Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F₁ families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from ‘Seyval blanc’, through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.

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.

Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). ‘Honeycrisp’ and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards this aim, we employed a pedigree-based approach using mostly germplasm related to ‘Honeycrisp.’ Two quantitative trait loci (QTL) were consistently identified on linkage groups (LGs) 2 and 16 across the 2014 and 2015 harvest years. The same QTL were identified for both storage disorders, indicating that they may be physiologically related. ‘Honeycrisp’ is homozygous for an identical by state haplotype at the LG2 QTL that was consistently associated with a deleterious effect on soft scald and soggy breakdown incidence. This haplotype was traced through SNP-confirmed pedigrees to the following cultivars: ‘Grimes Golden,’ ‘Northern Spy,’ ‘Rome Beauty,’ and ‘Fireside’ and is common in derived apple germplasm. Haplotypes at the LG16 QTL could not be adequately characterized due to variation between years combined with effects of this QTL being of relatively smaller size and being most evident in individuals that carry two copies of the deleterious haplotype at the LG2 QTL. These results suggest that limiting homozygosity of the deleterious haplotype at the LG2 QTL through marker-assisted breeding would be a valid strategy to limit soft scald and soggy breakdown incidences in apple seedling populations.

Fruit acidity and sweetness are important fruit quality traits in the apple and are therefore targets in apple breeding programs. Multiple quantitative trait loci (QTLs) associated with titratable acidity (TA) and soluble solids content (SSC) have been previously detected. In this study a pedigree-based QTL analysis approach was used to validate QTLs associated with TA and SSC in a ‘Honeycrisp’-derived germplasm set. TA and SSC data collected from 2014 to 2018 and curated genome-wide single nucleotide polymorphism (SNP) data were leveraged to validate three TA QTLs on linkage groups (LGs) 1, 8, and 16 and three SSC QTLs on LGs 1, 13, and 16. TA and SSC QTL haplotypes were characterized in six University of Minnesota apple breeding families representing eight breeding parents including ‘Honeycrisp’ and ‘Minneiska’. Six high-TA haplotypes, four low-TA haplotypes, 14 high-SSC haplotypes, and eight low-SSC haplotypes were characterized. The results of this study will enable more informed selection in apple breeding programs.