‘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).

Genomic prediction models that fit multiple environments globally are valuable tools for assessing cultivar performance across diverse and variable growing conditions. We analyzed 2,064 strawberry (Fragaria × ananassa) accessions genotyped with 12,591 SNP markers. Soluble solids content (SSC) was measured in multi-year trials conducted at seven locations spanning the U.S., Europe, and Australia. Population structure analysis grouped accessions into two major clusters corresponding to subtropical and temperate origins, which was confirmed by significant differences in allele frequency distributions. To improve prediction accuracy across environments, we developed factor analytic models focusing on genotype-by-environment interactions rather than covariance between sub-populations. We compared three genomic prediction approaches: (i) a standard GBLUP model (Gfa), (ii) a GBLUP model incorporating principal component analysis eigenvalues and re-parameterization (Pfa), and (iii) a multi-population GBLUP model that fits sub-population genomic relationship matrices (Wfa). The Pfa and Wfa models achieved the highest prediction accuracy (r = 0.8) for SSC, outperforming individual environment models and the standard GBLUP. These findings demonstrate that accounting for population structure and genotype-by-environment interactions enhances multi-environment genomic prediction and supports practical implementation of genomic selection in global strawberry improvement programs.

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.

U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. An improved understanding of genetic control and the stability of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, the analysis of a multiple-environment trial of a BR mapping population derived from a cross that combines wild ancestors introgressed with commercial cultivars on both sides of its pedigree has provided insights into genetic variation, genotype-by-environment interactions, quantitative trait loci (QTL), and QTL-by-environment interactions (QEI) of fruit quality traits among diverse field environments. The genetic components and stability of four fruit size traits and six fruit biochemistry traits were characterized in this mapping population following their evaluation over three years at four distinct locations representative of current U.S. BR production. This revealed relatively stable genetic control of the four fruit size traits across the tested production environments and less stable genetic control of the fruit biochemistry traits. Of the fifteen total QTL, eleven exhibited significant QEI. Closely overlapping QTL revealed the linkage of several fruit size traits: fruit mass, drupelet count, and seed fraction. These and related findings are expected to guide further genetic characterization of BR fruit quality, management of breeding germplasm, and development of improved BR cultivars for U.S. production.

‘Mini Blues’ highbush blueberry (Vaccinium sp.) was released in 2016 as a high-quality, machine-harvestable alternative to lowbush (V. angustifolium Ait.) or other small-fruited highbush blueberry cultivars for processed markets. A planting was established in Oct. 2015 in western Oregon to evaluate the effects of pruning method on yield, machine-harvest efficiency (MHE), berry weight and total soluble solids (TSS), leaf tissue nutrients, pruning weight, pruning time, and costs. Plants were pruned for shape and to remove flower buds in 2015–16 and 2016–17. Pruning treatments began in 2017–18 and included: 1) conventional highbush pruning (HB); 2) removing one or two of the oldest canes per bush (Speed); 3) leaving plants to grow from 2017 to 2021 (Unpruned) before doing a hard renovation prune in 2021–22 (cutting the plants back to a height of ≈0.3 m and leaving the best 8–10 canes/plant); and 4) hedging after fruit harvest in 2018 (Hedge) and then unpruned afterward until renovation in 2021–22. The pattern of yield progression, observed wood aging, and reduced berry size after 4 years of no pruning indicated renovation was necessary in the unpruned and hedge treatments. Low growth was removed each year in all treatments, and hedging was only done in 2018 because it severely reduced yield the following year and, therefore, was not a viable option. An over-the-row machine harvester was used from 2018 to 2021. Speed-pruned plants, averaged over 4 years, had the greatest potential yield (3.75 kg/plant) compared with the other treatments (averaged 2.99 kg/plant) but had a similar yield as HB because more fruit remained on the bush after harvest with speed pruning. In 2021, speed pruning resulted in the highest yield (4.2 kg/plant), followed by HB (3.8 kg/plant) and the unpruned and hedge methods (averaged 3.1 kg/plant). MHE increased from 43% in 2018 to 74% in 2021, mainly because, as the plants aged, a larger proportion of the canopy was above the catcher plates on the harvester. On average, MHE was highest with HB pruning (70%), intermediate in the unpruned and speed-pruned plants (59%), and lowest in the hedged plants (49%). In 2021, ground drop loss was highest for hedge (18%), lowest for speed (14%), and intermediate for HB and unpruned (averaged 16%) methods. HB-pruned plants had heavier berries (0.64 g) than unpruned and hedge treatments (averaged 0.57 g) and a similar berry weight as the speed-pruned plants (0.61 g). Pruning had no effect on berry TSS. In contrast to leaf K, leaf Mg and Ca concentrations were lowest in HB and higher in all other treatments. In 2020–21, HB pruning required 471 h·ha−1, while speed pruning took 79 h·ha−1; the hedge and unpruned treatments required an average of 60 h·ha−1 to remove low-growing branches that would interfere with machine harvest. In 2021–22, renovation of the unpruned and hedge treatments took 290 h·ha−1. While leaving bushes unpruned during establishment appears to be a promising option for ‘Mini Blues’, further work is needed to evaluate fruit production after renovation and to determine how long the plants could remain unpruned thereafter. Speed pruning is also a good option, reducing pruning costs by 85%.

