The American cranberry (Vaccinium macrocarpon) is a commercially important berry species native to North America. Cranberry is a popular fruit crop with many known health benefits. Thus far, genotyping-by-sequencing (GBS) was the only high-throughput genotyping technique available in cranberry. While GBS is cost efficient, it has the disadvantage of producing variant calls that cannot be easily transferred between populations and across studies. In this study, we report the development of the first targeted high-throughput genotyping platform for cranberry. The Flex-Seq genotyping technology offers repeatable, high-recovery, and high-density single nucleotide polymorphisms as well as concomitant haplotypes. The cranberry Flex-Seq platform contains 17,502 loci, boasting a recovery rate of 99.8% in a diversity panel of 192 cranberry accessions. The level of incompatible marker inheritance in 22 analyzed parent-offspring trios ranged from 1.1% to 13%, with an average of 5.5%. Nine of the 22 crosses had an excess of incompatible markers, indicating inconsistent parentage that could be investigated further. In quantitative trait loci (QTLs) analyses, Flex-Seq identified a greater number of QTLs compared to previously used GBS as well as higher overall logarithm of odds scores for overlapping QTLs. In addition, construction of locus haplotypes resulted in a substantial improvement in resolving the relatedness of cranberry accessions. This platform will aid in utilizing the untapped potential of wild cranberry, mapping key traits with higher precision, and ensuring robust characterization of accessions. The developed genotyping platform will help in the rapid improvement of cranberry cultivars to benefit breeders, growers, and consumers.

Prickles on blackberry and raspberry canes make pruning, harvesting, and handling more difficult and can increase labor costs for growers. The trait has been challenging to improve in these clonal crops because it is recessive and linked to undesirable agronomic traits. In blackberry and red raspberry, breeding programs have used recessive mutants at the S locus to generate prickleless cultivars for the last century. In this study, we identified independent loss-of-function mutations in a WUSCHEL-LIKE HOMEOBOX transcription factor, WOX1 , as the genetic basis of the prickleless S locus in both blackberry and red raspberry. We mapped the S locus using integrated genome-wide association, bulked segregant analysis, and identity-by-descent analyses informed by breeding pedigrees. Additionally, we generated a genome sequence from Luther Burbank’s prickleless blackberry variety Burbank Thornless that contained an additional allele of WOX1 . To verify the gene’s role, we used gene editing to knock out WOX1 in an elite prickled commercial blackberry line. All edited plants were prickleless and lacked glandular trichomes, confirming that WOX1 controls a joint developmental pathway. Other plant traits were unchanged, indicating WOX1 is a specific and safe target for improvement. Gene editing can enable breeders to remove prickles directly from elite varieties, reducing the need for extensive breeding cycles and delivering safer, easier-to-harvest cultivars to growers.

The fresh-market blackberry ( Rubus subgenus Rubus ) industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 (∼33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32-35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved Rubus argutus ‘Hillquist’ genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3′ UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers ( PF1 and PF2 ), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus , and deliver diagnostic markers that can be immediately deployed in breeding programs.

Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multiallelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Comparative analyses of these databases highlighted the advantages of microhaplotypes in capturing greater allelic diversity, resolving fine-scale population structures, and improving linkage map construction. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.

Indoor farming enables consistent production of superior-quality strawberries through optimized conditions. As strawberry growth, production, and quality can be largely affected by both genotype and environment, it is important to identify cultivars with traits desirable for indoor production. Twenty-three publicly available strawberry ( Fragaria × ananassa ) cultivars were selected from the USDA-ARS National Clonal Germplasm Repository as possible genetic resources for future breeding for indoor production and evaluated in a walk-in growth chamber with sole source electric lighting. Among strawberry cultivars examined, ‘Mara des Bois’ had desirable traits for indoor farming, including long-day photoperiodic response, early production, higher average weekly yield, and low sensitivity to dormancy-inducing photoperiod. Fruit quality traits, including size, calyx area, shape, color, total soluble solid content (Brix), titratable acidity (TA), and firmness were evaluated. ‘Chandler’ produced the largest fruit, ‘Sweet Sunrise’ showed the lowest calyx-to-fruit area ratio, and ‘Benton’, ‘Hood’, ‘Mara des Bois’, ‘NW 90054-37’, and ‘Puget Beauty’ fruit had a relatively high Brix-to-TA ratio. Correlations among productivity, quality, and morphological characteristics revealed the potential to enhance both productivity and quality by optimizing environmental conditions. The information on strawberry plant growth, development, and fruit production provided in this study can assist indoor growers in cultivar selection and potentially contribute to the development of new strawberry cultivars that thrive in indoor production environments.

Blueberry is promoted as a super food with several health properties derived from chlorogenic acid and anthocyanin. Previous studies indicated that anthocyanin acylation and the content of chlorogenic acid could affect their level of absorption and biological activity. In this study, a genome-wide association study was performed to identify loci associated with anthocyanin and chlorogenic acid and characterize the candidate genes controlling anthocyanin acylation. Two stable loci controlling anthocyanin acylation and glucose specific glycosylation were confirmed on chromosomes 2 and 4, respectively, while no stable loci associated with chlorogenic acid were identified. Two acyl-CoA acyltransferases named VcBAHD-AT1 and VcBAHD-AT4 were identified as best candidate genes controlling anthocyanin acylation. Interestingly, the two genes clustered in acyl-CoA acyltransferases clade III, a clade that is not commonly associated with anthocyanin acylation. A virus-induced gene silencing approach optimized for silencing VcBAHD-AT1 and VcBAHD-AT4 in the whole blueberry fruits, confirmed the role of these two genes in anthocyanin acylation. Overall, this study establishes the foundation to develop a molecular marker to select for higher acylated anthocyanin and delivered a method for rapid functional characterization of genes associated with other fruit related traits in blueberry. Also, the study adds evidence that during the evolution of acyl-CoA acyltransferases multiple routes led to the emergence and/or fixation of the anthocyanin acyltransferase activity. These outcomes advance knowledge about the genes controlling anthocyanin acylation in blueberries and that extend to other plants. Selecting new blueberry cultivars with higher acylated anthocyanin levels could potentially increase absorption of this health-related bioactive.

‘Thunderhead’ is an erect primocane fruiting blackberry (Rubus subg. Rubus) that produces high yields of berries with excellent firmness and fruit quality for the fresh market. ‘Thunderhead’ is the first erect primocane fruiting blackberry released by the US Department of Agriculture (USDA)–Agricultural Research Service (ARS) Horticultural Crops Production and Genetic Improvement Research Unit (HCPGIRU) breeding program in Oregon, USA. The cultivar contains a genetic background derived primarily from eastern US primocane fruiting blackberry germplasm (developed previously by John Clark at the University of Arkansas System Division of Agriculture, AR, USA) that is predominantly tetraploid (2n = 4x = 28), erect in cane architecture, and has a hybrid mixture of Rubus backgrounds, including strong contributions from species native to eastern and southeastern North America (Rubus argutus, Rubus trivialis).

Developing cultivars that are resistant to multiple biotic stresses is an important objective in raspberry plant breeding. Diseases such as Raspberry bushy dwarf virus and Phytophthora root rot have long been a high priority for raspberry breeding programs, whereas other pests, such as spotted wing Drosophila and the root lesion nematode, have been considered more recently. Breeding for improved resistance to these stresses has relied primarily on conventional breeding methods. However, rapid technological progress and increased access and affordability of genomic and phenomic methodologies may accelerate breeding and improve selection efficiency for genetic resistance to pests and pathogens. Such advancements are understudied for application in raspberry, but are emerging as a significant research interest. We review the current state of plant breeding research for the most significant diseases and pests affecting raspberry production in the Pacific Northwest of North America. In addition, we discuss new and relevant plant breeding methodologies that could contribute to future breeding objectives.

