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.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0586-4) contains supplementary material, which is available to authorized users.

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.

Intermediate wheatgrass [IWG; Thinopyrum intermedium (Host) Barkworth & D.R. Dewey subsp. intermedium] is being developed as a new perennial grain crop that has a large allohexaploid genome similar to that of wheat (Triticum aestivum L.). Breeding for increased seed weight is one of the primary goals for improving grain yield of IWG. As a new crop, however, the genetic architecture of seed weight and size has not been characterized, and selective breeding of IWG may be more intricate than wheat because of its self-incompatible mating system and perennial growth habit. Here, seed weight, seed area size, seed width, and seed length were evaluated across multiple years, in a heterogeneous breeding population comprised of 1126 genets and two clonally replicated biparental populations comprised of 172 and 265 genets. Among 10,171 DNA markers discovered using genotypingby-sequencing (GBS) in the breeding population, 4731 markers were present in a consensus genetic map previously constructed using seven full-sib populations. Thirty-three quantitative trait loci (QTL) associated with seed weight and size were identified using association mapping (AM), of which 23 were verified using linkage mapping in the biparental populations. About 37.6% of seed weight variation in the breeding population was explained by 15 QTL, 12 of which also contributed to either seed length or seed width. When performing either phenotypic selection or genomic selection for seed weight, we observed the frequency of favorable QTL alleles were increased to >46%. Thus, by combining AM and genomic selection, we can effectively select the favorable QTL alleles for seed weight and size in IWG breeding populations. Intermediate wheatgrass (2n = 6x = 42) is a new perennial grain crop (Wagoner, 1990;Kantar et al., 2016). Compared with annual grain crops, it has an extended growing season and deep roots, which increase carbon sequestration and help prevent runoff and improve water quality (Glover et al., 2010;Culman et al., 2013). Moreover, Core Ideas• Twenty-three shared QTL were identified using linkage and association mapping• Overlapped QTL explained the high genetic correlation among seed weight and size• QTL responded positively to either phenotypic selection or genomic selection• Combining association mapping and genomic selection would increase genetic gain

Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. ‘Honeycrisp’ inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent ‘Frostbite’. The highly resistant IBP ‘Enterprise’ had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.

Background and Aims: A hybrid grapevine biparental mapping population was evaluated for resistance to grape phylloxera (Daktulosphaira vitifoliae Fitch) in the greenhouse and in the field. The family (n = 125) was derived from a cross of two University of Minnesota breeding selections from a complex pedigree with multiple Vitis species. Methods and Results: The vines were evaluated for foliar phylloxera severity using visual rating in the field for multiple years. In the greenhouse, a replicated experimental design was used to quantify phylloxera severity using different traits including number of galls per plant, area under the disease progress curve, proportion of leaves with galls, average number of galls per leaf and visual rating. The plants used in the greenhouse experiment were also visually rated for root infestation. Conclusions: Quantitative trait loci (QTL) mapping for the foliar resistance traits (reduced severity) routinely identified the region spanning~10 to 30 cM on linkage group (LG) 14 to be associated with resistance, and inherited from the mother parent MN1264. The plants used in the greenhouse experiment were also visually rated for root infestation, and subsequent QTL mapping identified regions on LG 5 of the maternal map and LG 10 of the paternal map (MN1246) associated with root resistance.Significance of the Study: The new QTLs identified in this report are potential novel sources of resistance and the first report of QTL for foliar phylloxera resistance in a hybrid grapegrowing region of North America. Molecular markers linked to resistance can be utilised in marker-assisted breeding.

Breeding resistant apple cultivars is a long-term solution to fire blight, a devastating bacterial disease caused by Erwinia amylovora. However, most resistance sources have been characterized in wild genetic backgrounds with poor fruit quality. Additionally, strong influences of environment and tree vigor on susceptibility, quantitative resistance, and the disease's erratic nature make phenotyping challenging. This study examined levels of resistance/susceptibility to fire blight among and within 32 full-sib families (n = 314 seedlings) in a pedigree-connected apple germplasm set. In 2016 and 2017, multiple actively-growing shoots per tree (approximately 3 trees per seedling) were challenged with E. amylovora. Responses were quantified as proportions of current season's shoot lengths that were blighted (SLB). Within a year, seedling responses were estimated using mean adjusted SLB best linear unbiased predictions (adjusted SLB BLUPs). Responses ranged from highly resistant to highly susceptible (0.04-0.97 adjusted SLB BLUPs across years) and were relatively consistent between years (Spearman's R 2 = 0.55). Kmeans clustering was used to classify seedlings into resistance/susceptibility groups based on incidence, adjusted SLB BLUPs, maximum SLB, and maximum age of wood infected. Most families, including crosses between susceptible parents, demonstrated quantitative variation for resistance/susceptibility. Families derived from 'Enterprise' demonstrated low relative susceptibility. Depending on the year and model, average narrow-sense heritability estimates ranged from 0.22-0.49. Phenotypic information (1) increases understanding of variation and inheritance of resistance/susceptibility to fire blight in germplasm relevant to US apple breeding programs and (2) could be used in pedigree-informed QTL analyses to detect loci associated with resistance/ susceptibility.

Fruit texture is a major target of apple (Malus domestica) breeding programs due to its influence on consumer preference. This multitrait feature is typically rated using sensory assessment, which is subjective and prone to biases. Instrumental measurements have predominantly targeted firmness of the outer region of fruit cortex using industry standard Magness–Taylor-type penetrometers, while other metrics remain largely unused. Additionally, there have been limited reports on correlating sensory attributes with instrumental metrics on many diverse apple selections. This report is the first to correlate multiyear historical fruit texture information of instrumental metrics and sensory assessment in an apple breeding program. Through 11 years of routine fruit quality evaluation at the Washington State University apple breeding program, physical textural data of 84,552 fruit acquired from computerized penetrometers were correlated with sensory assessment. Correlations among various instrumental metrics are high (0.63 ≤ r ≤ 1.00; P < 0.0001). In correlating instrumental outputs with sensory data, there is a significant correlation (r = 0.43; P < 0.0001) between the instrumental crispness value and sensory crispness. Additionally, instrumental hardness traits are significantly correlated (0.61 ≤ r ≤ 0.69; P < 0.0001) with sensory hardness. Outputs from two versions of computerized penetrometers were tested and shown to have no statistical differences. Overall, this report demonstrates potential use of instrumental metrics as firmness and crispness estimates for selecting apples of diverse backgrounds in a breeding program. However, in testing a large number and diversity of fruit, experimenters should perform data curation and account for lower limits/thresholds of the instrument.

Grapevine (Vitis spp.) contains a wealth of phytochemicals that have received considerable attention due to health-promoting properties and biological activities as phytoalexins. To date, the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited. Here, metabolic quantitative trait locus (mQTL) mapping was conducted using grapevine stems of a segregating F2 population. Metabolic profiling of grapevine stems was performed using liquid chromatography–high-resolution mass spectrometry (LC-HRMS), resulting in the detection of 1317 ions/features. In total, 19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software, resulting in the identification of four mQTLs. Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18, accounting for phenotypic variances of 29.0% and 38.4%. Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18. This 2.8-Mbp region contains 48 genes with R-gene motifs, including variants of TIR, NBS, and LRR, that might potentially confer resistance to powdery mildew, downy mildew, or other pathogens. The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites, including phytoalexins. In addition, haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.