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

Authors

Jason D. Fiedler, North Dakota State UniversityFollow
Christina Lanzatella, USDA Crop Improvement and Genetics Research Unit
Serge J. Edme, USDA-ARS Wheat, Sorghum and Forage Research UnitFollow
Nathan A. Palmer, USDA-ARS Wheat, Sorghum and Forage Research UnitFollow
Gautam Sarath, USDA-ARS Wheat, Sorghum and Forage Research UnitFollow
Rob Mitchell, USDA-ARS Wheat, Sorghum and Forage Research UnitFollow
Christian M. Tobias, USDA-ARS, Genomics and Gene Discovery Research UnitFollow

ORCID IDs

0000-0002-7881-750X

Date of this Version

2018

Citation

BMC Plant Biology (2018) 18:142

Comments

© The Author(s).

Open access

https://doi.org/10.1186/s12870-018-1360-z

Abstract

Background: 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.

Results: 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.

Conclusions: 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.