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

BMC Plant Biology

卷:18

Jason D. Fiedler¹  Christina Lanzatella²  Christian M. Tobias²  Rob Mitchell³  Nathan A. Palmer³  Gautam Sarath³  Serge J. Edmé³ 

[1] Department of Plant Sciences, North Dakota State University;

[2] USDA-ARS Crop Improvement and Genetics Research Unit, Western Regional Research Center;

[3] USDA-ARS Wheat, Sorghum and Forage Research Unit, 251 Filley Hall/Food Ind. University of Nebraska;

关键词: Perennial;    Biomass;    Biofuel;    Panicum;    Polycross;   

DOI  :  10.1186/s12870-018-1360-z

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown