ORCiD logo [2];  [1];  [3]; ORCiD logo [4];  [5];  [6]; ORCiD logo [5];  [6];  [5];  [1];  [1];  [7];  [1];  [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Plant Systems Biology Group. Biosciences Division
  2. Oregon State Univ., Corvallis, OR (United States). Dept. of Forest Ecosystems and Society
  3. Univ. of Tennessee, Knoxville, TN (United States). The Bredesen Center for Interdisciplinary Research and Graduate Education
  4. Michigan Technological Univ., Houghton, MI (United States). School of Forest Resources and Environmental Science
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Biology Group. Biosciences Division
  6. Univ. of Tennessee, Knoxville, TN (United States). The Bredesen Center for Interdisciplinary Research and Graduate Education; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Biology Group. Biosciences Division
  7. Oak Ridge Associated Universities, Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); ORNL Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1468129
Grant/Contract Number:  
[AC05-00OR22725]
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
[ Journal Volume: 13; Journal Issue: 8]; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; genome-wide association studies; Arabidopsis thaliana; gene regulation; auxins; gene expression; leaves; transcription factors; genetic networks

Citation Formats

Tuskan, Gerald A., Mewalal, Ritesh, Gunter, Lee E., Palla, Kaitlin J., Carter, Kelsey, Jacobson, Daniel A., Jones, Piet C., Garcia, Benjamin J., Weighill, Deborah A., Hyatt, Philip D., Yang, Yongil, Zhang, Jin, Reis, Nicholas, Chen, Jin-Gui, and Muchero, Wellington. Defining the genetic components of callus formation: A GWAS approach. United States: N. p., 2018. Web. doi:10.1371/journal.pone.0202519.
Tuskan, Gerald A., Mewalal, Ritesh, Gunter, Lee E., Palla, Kaitlin J., Carter, Kelsey, Jacobson, Daniel A., Jones, Piet C., Garcia, Benjamin J., Weighill, Deborah A., Hyatt, Philip D., Yang, Yongil, Zhang, Jin, Reis, Nicholas, Chen, Jin-Gui, & Muchero, Wellington. Defining the genetic components of callus formation: A GWAS approach. United States. doi:10.1371/journal.pone.0202519.
Tuskan, Gerald A., Mewalal, Ritesh, Gunter, Lee E., Palla, Kaitlin J., Carter, Kelsey, Jacobson, Daniel A., Jones, Piet C., Garcia, Benjamin J., Weighill, Deborah A., Hyatt, Philip D., Yang, Yongil, Zhang, Jin, Reis, Nicholas, Chen, Jin-Gui, and Muchero, Wellington. Fri . "Defining the genetic components of callus formation: A GWAS approach". United States. doi:10.1371/journal.pone.0202519. https://www.osti.gov/servlets/purl/1468129.
@article{osti_1468129,
title = {Defining the genetic components of callus formation: A GWAS approach},
author = {Tuskan, Gerald A. and Mewalal, Ritesh and Gunter, Lee E. and Palla, Kaitlin J. and Carter, Kelsey and Jacobson, Daniel A. and Jones, Piet C. and Garcia, Benjamin J. and Weighill, Deborah A. and Hyatt, Philip D. and Yang, Yongil and Zhang, Jin and Reis, Nicholas and Chen, Jin-Gui and Muchero, Wellington},
abstractNote = {A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide–log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.},
doi = {10.1371/journal.pone.0202519},
journal = {PLoS ONE},
number = [8],
volume = [13],
place = {United States},
year = {2018},
month = {8}
}

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