Abstract Blueberry is promoted as a super food with several health properties derived from chlorogenic acid and anthocyanin. Previous studies indicated that anthocyanin acylation and the content of chlorogenic acid could affect their level of absorption and biological activity. In this study, a genome-wide association study was performed to identify loci associated with anthocyanin and chlorogenic acid and characterize the candidate genes controlling anthocyanin acylation. Two stable loci controlling anthocyanin acylation and glucose specific glycosylation were confirmed on chromosomes 2 and 4, respectively, while no stable loci associated with chlorogenic acid were identified. Two acyl-CoA acyltransferases named VcBAHD-AT1 and VcBAHD-AT4, were identified as best candidate genes controlling anthocyanin acylation. Interestingly, the two genes clustered in acyl-CoA acyltransferases clade III, a clade that is not commonly associated with anthocyanin acylation. A Virus-induced gene silencing approach optimized for silencing VcBAHD-AT1 and VcBAHD-AT4 in the whole blueberry fruits, confirmed the role of these two genes in anthocyanin acylation. Overall, this study establishes the foundation to develop a molecular marker to select for higher acylated anthocyanin and delivered a method for rapid functional characterization of genes associated with other fruit related traits in blueberry. Also, the study adds evidence that during the evolution of acyl-CoA acyltransferases multiple routes led to the emergence and/or fixation of the anthocyanin acyltransferase activity. These outcomes advance knowledge about the genes controlling anthocyanin acylation in blueberries and that extend to other plants. Selecting new blueberry cultivars with higher acylated anthocyanin levels could potentially increase absorption of this health related bioactive.

Cranberry (Vaccinium macrocarpon Aiton), a native North American fruit crop, has gained global popularity due to its unique flavor and health benefits. As the market expands for new cranberry products, the requirements to produce varieties that meet new standards have increased. DNA-assisted breeding in cranberry has been limited due to the lack of cost-effective genotyping tools. To address this gap, Breeding Insight developed and validated a 3K DArTag panel. Target loci were strategically selected from 507K single-nucleotide polymorphisms (SNPs), generated from resequencing 53 diverse cultivated cranberry accessions. Selection criteria prioritized even genomic distribution, genic regions, maximum genetic diversity among North American breeding germplasm, and markers associated with known quantitative trait loci. The cranberry 3K DArTag panel was validated using a diverse collection of cranberry accessions, interspecific hybrids, and two F1 populations. The panel, optimized for cultivated V. macrocarpon, demonstrated a high average amplification rate (83.4%) and robust performance in its close relatives, Vaccinium microcarpum and Vaccinium oxycoccos, as well as somewhat lower but acceptable performance in interspecific hybrids. However, transferability to the more distant blueberry was limited. The panel successfully revealed expected ploidy levels and population structure among the tested materials. Two individual linkage maps and one consensus map were constructed for the mapping populations, with an average marker density of 0.68 markers per centimorgan. This cost-effective (∼$15/sample), rapid genotyping platform offers valuable capabilities for public and private breeding programs. Its open-access nature enables genetic datasets generated from the marker panel to be compared and integrated across projects and geographical boundaries.

Blueberry (Vaccinium spp.) is one of the most economically important berry crops worldwide. Validation of genetic mapping studies is often hindered by asynchronous marker technology. The development of a standardized genotyping platform that targets a specific set of polymorphic loci can be a practical solution to unify the scientific and breeding community toward blueberry improvement. The objective of this study was to develop and evaluate a targeted genotyping platform for cultivated blueberries that is affordable, reproducible, and sufficiently high density to warrant large-scale adoption for genomic studies. The Flex-Seq platform was developed in a two-step procedure that resulted in 22,000 loci that yielded 194,365 single nucleotide polymorphisms when assessed in a diversity set of 192 samples including cultivated and other related wild Vaccinium species. Locus recovery averaged 89.4% in the cultivated polyploid blueberry (northern highbush [NHB], southern highbush [SHB], and rabbiteye [RE]) and on average 88.8% were polymorphic. While recovery of these loci was lower in the other Vaccinium species assayed, recovery remained high and ranged between 60.8% and 70.4% depending on the taxonomic distance to the cultivated blueberry targeted in this platform. NHB had the highest mean number of variants per locus at 9.7, followed by RE with 9.1, SHB with 8.5, and a range between 7.7 and 8.5 in other species. As expected, the total number of unique-in-state haplotypes exceeded the total number of variants in the domesticated blueberries. Phylogenetic analysis using a subset of the SNPs and haplotypes mostly conformed to known relationships. The platform also offers flexibility about the number of loci, depth of sequencing for accurate dosage calling, loci and haplotype reconstruction from increased fragment length. This genotyping platform will accelerate the development and improvement of blueberry cultivars through genomic-assisted breeding tools.

