title: Accuracy and responses of genomic selection on key traits in apple breeding.
abstract: The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.
authors.affiliation: Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV , F-49071 Beaucouze, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Muranty
authors.affiliation: Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige , Trento, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.affiliation: Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV , F-49071 Beaucouze, France.
authors.forename: Inès Ben
authors.initials: IB
authors.lastname: Sadok
authors.affiliation: Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV , F-49071 Beaucouze, France.
authors.forename: Mehdi Al
authors.initials: MA
authors.lastname: Rifaï
authors.affiliation: Better3Fruit , Rillaar, Belgium.
authors.forename: Annemarie
authors.initials: A
authors.lastname: Auwerkerken
authors.affiliation: Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige , Trento, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Banchi
authors.affiliation: Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige , Trento, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.affiliation: DAFNAE, Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente , viale Università 16, 35020 Legnaro (PD), Università, degli Studi di Padova , Italy.
authors.forename: Piergiorgio
authors.initials: P
authors.lastname: Stevanato
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Center , Wageningen, The Netherlands.
authors.forename: W Eric
authors.initials: WE
authors.lastname: van de Weg
authors.affiliation: Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy; Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen, The Netherlands.
authors.forename: Mario
authors.initials: M
authors.lastname: Di Guardo
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited , Private Bag 1401, Havelock North 4157, New Zealand.
authors.forename: Satish
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV , F-49071 Beaucouze, France.
authors.forename: François
authors.initials: F
authors.lastname: Laurens
authors.affiliation: Biometris, Wageningen University and Research Center , Wageningen, The Netherlands.
authors.forename: Marco C A M
authors.initials: MC
authors.lastname: Bink