Juvenility, maturation, and rejuvenation in woody plants, Horticultural Reviews, pp.109-155, 1985. ,
Towards genomic selection in apple (Malus 3 domestica Borkh.) breeding programmes: prospects, challenges and strategies, Tree Genet Genomes, vol.8, pp.1-14, 2012. ,
Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops, Hort Res, vol.1, p.14022, 2014. ,
Efficiency of marker-assisted selection in the improvement of quantitative traits, Genetics, vol.124, pp.743-756, 1990. ,
Potential for marker-assisted selection for forest tree breeding: lessons from 20 years of MAS in crops, Tree Genet Genomes, vol.10, pp.1491-1510, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02635335
Breeding elite lines of apple carrying pyramided homozygous resistance genes against apple scab and resistance against powdery mildew and fire blight, Plant Mol Biol Report, vol.33, pp.1573-1583, 2015. ,
Prediction of total genetic value using genomewide dense marker maps, Genetics, vol.157, pp.1819-1829, 2001. ,
Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines, BMC Genomics, vol.13, p.452, 2012. ,
Prospects for genomewide selection for quantitative traits in maize, Crop Sci, vol.47, pp.1082-1090, 2007. ,
Genome-based prediction of testcross values in maize, Theor Appl Genet, vol.123, pp.339-350, 2011. ,
Evaluation of genome-wide selection efficiency in maize nested association mapping populations, Theor Appl Genet, vol.124, pp.261-275, 2012. ,
Ridge regression and extensions for genomewide selection in maize, Crop Sci, vol.49, p.1165, 2009. ,
Accuracy of genomic selection in European maize elite breeding populations, Theor Appl Genet, vol.124, pp.769-776, 2012. ,
Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study, Genetics, vol.182, pp.355-364, 2009. ,
Genomic selection accuracy for grain quality traits in biparental wheat populations, Crop Sci, vol.51, pp.2597-2606, 2011. ,
Accuracy of genomic selection models in a large population of open-pollinated families in white spruce, Heredity, vol.113, pp.343-352, 2014. ,
Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica, Tree Genet Genomes, vol.7, pp.747-758, 2011. ,
Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.), Genetics, vol.190, pp.1503-1510, 2012. ,
Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees, New Phytol, vol.194, pp.116-128, 2012. ,
Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches, PLoS One, vol.9, p.112227, 2014. ,
Genomic selection prediction accuracy in a perennial crop: case study of oil palm, Elaeis guineensis Jacq.). Theor Appl Genet, vol.128, pp.397-410, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02637338
Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia, Breed Sci, vol.63, pp.125-140, 2013. ,
Genomic selection for fruit quality traits in apple (Malus 3 domestica Borkh.), PLoS One, vol.7, p.36674, 2012. ,
marker-assisted, and pedigree-BLUP selection methods for b-glucan concentration in elite oat, Crop Sci, vol.53, pp.1894-1906, 2013. ,
The European project HiDRAS: innovative multidisciplinary approaches to breeding high quality disease resistant apples, XI Eucarpia Symposium on Fruit Breeding and Genetics, vol.663, pp.327-330, 2003. ,
Multiple QTL mapping in related plant populations via a pedigree-analysis approach, Theor Appl Genet, vol.104, pp.751-762, 2002. ,
Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe, Tree Genet Genomes, vol.5, pp.659-672, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-02668152
Pedimap: software for the visualization of genetic and phenotypic data in pedigrees, J Hered, vol.103, pp.903-907, 2012. ,
Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple, Theor Appl Genet, vol.127, pp.1073-1090, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02637406
Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus 3 domestica Borkh), PLoS One, vol.9, p.110377, 2014. ,
Genome-wide SNP detection, validation, and development of an 8K SNP array for apple, PLoS One, vol.7, p.31745, 2012. ,
A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation, Genet Sel Evol, vol.44, p.9, 2012. ,
breedR: statistical methods for forest genetic resources analysts. R package version 0.7-9 ,
R: a language and environment for statistical computing ,
, Vienna: R Foundation for Statistical Computing, 2014.
Pedigree: pedigree functions ,
The importance of identity-by-state information for the accuracy of genomic selection, Genet Sel Evol, vol.44, p.28, 2012. ,
Allele coding in genomic evaluation, Genet Sel Evol, vol.43, p.25, 2011. ,
The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes, Genet Sel Evol, vol.44, p.4, 2012. ,
Extension of the Bayesian alphabet for genomic selection, BMC Bioinf, vol.12, p.186, 2011. ,
The impact of genetic relationship information on genomic breeding values in German Holstein cattle, Genet Sel Evol, vol.42, p.5, 2010. ,
Reliability of direct genomic values for animals with different relationships within and to the reference population, J Dairy Sci, vol.95, pp.389-400, 2012. ,
Persistence of accuracy of genomic estimated breeding values over generations in layer chickens, Genet Sel Evol, vol.43, p.23, 2011. ,
Evaluation of genomic selection training population designs and genotyping strategies in plant breeding programs using simulation, Crop Sci, vol.54, p.1476, 2014. ,
Mapping quantitative physiological traits in apple (Malus 3 domestica Borkh.), Plant Mol Biol, vol.52, pp.511-526, 2003. ,
MetaQTL analysis provides a compendium of genomic loci controlling fruit quality traits in apple, Tree Genet Genomes, vol.11, p.819, 2015. ,
Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures, New Phytol, vol.178, pp.302-314, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02667629
Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments, Mol Breed, vol.17, pp.329-339, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-02664978
Quantitative trait loci (QTL) analysis reveals both broad-spectrum and isolate-specific QTL for scab resistance in an apple progeny challenged with eight isolates of Venturia inaequalis, Phytopathology, vol.94, pp.370-379, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-02675316
Two distinct major QTL for resistance to fire blight co-localize on linkage group 12 in apple genotypes 'Evereste' and Malus floribunda clone 821, Genome, vol.52, pp.139-147, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-02662432
Identification and stability of QTLs for fruit quality traits in apple, Tree Genet Genomes, vol.4, pp.647-661, 2008. ,
QTL dynamics for fruit firmness and softening around an ethylene-dependent polygalacturonase gene in apple (Malus 3 domestica Borkh.), J Exp Bot, vol.61, pp.3029-3039, 2010. ,
Deciphering the genetic determinism of bud phenology in apple progenies: a new insight into chilling and heat requirement effects on flowering dates and positional candidate genes, New Phytol, vol.192, pp.378-392, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02645003
Molecular-marker analysis of quantitative traits for growth and development in juvenile apple trees, Theor Appl Genet, vol.96, pp.1027-1035, 1998. ,
Genome-enabled estimates of additive and non-additive genetic variances and prediction of apple phenotypes across environments, G3 GenesGenomesGenetics, vol.5, pp.2711-2718, 2015. ,
Mapping genes for complex traits in domestic animals and their use in breeding programmes, Nat Rev Genet, vol.10, pp.381-391, 2009. ,
Linkage disequilibrium with linkage analysis of multiline crosses reveals different multiallelic QTL for hybrid performance in the flint and dent heterotic groups of maize, Genetics, vol.198, pp.1717-1734, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02637060
Accuracy of predicting the genetic risk of disease using a genome-wide approach, PLoS One, vol.3, p.3395, 2008. ,
Using the genomic relationship matrix to predict the accuracy of genomic selection, J Anim Breed Genet, vol.128, pp.409-421, 2011. ,
Genomic selection in forest tree breeding, Tree Genet Genomes, vol.7, pp.241-255, 2011. ,
Is the use of formulae a reliable way to predict the accuracy of genomic selection?, J Anim Breed Genet, vol.132, pp.207-217, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01194037
Threshold models for genome-enabled prediction of ordinal categorical traits in plant breeding, G3 GenesGenomesGenetics, vol.5, pp.291-300, 2015. ,
Bayesian methods for estimating GEBVs of threshold traits, Heredity, vol.110, pp.213-219, 2013. ,
Reduction in accuracy of genomic prediction for ordered categorical data compared to continuous observations, Genet Sel Evol, vol.46, p.37, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01341262
Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple, Theor Appl Genet, vol.96, pp.1077-1085, 1998. ,
Genomeenabled predictions for binomial traits in sugar beet populations, BMC Genet, vol.15, p.87, 2014. ,
Genomic selection using low-density marker panels, Genetics, vol.182, pp.343-353, 2009. ,
Practical implementation of cost-effective genomic selection in commercial pig breeding using imputation, J Anim Sci, vol.91, pp.3583-3592, 2013. ,
Founding clones, inbreeding, coancestry, and status number of modern apple cultivars, J Am Soc Hortic Sci, vol.121, pp.773-782, 1996. ,
Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes, Mol Breed, vol.24, pp.337-347, 2009. ,
Inbreeding in genome-wide selection, J Anim Breed Genet, vol.124, pp.369-376, 2007. ,
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