DOI: 10.5061/dryad.ms580
title: Data from: Assessing the expected response to genomic selection of individuals and families in Eucalyptus breeding with an additive-dominant model

description: We report a genomic selection (GS) study of growth and wood quality traits
 in an outbred F2 hybrid Eucalyptus population (n=768) using high-density
 single-nucleotide polymorphism (SNP) genotyping. Going beyond previous
 reports in forest trees, models were developed for different selection
 targets, namely, families, individuals within families and individuals
 across the entire population using a genomic model including dominance. To
 provide a more breeder-intelligible assessment of the performance of GS we
 calculated the expected response as the percentage gain over the
 population average expected genetic value (EGV) for different proportions
 of genomically selected individuals, using a rigorous cross-validation
 (CV) scheme that removed relatedness between training and validation sets.
 Predictive abilities (PAs) were 0.40–0.57 for individual selection and
 0.56–0.75 for family selection. PAs under an additive+dominance model
 improved predictions by 5 to 14% for growth depending on the selection
 target, but no improvement was seen for wood traits. The good performance
 of GS with no relatedness in CV suggested that our average SNP density
 (~25 kb) captured some short-range linkage disequilibrium. Truncation GS
 successfully selected individuals with an average EGV significantly higher
 than the population average. Response to GS on a per year basis was ~100%
 more efficient than by phenotypic selection and more so with higher
 selection intensities. These results contribute further experimental data
 supporting the positive prospects of GS in forest trees. Because
 generation times are long, traits are complex and costs of DNA genotyping
 are plummeting, genomic prediction has good perspectives of adoption in
 tree breeding practice.
description: SNP Data for 24,806
 polymorphic SNPsSNP Data for 24,806
 polymorphic SNPs in 768 individuals of the 856 individuals used in the
 study. SNP data were generated using the EuCHIP60K. You will find detailed
 info on the SNP contained in this chip (genome location, target SNP,
 flanking sequence) in Silva-Junior et al. (2015). A flexible multi-species
 genome-wide 60K SNP chip developed from pooled resequencing 240 Eucalyptus
 tree genomes across 12 species. New Phytologist 206(4): 1527-1540. Please
 note that SNP data was available for 768 trees of the 856 trees
 phenotyped, as described in the paperSNP_Data.txtPedigree data for the populationExpected pedigree data for the experimental population of full sib families based on the pedigree registered by the breeder. Individuals used in the study go from ID 11 to 856.Pedigree_data.txtPhenotypic data for the 856 treesPhenotypic data for the 856 trees of the experimental population. Data include information on the progeny trial (called landscape in the datafile), block,soil type, planting spacing, age at measurement in years, followed by the trait data, mean annual volume growth increment (MAI), basic wood density (BWD) and screened cellulose pulp yield (SPY). Please note that SNP data were available only for 768 trees of these 856 phenotyped trees as described in the paperPhenotypic_data.txt