Accuracy and responses of genomic selection on key traits in apple breeding

Hélène Muranty, Michela Troggio, Inès Ben Sadok, Mehdi Al Rifaï, Annemarie Auwerkerken, E. Banchi, Riccardo Velasco, P. Stevanato, W.E. van de Weg, M. Di Guardo, S. Kumar, François Laurens, M.C.A.M. Bink

Research output: Contribution to journalArticleAcademicpeer-review

36 Citations (Scopus)

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.
Original languageEnglish
Article number15060
JournalHorticulture Research
Volume2
DOIs
Publication statusPublished - 2015

Fingerprint

Malus
marker-assisted selection
Breeding
apples
Single Nucleotide Polymorphism
Fruits
prediction
breeding
Fruit
heritability
selection response
fruit trees
breeding value
genomics
Crops
phenotype
selection intensity
crops
phenotypic variation
Population

Cite this

Muranty, H., Troggio, M., Ben Sadok, I., Al Rifaï, M., Auwerkerken, A., Banchi, E., ... Bink, M. C. A. M. (2015). Accuracy and responses of genomic selection on key traits in apple breeding. Horticulture Research, 2, [15060]. https://doi.org/10.1038/hortres.2015.60
Muranty, Hélène ; Troggio, Michela ; Ben Sadok, Inès ; Al Rifaï, Mehdi ; Auwerkerken, Annemarie ; Banchi, E. ; Velasco, Riccardo ; Stevanato, P. ; van de Weg, W.E. ; Di Guardo, M. ; Kumar, S. ; Laurens, François ; Bink, M.C.A.M. / Accuracy and responses of genomic selection on key traits in apple breeding. In: Horticulture Research. 2015 ; Vol. 2.
@article{64c5078584ab495a9efb3ee82868ef31,
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.",
author = "H{\'e}l{\`e}ne Muranty and Michela Troggio and {Ben Sadok}, In{\`e}s and {Al Rifa{\"i}}, Mehdi and Annemarie Auwerkerken and E. Banchi and Riccardo Velasco and P. Stevanato and {van de Weg}, W.E. and {Di Guardo}, M. and S. Kumar and Fran{\cc}ois Laurens and M.C.A.M. Bink",
year = "2015",
doi = "10.1038/hortres.2015.60",
language = "English",
volume = "2",
journal = "Horticulture Research",
issn = "2052-7276",
publisher = "Nature Publishing Group",

}

Muranty, H, Troggio, M, Ben Sadok, I, Al Rifaï, M, Auwerkerken, A, Banchi, E, Velasco, R, Stevanato, P, van de Weg, WE, Di Guardo, M, Kumar, S, Laurens, F & Bink, MCAM 2015, 'Accuracy and responses of genomic selection on key traits in apple breeding' Horticulture Research, vol. 2, 15060. https://doi.org/10.1038/hortres.2015.60

Accuracy and responses of genomic selection on key traits in apple breeding. / Muranty, Hélène; Troggio, Michela; Ben Sadok, Inès; Al Rifaï, Mehdi; Auwerkerken, Annemarie; Banchi, E.; Velasco, Riccardo; Stevanato, P.; van de Weg, W.E.; Di Guardo, M.; Kumar, S.; Laurens, François; Bink, M.C.A.M.

In: Horticulture Research, Vol. 2, 15060, 2015.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Accuracy and responses of genomic selection on key traits in apple breeding

AU - Muranty, Hélène

AU - Troggio, Michela

AU - Ben Sadok, Inès

AU - Al Rifaï, Mehdi

AU - Auwerkerken, Annemarie

AU - Banchi, E.

AU - Velasco, Riccardo

AU - Stevanato, P.

AU - van de Weg, W.E.

AU - Di Guardo, M.

AU - Kumar, S.

AU - Laurens, François

AU - Bink, M.C.A.M.

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

U2 - 10.1038/hortres.2015.60

DO - 10.1038/hortres.2015.60

M3 - Article

VL - 2

JO - Horticulture Research

JF - Horticulture Research

SN - 2052-7276

M1 - 15060

ER -

Muranty H, Troggio M, Ben Sadok I, Al Rifaï M, Auwerkerken A, Banchi E et al. Accuracy and responses of genomic selection on key traits in apple breeding. Horticulture Research. 2015;2. 15060. https://doi.org/10.1038/hortres.2015.60