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Title: Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree

Abstract

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To reflect how this process can be accelerated, we employed a genome-wide association mapping of ca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among crucial associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1];  [3]; ORCiD logo [1];  [3]; ORCiD logo [1];  [4];  [4];  [4];  [3]; ORCiD logo [3];  [2]; ORCiD logo [2];  [5];  [5];  [1];  [1];  [6]; ORCiD logo [7] more »; ORCiD logo [8] « less
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Oregon State Univ., Corvallis, OR (United States)
  3. Univ. of Georgia, Athens, GA (United States)
  4. North Dakota State Univ., Fargo, ND (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. Oregon State Univ., Corvallis, OR (United States); North Dakota State Univ., Fargo, ND (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1545198
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; SC0015662; FG02-93ER20097
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 45; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
septoria canker; invasive disease; association mapping; disease resistance; Populus trichocarpa

Citation Formats

Muchero, Wellington, Sondreli, Kelsey L., Chen, Jin-Gui, Urbanowicz, Breeanna R., Zhang, Jin, Singan, Vasanth, Yang, Yongil, Brueggeman, Robert S., Franco-Coronado, Juan, Abraham, Nivi, Yang, Jeong-Yeh, Moremen, Kelley W., Weisberg, Alexandra J., Chang, Jeff H., Lindquist, Erika, Barry, Kerrie, Ranjan, Priya, Jawdy, Sara, Schmutz, Jeremy, Tuskan, Gerald A., and LeBoldus, Jared M. Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree. United States: N. p., 2018. Web. doi:10.1073/pnas.1804428115.
Muchero, Wellington, Sondreli, Kelsey L., Chen, Jin-Gui, Urbanowicz, Breeanna R., Zhang, Jin, Singan, Vasanth, Yang, Yongil, Brueggeman, Robert S., Franco-Coronado, Juan, Abraham, Nivi, Yang, Jeong-Yeh, Moremen, Kelley W., Weisberg, Alexandra J., Chang, Jeff H., Lindquist, Erika, Barry, Kerrie, Ranjan, Priya, Jawdy, Sara, Schmutz, Jeremy, Tuskan, Gerald A., & LeBoldus, Jared M. Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree. United States. doi:10.1073/pnas.1804428115.
Muchero, Wellington, Sondreli, Kelsey L., Chen, Jin-Gui, Urbanowicz, Breeanna R., Zhang, Jin, Singan, Vasanth, Yang, Yongil, Brueggeman, Robert S., Franco-Coronado, Juan, Abraham, Nivi, Yang, Jeong-Yeh, Moremen, Kelley W., Weisberg, Alexandra J., Chang, Jeff H., Lindquist, Erika, Barry, Kerrie, Ranjan, Priya, Jawdy, Sara, Schmutz, Jeremy, Tuskan, Gerald A., and LeBoldus, Jared M. Thu . "Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree". United States. doi:10.1073/pnas.1804428115. https://www.osti.gov/servlets/purl/1545198.
@article{osti_1545198,
title = {Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree},
author = {Muchero, Wellington and Sondreli, Kelsey L. and Chen, Jin-Gui and Urbanowicz, Breeanna R. and Zhang, Jin and Singan, Vasanth and Yang, Yongil and Brueggeman, Robert S. and Franco-Coronado, Juan and Abraham, Nivi and Yang, Jeong-Yeh and Moremen, Kelley W. and Weisberg, Alexandra J. and Chang, Jeff H. and Lindquist, Erika and Barry, Kerrie and Ranjan, Priya and Jawdy, Sara and Schmutz, Jeremy and Tuskan, Gerald A. and LeBoldus, Jared M.},
abstractNote = {Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To reflect how this process can be accelerated, we employed a genome-wide association mapping ofca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among crucial associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.},
doi = {10.1073/pnas.1804428115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 45,
volume = 115,
place = {United States},
year = {2018},
month = {10}
}

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Works referenced in this record:

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
journal, August 2012