Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture

Haichao Guo; Habtamu Ayalew; Anand Seethepalli; Kundan Dhakal; Marcus Griffiths; Xue Feng Ma; Larry M. York

doi:10.1111/nph.17329

Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture

Haichao Guo, Habtamu Ayalew, Anand Seethepalli, Kundan Dhakal, Marcus Griffiths, Xue Feng Ma, Larry M. York

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

The root economics space is a useful framework for plant ecology but is rarely considered for crop ecophysiology. In order to understand root trait integration in winter wheat, we combined functional phenomics with trait economic theory, utilizing genetic variation, high-throughput phenotyping, and multivariate analyses. We phenotyped a diversity panel of 276 genotypes for root respiration and architectural traits using a novel high-throughput method for CO₂ flux and the open-source software RhizoVision Explorer to analyze scanned images. We uncovered substantial variation in specific root respiration (SRR) and specific root length (SRL), which were primary indicators of root metabolic and structural costs. Multiple linear regression analysis indicated that lateral root tips had the greatest SRR, and the residuals from this model were used as a new trait. Specific root respiration was negatively correlated with plant mass. Network analysis, using a Gaussian graphical model, identified root weight, SRL, diameter, and SRR as hub traits. Univariate and multivariate genetic analyses identified genetic regions associated with SRR, SRL, and root branching frequency, and proposed gene candidates. Combining functional phenomics and root economics is a promising approach to improving our understanding of crop ecophysiology. We identified root traits and genomic regions that could be harnessed to breed more efficient crops for sustainable agroecosystems.

Original language	English
Pages (from-to)	98-112
Number of pages	15
Journal	New Phytologist
Volume	232
Issue number	1
DOIs	https://doi.org/10.1111/nph.17329
State	Published - Oct 2021
Externally published	Yes

Funding

This research was supported by the Noble Research Institute, LLC. The authors wish to acknowledge David McSweeney and Karen Hartman of the Greenhouse Core Facility for assistance provided during the experiment, Nick Krom of the Scientific Computing Department for assistance with Blast searches for candidate genes, and contributions from Yaxin Ge, Michael Cloyde, Na Ding, Xinji Zhang, Guangming Li and Wangqi Huang for data acquisition and sampling. LMY thanks the sROOT working group hosted by the iDiv in Leipzig, Germany for their stimulating discussion that impacted this work.

Funders	Funder number
Noble Research Institute

Keywords

genome-wide association studies (GWAS)
multi-trait
root architecture
root respiration
winter wheat

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1111/nph.17329

Cite this

@article{c134a5fbbaad4635bac4988746769c84,

title = "Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture",

abstract = "The root economics space is a useful framework for plant ecology but is rarely considered for crop ecophysiology. In order to understand root trait integration in winter wheat, we combined functional phenomics with trait economic theory, utilizing genetic variation, high-throughput phenotyping, and multivariate analyses. We phenotyped a diversity panel of 276 genotypes for root respiration and architectural traits using a novel high-throughput method for CO2 flux and the open-source software RhizoVision Explorer to analyze scanned images. We uncovered substantial variation in specific root respiration (SRR) and specific root length (SRL), which were primary indicators of root metabolic and structural costs. Multiple linear regression analysis indicated that lateral root tips had the greatest SRR, and the residuals from this model were used as a new trait. Specific root respiration was negatively correlated with plant mass. Network analysis, using a Gaussian graphical model, identified root weight, SRL, diameter, and SRR as hub traits. Univariate and multivariate genetic analyses identified genetic regions associated with SRR, SRL, and root branching frequency, and proposed gene candidates. Combining functional phenomics and root economics is a promising approach to improving our understanding of crop ecophysiology. We identified root traits and genomic regions that could be harnessed to breed more efficient crops for sustainable agroecosystems.",

keywords = "genome-wide association studies (GWAS), multi-trait, root architecture, root respiration, winter wheat",

author = "Haichao Guo and Habtamu Ayalew and Anand Seethepalli and Kundan Dhakal and Marcus Griffiths and Ma, {Xue Feng} and York, {Larry M.}",

note = "Publisher Copyright: {\textcopyright} 2021 The Authors. New Phytologist {\textcopyright} 2021 New Phytologist Foundation",

year = "2021",

month = oct,

doi = "10.1111/nph.17329",

language = "English",

volume = "232",

pages = "98--112",

journal = "New Phytologist",

issn = "0028-646X",

publisher = "wiley",

number = "1",

}

TY - JOUR

T1 - Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture

AU - Guo, Haichao

AU - Ayalew, Habtamu

AU - Seethepalli, Anand

AU - Dhakal, Kundan

AU - Griffiths, Marcus

AU - Ma, Xue Feng

AU - York, Larry M.

PY - 2021/10

Y1 - 2021/10

N2 - The root economics space is a useful framework for plant ecology but is rarely considered for crop ecophysiology. In order to understand root trait integration in winter wheat, we combined functional phenomics with trait economic theory, utilizing genetic variation, high-throughput phenotyping, and multivariate analyses. We phenotyped a diversity panel of 276 genotypes for root respiration and architectural traits using a novel high-throughput method for CO2 flux and the open-source software RhizoVision Explorer to analyze scanned images. We uncovered substantial variation in specific root respiration (SRR) and specific root length (SRL), which were primary indicators of root metabolic and structural costs. Multiple linear regression analysis indicated that lateral root tips had the greatest SRR, and the residuals from this model were used as a new trait. Specific root respiration was negatively correlated with plant mass. Network analysis, using a Gaussian graphical model, identified root weight, SRL, diameter, and SRR as hub traits. Univariate and multivariate genetic analyses identified genetic regions associated with SRR, SRL, and root branching frequency, and proposed gene candidates. Combining functional phenomics and root economics is a promising approach to improving our understanding of crop ecophysiology. We identified root traits and genomic regions that could be harnessed to breed more efficient crops for sustainable agroecosystems.

AB - The root economics space is a useful framework for plant ecology but is rarely considered for crop ecophysiology. In order to understand root trait integration in winter wheat, we combined functional phenomics with trait economic theory, utilizing genetic variation, high-throughput phenotyping, and multivariate analyses. We phenotyped a diversity panel of 276 genotypes for root respiration and architectural traits using a novel high-throughput method for CO2 flux and the open-source software RhizoVision Explorer to analyze scanned images. We uncovered substantial variation in specific root respiration (SRR) and specific root length (SRL), which were primary indicators of root metabolic and structural costs. Multiple linear regression analysis indicated that lateral root tips had the greatest SRR, and the residuals from this model were used as a new trait. Specific root respiration was negatively correlated with plant mass. Network analysis, using a Gaussian graphical model, identified root weight, SRL, diameter, and SRR as hub traits. Univariate and multivariate genetic analyses identified genetic regions associated with SRR, SRL, and root branching frequency, and proposed gene candidates. Combining functional phenomics and root economics is a promising approach to improving our understanding of crop ecophysiology. We identified root traits and genomic regions that could be harnessed to breed more efficient crops for sustainable agroecosystems.

KW - genome-wide association studies (GWAS)

KW - multi-trait

KW - root architecture

KW - root respiration

KW - winter wheat

UR - http://www.scopus.com/inward/record.url?scp=85104117970&partnerID=8YFLogxK

U2 - 10.1111/nph.17329

DO - 10.1111/nph.17329

M3 - Article

C2 - 33683730

AN - SCOPUS:85104117970

SN - 0028-646X

VL - 232

SP - 98

EP - 112

JO - New Phytologist

JF - New Phytologist

IS - 1

ER -

Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture

Abstract

Funding

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this