Genomic Predictions for Root Vigor in Sugar Beet Accessions: A Pilot Study

Selection for root system traits is essential to improve not only the soil resource acquisition but also plant growth and productivity. Previous studies demonstrated a correlation between root vigor (root elongation rate and sulfate uptake following deprivation) and crop yield. In sugar beet breeding programs, genomic markers could be used to predict the future performance of seedlings -whether they will show high or low root vigor- from marker genotypes. A pilot study on the implementation of genomic selection for root vigor in sugar beet is being carried out with a set of 123 individual plants from high and low root vigor lines and 192 SNP (single nucleotide polymorphism) markers uniformly distributed along the Beta vulgaris genome. Missing genotypes were imputed using the haplotype-based method implemented in Beagle. Imputed data were edited for call-rate > 90% and MAF < 2.5%. Marker genotypes were used to estimate genomic relationships between sugar beet individual plants. The mean of genomic relationships was 0.365 (standard deviation: 0.248; coefficient of variation: 67.9%). The matrix G of genomic relationship is used to compute genomic predictions in GBLUP: a threshold model for the probability p of either having high or low root vigor is fitted (logit(p)=μ+Xg). The predictive ability of genomic predictions will be measured in a 5-fold cross validation scheme, repeated 100 times, as the correlation between observed and predicted phenotypes. Genomic predictions have already proven to be a powerful tool in crop species (e.g. maize) and promises to enhance breeding programs in sugar beet as well.