Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set

The apple(Malus×domestica)cultivar Honeycrisp has become important economically and as a breeding parent.An earlier study with SSR markers indicated the original recorded pedigree of‘Honeycrisp’was incorrect and‘Keepsake’was identified as one putative parent,the other being unknown.The objective of this study was to verify‘Keepsake’as a parent and identify and genetically describe the unknown parent and its grandparents.A multi-family based dense and high-quality integrated SNP map was created using the apple 8 K Illumina Infinium SNP array.This map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNP haplotypes and to identify pedigree relationships.‘Keepsake’was verified as one parent of‘Honeycrisp’and‘Duchess of Oldenburg’and‘Golden Delicious’were identified as grandparents through the unknown parent.Following this finding,siblings of‘Honeycrisp’were identified using the SNP data.Breeding records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection,MN1627.This selection is no longer available,but now is genetically described through imputed SNP haplotypes.We also present the mosaic grandparental composition of‘Honeycrisp’for each of its 17 chromosome pairs.This new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect‘Honeycrisp’with other cultivars used widely in apple breeding programs.The created SNP linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNP arrays.

Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

The timing of fruit maturity is an important trait in sweet cherry production and breeding.Phenotypic variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control,but that control might be complicated by phenotypic instability across environments.Although such genotype-by-environment interaction(G×E)is a common phenomenon in crop plants,knowledge about it is lacking for fruit maturity timing and other sweet cherry traits.In this study,1673 genome-wide SNP markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA,thus sampling eight‘environments’.The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic predictions.Linkage disequilibrium among marker loci declined rapidly with physical distance,and ordination of the relationship matrix suggested no strong structure among germplasm.The most parsimonious G×E model allowed heterogeneous genetic variance and pairwise covariances among environments.Narrow-sense genomic heritability was very high(0.60–0.83),as was accuracy of predicted breeding values(>0.62).Average correlation of additive effects among environments was high(0.96)and breeding values were highly correlated across locations.Results indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new environments.Limited G×E for this trait indicated that phenotypes of individuals will be stable across similar environments.Equivalent analyses for other sweet cherry traits,for which multiple years of data are commonly available among breeders and cultivar testers,would be informative for predicting performance of elite selections and cultivars in new environments.