1. Single-step genomic prediction of Eucalyptus dunnii using different identity-by-descent and identity-by-state relationship matrices
- Author
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Dino Palazzini, Juan Gabriel Rivas, Natalia Cristina Aguirre, Leonel Harrand, Esteban F. Cisneros, Gustavo Pedro Javier Oberschelp, Martín N. Garcia, Juan Adolfo Lopez, Esteban Javier Jurcic, Cintia V. Acuña, Pamela V. Villalba, Sebastián Munilla, Maria Carolina Martinez, Pablo S. Pathauer, Eduardo P. Cappa, and Susana N. Marcucci Poltri
- Subjects
0106 biological sciences ,0301 basic medicine ,Genotype ,Biology ,Best linear unbiased prediction ,010603 evolutionary biology ,01 natural sciences ,Identity by descent ,Article ,Standard deviation ,Eucalyptus dunnii ,03 medical and health sciences ,Statistics ,Genetics ,Genetics (clinical) ,Eucalyptus ,Genome ,Models, Genetic ,Covariance matrix ,Estimator ,Genomics ,Covariance ,Plant Breeding ,Phenotype ,030104 developmental biology ,Tree breeding - Abstract
Genomic selection based on the single-step genomic best linear unbiased prediction (ssGBLUP) approach is becoming an important tool in forest tree breeding. The quality of the variance components and the predictive ability of the estimated breeding values (GEBV) depends on how well marker-based genomic relationships describe the actual genetic relationships at unobserved causal loci. We investigated the performance of GEBV obtained when fitting models with genomic covariance matrices based on two identity-by-descent (IBD) and two identity-by-state (IBS) relationship measures. Multiple-trait multiple-site ssGBLUP models were fitted to diameter and stem straightness in five open-pollinated progeny trials of Eucalyptus dunnii, genotyped using the EUChip60K. We also fitted the conventional ABLUP model with a pedigree-based covariance matrix. Estimated relationships from the IBD estimators displayed consistently lower standard deviations than those from the IBS approaches. Although ssGBLUP based in IBS estimators resulted in higher trait-site heritabilities, the gain in accuracy of the relationships using IBD estimators has resulted in higher predictive ability and lower bias of GEBV, especially for low-heritability trait-site. ssGBLUP based on IBS and IBD approaches performed considerably better than the traditional ABLUP. In summary, our results advocate the use of the ssGBLUP approach jointly with the IBD relationship matrix in open-pollinated forest tree evaluation.
- Published
- 2021
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