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      Multi‐trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce

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          Abstract

          Plantation‐grown trees have to cope with an increasing pressure of pest and disease in the context of climate change, and breeding approaches using genomics may offer efficient and flexible tools to face this pressure. In the present study, we targeted genetic improvement of resistance of an introduced conifer species in Canada, Norway spruce ( Picea abies (L.) Karst.), to the native white pine weevil ( Pissodes strobi Peck). We developed single‐ and multi‐trait genomic selection (GS) models and selection indices considering the relationships between weevil resistance, intrinsic wood quality, and growth traits. Weevil resistance, acoustic velocity as a proxy for mechanical wood stiffness, and average wood density showed moderate‐to‐high heritability and low genotype‐by‐environment interactions. Weevil resistance was genetically positively correlated with tree height, height‐to‐diameter at breast height (DBH) ratio, and acoustic velocity. The accuracy of the different GS models tested (GBLUP, threshold GBLUP, Bayesian ridge regression, BayesCπ) was high and did not differ among each other. Multi‐trait models performed similarly as single‐trait models when all trees were phenotyped. However, when weevil attack data were not available for all trees, weevil resistance was more accurately predicted by integrating genetically correlated growth traits into multi‐trait GS models. A GS index that corresponded to the breeders’ priorities achieved near maximum gains for weevil resistance, acoustic velocity, and height growth, but a small decrease for DBH. The results of this study indicate that it is possible to breed for high‐quality, weevil‐resistant Norway spruce reforestation stock with high accuracy achieved from single‐trait or multi‐trait GS.

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          The ecology and evolution of plant tolerance to herbivory.

          The tolerance of plants to herbivory reflects the degree to which a plant can regrow and reproduce after damage from herbivores. Autoecological factors, as well as the influence of competitors and mutualists, affect the level of plant tolerance. Recent work indicates that there is a heritable basis for tolerance and that it can evolve in natural plant populations. Although tolerance is probably not a strict alternative to plant resistance, there could be inter- and intraspecific tradeoffs between these defensive strategies.
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            Shrinkage Estimation of the Realized Relationship Matrix

            The additive relationship matrix plays an important role in mixed model prediction of breeding values. For genotype matrix X (loci in columns), the product XX′ is widely used as a realized relationship matrix, but the scaling of this matrix is ambiguous. Our first objective was to derive a proper scaling such that the mean diagonal element equals 1+f, where f is the inbreeding coefficient of the current population. The result is a formula involving the covariance matrix for sampling genomic loci, which must be estimated with markers. Our second objective was to investigate whether shrinkage estimation of this covariance matrix can improve the accuracy of breeding value (GEBV) predictions with low-density markers. Using an analytical formula for shrinkage intensity that is optimal with respect to mean-squared error, simulations revealed that shrinkage can significantly increase GEBV accuracy in unstructured populations, but only for phenotyped lines; there was no benefit for unphenotyped lines. The accuracy gain from shrinkage increased with heritability, but at high heritability (> 0.6) this benefit was irrelevant because phenotypic accuracy was comparable. These trends were confirmed in a commercial pig population with progeny-test-estimated breeding values. For an anonymous trait where phenotypic accuracy was 0.58, shrinkage increased the average GEBV accuracy from 0.56 to 0.62 (SE < 0.00) when using random sets of 384 markers from a 60K array. We conclude that when moderate-accuracy phenotypes and low-density markers are available for the candidates of genomic selection, shrinkage estimation of the relationship matrix can improve genetic gain.
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              Performance of genomic selection in mice.

              Selection plans in plant and animal breeding are driven by genetic evaluation. Recent developments suggest using massive genetic marker information, known as "genomic selection." There is little evidence of its performance, though. We empirically compared three strategies for selection: (1) use of pedigree and phenotypic information, (2) use of genomewide markers and phenotypic information, and (3) the combination of both. We analyzed four traits from a heterogeneous mouse population (http://gscan.well.ox.ac.uk/), including 1884 individuals and 10,946 SNP markers. We used linear mixed models, using extensions of association analysis. Cross-validation techniques were used, providing assumption-free estimates of predictive ability. Sampling of validation and training data sets was carried out across and within families, which allows comparing across- and within-family information. Use of genomewide genetic markers increased predictive ability up to 0.22 across families and up to 0.03 within families. The latter is not statistically significant. These values are roughly comparable to increases of up to 0.57 (across family) and 0.14 (within family) in accuracy of prediction of genetic value. In this data set, within-family information was more accurate than across-family information, and populational linkage disequilibrium was not a completely accurate source of information for genetic evaluation. This fact questions some applications of genomic selection.
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                Author and article information

                Contributors
                Patrick.Lenz@canada.ca
                Journal
                Evol Appl
                Evol Appl
                10.1111/(ISSN)1752-4571
                EVA
                Evolutionary Applications
                John Wiley and Sons Inc. (Hoboken )
                1752-4571
                20 June 2019
                January 2020
                : 13
                : 1 , Forest genomics: Advancing climate adaptation, forest health, productivity and conservation ( doiID: 10.1111/eva.v13.1 )
                : 76-94
                Affiliations
                [ 1 ] Canadian Wood Fibre Centre Natural Resources Canada Québec Québec Canada
                [ 2 ] Canada Research Chair in Forest Genomics Institute of Integrative Biology and Systems, Centre for Forest Research Université Laval Québec Québec Canada
                [ 3 ] Ministère des Forêts, de la Faune et des Parcs Gouvernement du Québec, Direction de la recherche forestière Québec Québec Canada
                [ 4 ] Laurentian Forestry Centre Natural Resources Canada Québec Québec Canada
                Author notes
                [*] [* ] * Correspondence

                Patrick R. N. Lenz, Natural Resources Canada, Canadian Wood Fibre Centre, 1055 du PEPS, PO Box 10380, Québec, QC G1V 4C7, Canada.

                Email: Patrick.Lenz@ 123456canada.ca

                Author information
                https://orcid.org/0000-0002-0184-9247
                Article
                EVA12823
                10.1111/eva.12823
                6935592
                31892945
                1cd03f26-d4d2-48ab-9150-b018a89add58
                © 2019 Her Majesty the Queen in Right of Canada. Environmental DNA published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 07 November 2018
                : 18 April 2019
                : 15 May 2019
                Page count
                Figures: 5, Tables: 5, Pages: 19, Words: 17090
                Funding
                Funded by: Genome Canada , open-funder-registry 10.13039/100008762;
                Award ID: 6503
                Categories
                Special Issue Original Article
                Special Issue Original Articles
                Custom metadata
                2.0
                January 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.3 mode:remove_FC converted:29.12.2019

                Evolutionary Biology
                breeding,conifers,index selection,insect resistance,multi‐trait genomic selection,norway spruce,white pine weevil,wood quality

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