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Title: Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations

Abstract

Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. One way to achieve this is through genomic selection. However, the heritability of traits needs to be determined as well as the accuracy of prediction in order to determine if efficient selection is possible. Using five distinct switchgrass populations comprised of three lowland, one upland and one hybrid accession, the accuracy of genomic predictions under different cross-validation strategies and prediction methods was investigated. Individual genotypes were collected using GBS while kin-BLUP, partial least squares, sparse partial least squares, and BayesB methods were employed to predict yield, morphological, and NIRS-based compositional data collected in 2012–2013 from a replicated Nebraska field trial. Population structure was assessed by F statistics which ranged from 0.3952 between lowland and upland accessions to 0.0131 among the lowland accessions. Prediction accuracy ranged from 0.57–0.52 for cell wall soluble glucose and fructose respectively, to insignificant for traits with low repeatability. Ratios of heritability across to within-population ranged from 15 to 0.6. Accuracy was significantly affected by both cross-validation strategy and trait. Accounting for population structure with a cross-validation strategymore » constrained by accession resulted in accuracies that were 69% lower than apparent accuracies using unconstrained cross-validation. Less accurate genomic selection is anticipated when most of the phenotypic variation exists between populations such as with spring regreening and yield phenotypes.« less

Authors:
; ; ; ; ; ; ORCiD logo
Publication Date:
Research Org.:
US Dept. of Agriculture (USDA), Washington, DC (United States). Agricultural Research Service; Agricultural Research Service, Fort Collins, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1545363
Alternate Identifier(s):
OSTI ID: 1541878
Grant/Contract Number:  
SC0001490
Resource Type:
Accepted Manuscript
Journal Name:
BMC Plant Biology
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2229
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
Plant Sciences; Perennial; Biomass; Biofuel; Panicum; Polycross

Citation Formats

Fiedler, Jason D., Lanzatella, Christina, Edmé, Serge J., Palmer, Nathan A., Sarath, Gautam, Mitchell, Rob, and Tobias, Christian M. Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations. United States: N. p., 2018. Web. doi:10.1186/s12870-018-1360-z.
Fiedler, Jason D., Lanzatella, Christina, Edmé, Serge J., Palmer, Nathan A., Sarath, Gautam, Mitchell, Rob, & Tobias, Christian M. Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations. United States. doi:10.1186/s12870-018-1360-z.
Fiedler, Jason D., Lanzatella, Christina, Edmé, Serge J., Palmer, Nathan A., Sarath, Gautam, Mitchell, Rob, and Tobias, Christian M. Mon . "Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations". United States. doi:10.1186/s12870-018-1360-z. https://www.osti.gov/servlets/purl/1545363.
@article{osti_1545363,
title = {Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations},
author = {Fiedler, Jason D. and Lanzatella, Christina and Edmé, Serge J. and Palmer, Nathan A. and Sarath, Gautam and Mitchell, Rob and Tobias, Christian M.},
abstractNote = {Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. One way to achieve this is through genomic selection. However, the heritability of traits needs to be determined as well as the accuracy of prediction in order to determine if efficient selection is possible. Using five distinct switchgrass populations comprised of three lowland, one upland and one hybrid accession, the accuracy of genomic predictions under different cross-validation strategies and prediction methods was investigated. Individual genotypes were collected using GBS while kin-BLUP, partial least squares, sparse partial least squares, and BayesB methods were employed to predict yield, morphological, and NIRS-based compositional data collected in 2012–2013 from a replicated Nebraska field trial. Population structure was assessed by F statistics which ranged from 0.3952 between lowland and upland accessions to 0.0131 among the lowland accessions. Prediction accuracy ranged from 0.57–0.52 for cell wall soluble glucose and fructose respectively, to insignificant for traits with low repeatability. Ratios of heritability across to within-population ranged from 15 to 0.6. Accuracy was significantly affected by both cross-validation strategy and trait. Accounting for population structure with a cross-validation strategy constrained by accession resulted in accuracies that were 69% lower than apparent accuracies using unconstrained cross-validation. Less accurate genomic selection is anticipated when most of the phenotypic variation exists between populations such as with spring regreening and yield phenotypes.},
doi = {10.1186/s12870-018-1360-z},
journal = {BMC Plant Biology},
number = 1,
volume = 18,
place = {United States},
year = {2018},
month = {7}
}

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Works referenced in this record:

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