The global production and consumption of blueberry (Vaccinium spp.), a specialty crop known for its abundant bioactive and antioxidant compounds, has more than doubled over the last decade. To hold this momentum, plant breeders have begun to use quantitative genetics and molecular breeding to guide their decisions and select new cultivars that are improved for fruit quality. In this study, we leveraged our inferences on the genetic basis of fruit texture and chemical components by surveying large breeding populations from northern highbush blueberries (NHBs) and southern highbush blueberries (SHBs), the two dominant cultivated blueberries. After evaluating 1065 NHB genotypes planted at the Oregon State University, and 992 SHB genotypes maintained at the University of Florida for 17 texture-related traits, evaluated over multiple years, our contributions consist of the following: (i) we drew attention to differences between NHB and SHB materials and showed that both blueberry types can be differentiated using texture traits; (ii) we computed genetic parameters and shed light on the genetic architecture of important texture attributes, indicating that most traits had a complex nature with low to moderate heritability; (iii) using molecular breeding, we emphasized that prediction could be performed across populations; and finally (iv) the genomic association analyses pinpointed some genomic regions harboring potential candidate genes for texture that could be used for further validation studies. Altogether, the methods and approaches used here can guide future breeding efforts focused on maximizing texture improvements in blueberries.

The shelf-life of blueberry (Vaccinium corymbosum L.) fruits depends on changes in multiple fruit characteristics during storage, including texture, appearance of wrinkles and mold, and loss of water. These changes result in softening, decay, and change in flavor, which can negatively affect consumer acceptance. Therefore, understanding how breeders can select for new cultivars with extended shelf-life is crucial. In this study, 20 mechanical texture parameters and four fruit appearance traits (fruit weight, fruit scar diameter, fruit height and wrinkle) were measured at harvest and six weeks post-storage in two very large (N>2000) collections of northern and southern highbush blueberry (NHB, SHB, respectively) genotypes. The study is the first to assess shelf-life at the scale resembling the number, genetic structure and diversity of populations used in blueberry breeding programs. The results highlighted that post-storage changes are positively correlated with initial texture. The low storage temperature for SHB best explained a notable lower rate of changes for all parameters. Correlation analysis indicated that three main texture components representing the Young Modulus parameters (YMs), 'Distance to Maximum Force' (DFM) and 'Mean Internal Firmness' (MIF) contributed to blueberry texture. YMs and DFM likely represent textural characteristics of the external fruit structural components. Also, texture parameters YMs and DFM explained most of the phenotypic changes observed between harvest and post-storage, suggesting that changes during storage largely occurs in the more external layers of the berry. Changes for parameters correlated to size were highly predictable, while most of the texture parameters had a low to moderate predictability. The contribution of fruit chemistry parameters to predict texture and appearance traits at harvest and post-storage was very limited or not significant. The rate of water loss and appearance of wrinkles was higher in small size berries and was not affected by the size of the stem scar. Overall, selecting for high YMs, DFM, F1mm (Force at 1 mm), Maximum Force (FM), and large size at harvest can contribute to select berries with better mechanical texture and appearance in post-storage.

Pears ( Pyrus ) represent an important part of consumer diets, and have the fourth highest production of non-citrus fruits, measured by fresh weight, in the U.S. They are maintained clonally and grown as composite plants, consisting of a scion (fruit bearing) cultivar grafted onto a rootstock cultivar. Up to 98% of existing production relies on only a few scion and rootstock cultivars, leaving the standing crop vulnerable to threats. Pears are faced with a wide range of biotic and abiotic threats and production vulnerabilities, some of which can be limited by integrating resistance and horticultural traits from wild and cultivated materials from around the world. The National Clonal Germplasm Repository (NCGR Corvallis), part of the USDA-ARS National Plant Germplasm System, maintains a large Pyrus collection from across the globe, consisting of 2793 Pyrus accessions from 37 species. The collection represents an important resource for preservation, research, and breeding efforts for pears. The crop vulnerability status of pears in the U.S. is currently moderate to high, with increasing threats and challenges. Breeding and preservation efforts, along with genetic, crop protection and production research are, however, actively targeting these needs.

