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Title: Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

Abstract

Sorghum (Sorghum bicolor) is the fifth most commonly grown cereal crop worldwide in large part due to its remarkable stress tolerance. It requires significantly less water to yield well than other major cereal crops and can survive harsher drought conditions. For these reasons as well as its size, it has also been recently proposed as a new bioenergy crop. However, despite the fact that sorghum is usually grown for its drought tolerant qualities, the genetic basis of its drought tolerance is still largely a mystery. To uncover the genetic basis of drought tolerance in sorghum at a comprehensive and genome-wide level, we undertook a high-density phenomics GWAS in which a diversity panel of ~640 sorghum lines were phenotyped in central California once per week by aerial drone over the course of a growing season. Plant biomass, height, and leaf area were measured by the drone for individual field plots, replicated over two drought treatments and a control treatment. The resulting dataset of over 171,000 phenotypic data-points was analyzed along with GBS data on the 640 sorghum lines to reveal more than 200 high-quality, replicated and conserved GWAS associations. We also introduce here new data analysis and visualization tools for highlymore » dense phenotype datasets including a variation on the Manhattan plot we term the ‘Manhattan blot’. Our 200 associations include a number of very strong candidate genes, including those encoding heat shock proteins, antifreeze proteins, and other domains recognized as important to plant stress responses.« less

Authors:
 [1];  [2];  [3];  [2];  [2];  [4];  [5];  [6]; ORCiD logo [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Univ. of California, Parlier, CA (United States). Kearney Agricultural Research and Extension Center
  3. Blue River Technology, Sunnyvale, CA (United States)
  4. Chromatin Inc, Lubbock, TX (United States)
  5. Univ. of California, Five Points, CA (United States). West Side Research & Extension Center
  6. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Advanced Research Projects Agency - Energy (ARPA-E); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1489292
Alternate Identifier(s):
OSTI ID: 1559146
Report Number(s):
PNNL-SA-131382
Journal ID: ISSN 1471-2164
Grant/Contract Number:  
AC05-76RL01830; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 19; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Spindel, Jennifer E., Dahlberg, Jeffery, Colgan, Matthew, Hollingsworth, Joy, Sievert, Julie, Staggenborg, Scott H., Hutmacher, Robert, Jansson, Christer, and Vogel, John P. Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought. United States: N. p., 2018. Web. doi:10.1186/s12864-018-5055-5.
Spindel, Jennifer E., Dahlberg, Jeffery, Colgan, Matthew, Hollingsworth, Joy, Sievert, Julie, Staggenborg, Scott H., Hutmacher, Robert, Jansson, Christer, & Vogel, John P. Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought. United States. doi:10.1186/s12864-018-5055-5.
Spindel, Jennifer E., Dahlberg, Jeffery, Colgan, Matthew, Hollingsworth, Joy, Sievert, Julie, Staggenborg, Scott H., Hutmacher, Robert, Jansson, Christer, and Vogel, John P. Mon . "Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought". United States. doi:10.1186/s12864-018-5055-5. https://www.osti.gov/servlets/purl/1489292.
@article{osti_1489292,
title = {Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought},
author = {Spindel, Jennifer E. and Dahlberg, Jeffery and Colgan, Matthew and Hollingsworth, Joy and Sievert, Julie and Staggenborg, Scott H. and Hutmacher, Robert and Jansson, Christer and Vogel, John P.},
abstractNote = {Sorghum (Sorghum bicolor) is the fifth most commonly grown cereal crop worldwide in large part due to its remarkable stress tolerance. It requires significantly less water to yield well than other major cereal crops and can survive harsher drought conditions. For these reasons as well as its size, it has also been recently proposed as a new bioenergy crop. However, despite the fact that sorghum is usually grown for its drought tolerant qualities, the genetic basis of its drought tolerance is still largely a mystery. To uncover the genetic basis of drought tolerance in sorghum at a comprehensive and genome-wide level, we undertook a high-density phenomics GWAS in which a diversity panel of ~640 sorghum lines were phenotyped in central California once per week by aerial drone over the course of a growing season. Plant biomass, height, and leaf area were measured by the drone for individual field plots, replicated over two drought treatments and a control treatment. The resulting dataset of over 171,000 phenotypic data-points was analyzed along with GBS data on the 640 sorghum lines to reveal more than 200 high-quality, replicated and conserved GWAS associations. We also introduce here new data analysis and visualization tools for highly dense phenotype datasets including a variation on the Manhattan plot we term the ‘Manhattan blot’. Our 200 associations include a number of very strong candidate genes, including those encoding heat shock proteins, antifreeze proteins, and other domains recognized as important to plant stress responses.},
doi = {10.1186/s12864-018-5055-5},
journal = {BMC Genomics},
issn = {1471-2164},
number = 1,
volume = 19,
place = {United States},
year = {2018},
month = {9}
}

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Works referenced in this record:

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011