Lenz2020

Reference

Lenz, P.R.N., Nadeau, S., Azaiez, A., Gerardi, S., Deslauriers, M., Perron, M., Isabel, N., Beaulieu, J., Bousquet, J. (2020) Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce. Heredity, 124(4):562-578. (Scopus )

Abstract

Genomic selection (GS) has a large potential for improving the prediction accuracy of breeding values and significantly reducing the length of breeding cycles. In this context, the choice of mating designs becomes critical to improve the efficiency of breeding operations and to obtain the largest genetic gains per time unit. Polycross mating designs have been traditionally used in tree and plant breeding to perform backward selection of the female parents. The possibility to use genetic markers for paternity identification and for building genomic prediction models should allow for a broader use of polycross tests in forward selection schemes. We compared the accuracies of genomic predictions of offspring’s breeding values from a polycross and a full-sib (partial diallel) mating design with similar genetic background in white spruce (Picea glauca). Trees were phenotyped for growth and wood quality traits, and genotyped for 4092 SNPs representing as many gene loci distributed across the 12 spruce chromosomes. For the polycross progeny test, heritability estimates were smaller, but more precise using the genomic BLUP (GBLUP) model as compared with pedigree-based models accounting for the maternal pedigree or for the reconstructed full pedigree. Cross-validations showed that GBLUP predictions were 22–52% more accurate than predictions based on the maternal pedigree, and 5–7% more accurate than predictions using the reconstructed full pedigree. The accuracies of GBLUP predictions were high and in the same range for most traits between the polycross (0.61–0.70) and full-sib progeny tests (0.61–0.74). However, higher genetic gains per time unit were expected from the polycross mating design given the shorter time needed to conduct crosses. Considering the operational advantages of the polycross design in terms of easier handling of crosses and lower associated costs for test establishment, we believe that this mating scheme offers great opportunities for the development and operational application of forward GS. © 2020, The Author(s).

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@ARTICLE { Lenz2020,
    AUTHOR = { Lenz, P.R.N. and Nadeau, S. and Azaiez, A. and Gerardi, S. and Deslauriers, M. and Perron, M. and Isabel, N. and Beaulieu, J. and Bousquet, J. },
    JOURNAL = { Heredity },
    TITLE = { Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce },
    YEAR = { 2020 },
    NOTE = { cited By 1 },
    NUMBER = { 4 },
    PAGES = { 562-578 },
    VOLUME = { 124 },
    ABSTRACT = { Genomic selection (GS) has a large potential for improving the prediction accuracy of breeding values and significantly reducing the length of breeding cycles. In this context, the choice of mating designs becomes critical to improve the efficiency of breeding operations and to obtain the largest genetic gains per time unit. Polycross mating designs have been traditionally used in tree and plant breeding to perform backward selection of the female parents. The possibility to use genetic markers for paternity identification and for building genomic prediction models should allow for a broader use of polycross tests in forward selection schemes. We compared the accuracies of genomic predictions of offspring’s breeding values from a polycross and a full-sib (partial diallel) mating design with similar genetic background in white spruce (Picea glauca). Trees were phenotyped for growth and wood quality traits, and genotyped for 4092 SNPs representing as many gene loci distributed across the 12 spruce chromosomes. For the polycross progeny test, heritability estimates were smaller, but more precise using the genomic BLUP (GBLUP) model as compared with pedigree-based models accounting for the maternal pedigree or for the reconstructed full pedigree. Cross-validations showed that GBLUP predictions were 22–52% more accurate than predictions based on the maternal pedigree, and 5–7% more accurate than predictions using the reconstructed full pedigree. The accuracies of GBLUP predictions were high and in the same range for most traits between the polycross (0.61–0.70) and full-sib progeny tests (0.61–0.74). However, higher genetic gains per time unit were expected from the polycross mating design given the shorter time needed to conduct crosses. Considering the operational advantages of the polycross design in terms of easier handling of crosses and lower associated costs for test establishment, we believe that this mating scheme offers great opportunities for the development and operational application of forward GS. © 2020, The Author(s). },
    AFFILIATION = { Natural Resources Canada, Canadian Wood Fibre Centre, 1055 rue Du PEPS, P.O. Box 10380QC G1V 4C7, Canada; Canada Research Chair in Forest Genomics, Institute of Systems and Integrative Biology, and Centre for Forest Research, Université Laval, 1030 Avenue de la MédecineQC G1V 0A6, Canada; Ministère des Forêts, de la Faune et des Parcs, Gouvernement du Québec, Direction de la recherche forestière, 2700 rue EinsteinQC G1P 3W8, Canada; Natural Resources Canada, Laurentian Forestry Centre, 1055 rue Du PEPS, P.O. Box 10380QC G1V 4C7, Canada },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1038/s41437-019-0290-3 },
    SOURCE = { Scopus },
    URL = { https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078098204&doi=10.1038%2fs41437-019-0290-3&partnerID=40&md5=ea1084a28a6fd9affdc9119eccc21cad },
}

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