Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

• Published in: The New phytologist Vol. 193; no. 3; pp. 617 - 624
• Main Authors: Resende, M. F. R. Jr, Muñoz, P, Acosta, J. J, Peter, G. F, Davis, J. M, Grattapaglia, D, Resende, M. D. V, Kirst, M
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-02-2012; New Phytologist Trust; Wiley Subscription Services, Inc
• Subjects: Age; Agriculture; Breeding; Domestication; Environment; Environment models; Estimate reliability; Evolutionary genetics; Feasibility studies; Genetic improvement; genomic selection; Genomics; Genomics - methods; genotype by environment interaction; Genotypes; Height; Inheritance Patterns - genetics; Linear Models; marker-assisted selection; Model accuracy; model estimation; Modeling; Models, Genetic; Nucleotides; Phenotype; Phenotypes; Phenotypic traits; Pine trees; Pinus - anatomy & histology; Pinus - genetics; Pinus - growth & development; Pinus taeda; plant breeding; Polymorphism; Population genetics; prediction; Prediction models; Quantitative trait loci; Quantitative Trait, Heritable; Reproducibility of Results; Reproductive cycle; Selection, Genetic; Single-nucleotide polymorphism; Time Factors; trees; Trees - genetics; Trees - growth & development
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/j.1469-8137.2011.03895.x

• Genomic selection is increasingly considered vital to accelerate genetic improvement. However, it is unknown how accurate genomic selection prediction models remain when used across environments and ages. This knowledge is critical for breeders to apply this strategy in genetic improvement. • Here, we evaluated the utility of genomic selection in a Pinus taeda population of c. 800 individuals clonally replicated and grown on four sites, and genotyped for 4825 single‐nucleotide polymorphism (SNP) markers. Prediction models were estimated for diameter and height at multiple ages using genomic random regression best linear unbiased predictor (BLUP). • Accuracies of prediction models ranged from 0.65 to 0.75 for diameter, and 0.63 to 0.74 for height. The selection efficiency per unit time was estimated as 53–112% higher using genomic selection compared with phenotypic selection, assuming a reduction of 50% in the breeding cycle. Accuracies remained high across environments as long as they were used within the same breeding zone. However, models generated at early ages did not perform well to predict phenotypes at age 6 yr. • These results demonstrate the feasibility and remarkable gain that can be achieved by incorporating genomic selection in breeding programs, as long as models are used at the relevant selection age and within the breeding zone in which they were estimated.