An initial cross of V. darrowii ‘Johnblue’ (Darrow’s blueberry) × V. vitis-idaea ‘Red Sunset’ (lingonberry) produced more than 30 true intersectional diploid hybrids as confirmed by molecular markers. The most vigorous of these hybrids was extensively evaluated. This hybrid, US 2535-A, was floriferous and morphologically intermediate to the respective parents. Examination of pollen suggested low male fertility. Numerous crosses using the hybrid as a female reflected similarly low fertility and potential crossing barriers. Stylar examination suggested blockage of pollen tube growth in self-pollinations and significantly retarded growth in backcross pollinations. Nonetheless, two confirmed hybrid offspring were produced using the F1 hybrid as a female in crosses with V. vitis-idaea and V. darrowii, respectively. In a second set of crosses utilizing additional V. darrowii and V. vitis-idaea genotypes, another 23 verified hybrids in seven parental combinations were produced. Hybrids such as the ones presented offer the potential for generating de novo interspecific fruit types in blueberry and/or broadening the adaptation of lingonberry.

Small public breeding programmes have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here we report the creation of a DArTag panel of 3,000 loci distributed across the tetraploid genome of blueberry (Vaccinium corymbosum) for use in molecular breeding and genomic prediction. The creation of this marker panel brings cost-effective and rapid genotyping capabilities to public and private breeding programmes. The open access provided by this platform will allow genetic data sets generated on the marker panel to be compared and joined across projects, institutions and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of blueberry.

Understanding consumers’ preferences for fruit quality attributes is key to informing breeding efforts, meeting consumer preferences, and promoting increased market demand. The objective of this study was to assess the effect of fruit quality traits and hedonic sensory evaluation on consumers’ willingness to pay (WTP) for a selection of fresh northern and southern highbush blueberry cultivars. The WTP was elicited by using a double-bounded contingent valuation conducted in conjunction with a consumer sensory test. Two types of models were estimated using either sensory evaluations (i.e., consumer preference and consumer intensity) or instrumental measurement data (i.e., measures of soluble solids, titratable acidity, sugars, acids, and firmness) as explanatory variables to model WTP. Results using sensory evaluations indicated that flavor liking, flavor intensity, and sweetness intensity are key factors that influence consumers’ acceptance and WTP for blueberries. A regression analysis using instrumental measurements indicated that measures related to sweetness and acidity traits are important factors that determine WTP. Higher WTP was associated with higher total sugar content across different levels of total organic acid. The WTP increases with organic acid content, because this is needed for enhanced flavor; however, WTP declines at high concentrations of organic acid. Except for extreme values of firmness, the WTP increased as measures of fruit firmness increased, indicating a consumer preference for firmer blueberries. Overall, the results provided new insights into the relationships between consumer preference and WTP and fruit quality benchmarks to select for improved quality.

Breeding programs around the world continually collect data on large numbers of individuals. To be able to combine data collected across regions, years, and experiments, research communities develop standard operating procedures for data collection and measurement. One such method is a crop ontology, or a standardized vocabulary for collecting data on commonly measured traits. The ontology is also computer readable to facilitate the use of data management systems such as databases. Blueberry breeders and researchers across the United States have come together to develop the first standardized crop ontology in blueberry ( Vaccinium spp.). We provide an overview and report on the construction of the first blueberry crop ontology and the 178 traits and methods included within. Researchers of Vaccinium species—such as other blueberry species, cranberry, lingonberry, and bilberry—can use the described crop ontology to collect phenotypic data of greater quality and consistency, interoperability, and computer readability. Crop ontologies, as a shared data language, benefit the entire worldwide research community by enabling collaborative meta-analyses that can be used with genomic data for quantitative trait loci, genome-wide association studies, and genomic selection analysis.