2022 journal article

Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture

G3 Genes|Genomes|Genetics.

co-author countries: United States of America πŸ‡ΊπŸ‡Έ

Ed(s): A. Lipka

author keywords: QTL; loblolly pine; linkage disequilibrium; genomic relationships; cloned progeny tests; cross-validation; GBLUP; GWAS; Genomic Prediction; GenPred; Shared Data Resource
MeSH headings : Genome-Wide Association Study; Genotype; Linkage Disequilibrium; Models, Genetic; Phenotype; Pinus taeda / genetics; Plant Breeding; Polymorphism, Single Nucleotide
Source: ORCID
Added: December 11, 2021

Abstract Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from random (20% vs 80%) cross validation within the training population were 0.56 and 0.78 for height and stem form, respectively. Removal of all full-sib relatives within the training population resulted in ∼50% reduction in their genomic prediction ability for both traits. The average prediction ability for all 451 individual trees was 0.29 for height and 0.57 for stem form. The degree of genetic linkage (full-sib family, half sib family, unrelated) between the training and validation sets had a strong impact on prediction ability for stem form but not for height. A dominant dwarfing allele, the first to be reported in a conifer species, was discovered via genome-wide association studies on linkage Group 5 that conferred a 0.33-m mean height reduction. However, the QTL was family specific. The rapid decay of linkage disequilibrium, large genome size, and inconsistencies in marker-QTL linkage phase suggest that large, diverse training populations are needed for genomic selection in Pinus taeda L.