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Title: 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture

Abstract

Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height, leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquiremore » shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.« less

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Texas A & M Univ., College Station, TX (United States). Interdisciplinary Program in Genetics and Biochemistry and Biophysics Department
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States; Texas A & M Univ., College Station, TX (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:
1427723
Grant/Contract Number:  
FC02-07ER64494; AR0000596
Resource Type:
Accepted Manuscript
Journal Name:
Plant Physiology (Bethesda)
Additional Journal Information:
Journal Name: Plant Physiology (Bethesda); Journal Volume: 172; Journal Issue: 2; Journal ID: ISSN 0032-0889
Publisher:
American Society of Plant Biologists
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Mccormick, Ryan F., Truong, Sandra K., and Mullet, John E. 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture. United States: N. p., 2016. Web. doi:10.1104/pp.16.00948.
Mccormick, Ryan F., Truong, Sandra K., & Mullet, John E. 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture. United States. doi:10.1104/pp.16.00948.
Mccormick, Ryan F., Truong, Sandra K., and Mullet, John E. Mon . "3D sorghum reconstructions from depth images identify QTL regulating shoot architecture". United States. doi:10.1104/pp.16.00948. https://www.osti.gov/servlets/purl/1427723.
@article{osti_1427723,
title = {3D sorghum reconstructions from depth images identify QTL regulating shoot architecture},
author = {Mccormick, Ryan F. and Truong, Sandra K. and Mullet, John E.},
abstractNote = {Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height, leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.},
doi = {10.1104/pp.16.00948},
journal = {Plant Physiology (Bethesda)},
number = 2,
volume = 172,
place = {United States},
year = {2016},
month = {8}
}

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Cited by: 16 works
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Works referenced in this record:

Data from: 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture
dataset, September 2016

  • McCormick, Ryan F.; Truong, Sandra K.; Mullet, John E.
  • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1104/pp.16.00948, 6 files
  • DOI: 10.5061/dryad.9vs26

    Works referencing / citing this record:

    Data from: 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture
    dataset, September 2016

    • McCormick, Ryan F.; Truong, Sandra K.; Mullet, John E.
    • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1104/pp.16.00948, 6 files
    • DOI: 10.5061/dryad.9vs26