Genomic Prediction for Winter Survival of Lowland Switchgrass in the Northern USA

Abstract

The lowland ecotype of switchgrass has generated considerable interest because of its higher biomass yield and late flowering characteristics compared to the upland ecotype. However, lowland ecotypes planted in northern latitudes exhibit very low winter survival. Implementation of genomic selection could potentially enhance switchgrass breeding for winter survival by reducing generation time while eliminating the dependence on weather. The objectives of this study were to assess the potential of genomic selection for winter survival in lowland switchgrass by combining multiple populations in the training set and applying the selected model in two independent testing datasets for validation. Marker data were generated using exome capture sequencing. Validation was conducted using (1) indirect indicators of winter adaptation based on geographic and climatic variables of accessions from different source locations and (2) winter survival estimates of the phenotype. The prediction accuracies were significantly higher when the training dataset comprising all populations was used in fivefold cross validation but its application was not useful in the independent validation dataset. Nevertheless, modeling for population heterogeneity improved the prediction accuracy to some extent but the genetic relationship between the training and validation populations was found to be more influential. The predicted winter survival of lowland switchgrass indicated latitudinal and longitudinal variability, with the northeast USA the region for most cold tolerant lowland populations. Our results suggested that GS could provide valuable opportunities for improving winter survival and accelerate the lowland switchgrass breeding programs toward the development of cold tolerant cultivars suitable for northern latitudes.

Keywords

• Genomic Prediction
• exome capture
• population structure
• winter survival
• GBLUP
• GenPred
• Shared Data Resources