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Description
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This is the Norway spruce dataset used in our study to demonstrate a novel formulation to select an optimal subset of individuals under a strict maximum tolerable pairwise genomic relationship threshold. The dataset was obtained from a breeding population of Norway spruce (Picea abies) managed by the Norwegian Forest Seed Center. The material consists of two progeny trials testing half-sib families from pollen-mix matings conducted in a seed orchard in 1983 (Steffenrem et al. 2016). In the orchard, 121 parental genotypes were crossed with the pollen mix from 17 additional parental genotypes. Progenies were planted at three sites, of which two were included in this material (site 2: “Braset”, 60.88N, 11.21E, 400 m elevation, site 3: “Jord”, 59.64N, 10.72E, 95 m elevation), as single-tree plots completely randomized within 30 replicates on each site. Trees heights at 16 year from planting were measured in 2001. A total of approximately 47,000 SNP markers covering the genome (Bernhardsson et al. 2021) were obtained for the parents still available in 2023, and 1,671 progenies grown at the two progeny test sites. For the estimation of a “Van Raden” relationship matrix, an imputation and filtering procedure was performed, resulting in 39,000 SNP markers with a call rate greater than 0.95 and minor allele frequency greater than 0.05. Relationship analysis was conducted using the R package SNPready (Granato and Fritsche-Neto 2022). Expected relationships for half-sibs, full-sibs, parent-progeny and ramets of the same clone were around 0.25, 0.50, 0.50 and 1, respectively. Within the parental generation, some genotypes were duplicated in the breeding arboretum which caused some relationships within this generation to be near 1. Genomic breeding values (GBLUPs) for height at 16 years were estimated using ASReml-R, utilizing G matrix in the “Animal model” (Butler et al. 2023) with site as fixed effect, replicate (within site) as random effect. The heritability of the trait was estimated to 0.21 (standard error 0.045), which is typical for this trait. The breeding values were expressed as deviations from the population mean in meters.
References:
Bernhardsson, C., Zan, Y. J., Chen, Z. Q., Ingvarsson, P. K., & Wu, H. X. (2021). Molecular Ecology Resources, 21(3), 880-896. https://doi.org/https://doi.org/10.1111/1755-0998.13292
Butler, D. G., Cullis, B. R., Gilmour, A. R., Gogel, B. J., & Thompson, A. (2023). ASReml-R Reference Manual Version 4.2. In VSN International Ltd. https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/ASReml-R-Reference-Manual-4.2.pdf
Granato, I., & Fritsche-Neto, R. (2022). 'snpReady': Preparing Genotypic Datasets in Order to Run Genomic Analsysis. R package version 0.9.6
Steffenrem, A., Solheim, H., & Skrøppa, T. (2016). European Journal of Forest Research, 135(5), 815-825. https://doi.org/https://doi.org/10.1007/s10342-016-0975-6 (2026-03-01) (2026-03-01)
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