Abstract Charcoal rot caused by Macrophomina phaseolinais an increasing economic problem in annualized strawberry production systems around the world. Currently there are no effective postfumigation chemical controls for managing charcoal rot, and no information is available on the genetic architecture of resistance to M. phaseolina in strawberry (Fragaria ×ananassa). In this study, three multiparental discovery populations and two validation populations were inoculated at planting and evaluated for mortality in three consecutive growing seasons. Genome-wide SNP genotyping and pedigree-based analysis with FlexQTL™ software were performed. Two large-effect quantitative trait loci (QTL) increasing charcoal rot resistance were discovered and validated in cultivated germplasm. FaRMp1 was located on linkage group 2A in the interval 20.4to 24.9 cM, while FaRMp2 was located on linkage group 4B in the interval 41.1to 61.2 cM. Together these QTLs explained 27% and 17% of the phenotypic variance in two discovery populations consisting of elite breeding germplasm. For both QTLs, the resistant allele showed some evidence of partial dominance, but no significant interaction was detected between the two loci. As the dosage of resistant alleles increased from 0 to 4 across the two QTLs, mortality decreased regardless of the combination of alleles.A third locus, FaRMp3 on 4D, was discovered in FVC 11–58, a reconstituted F.×ananassa originating from diverse F. virginiana and F. chiloensis accessions. This locus accounted for 44% of phenotypic variation in four segregating crosses. These findings will form the basis for DNA-informed breeding for resistance to charcoal rot in cultivated strawberry.

The application of molecular breeding in blackberry is a complex problem due to polyploidy, multisomic inheritance, and heterozygosity. However, recent advances in computational tools for mapping and quantitative trait loci analyses in polyploids and development of genomic resources for Rubus crops have removed many of these barriers. The objective of this project was to develop high-quality draft genomes for two diploid blackberry accessions and a polyploid resequencing panel. The diploid accessions chosen for reference genome development, `Burbank Thornless' (R. ulmifolius inermis, PI 554060) and `Hillquist' (R. argutus, PI 553951), represented important sources of thornlessness and primocane fruiting in fresh-market blackberry breeding programs. The genome sizes were estimated to be 405 Mb in `Burbank Thornless' and 376 Mb in `Hillquist' using nuclear flow cytometry. Single-molecule realtime (SMRT) sequencing technology generated similar to 80X genome coverage for each genome. The reads were assembled using Falcon-unzip and Purge Haplotigs into a 341 Mb genome with contig N50 of 1.19 Mb for `Burbank Thornless' and a 297 Mb genome with contig N50 of 650 kb for `Hillquist'. Chromosome-level assemblies for both accessions are being developed using 10X genomic and Hi-C scaffolding tools. Genome annotation will be performed using diverse tissue samples collected from `Hillquist' and ` Burbank Thornless'. Breeders can use these resources in combination with new computational tools and genotyping strategies for polyploid crops to develop effective molecular breeding strategies for blackberry.

The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.

The USDA-ARS blackberry breeding program, begun in the 1920s, was largely established from germplasm derived from Rubus ursinus (western US trailing dewberry) and its hybrids with R. idaeus (red raspberry) such as `Loganberry'. Over the decades, other species have been mixed in with varying levels of success. For example, the source of thornlessness primarily used in the mid-1900s was from `Austin Thornless', an octoploid from a R. baileyanus x R. argutus hybrid. In the late 1980s, the thornless `Lincoln Logan', began to be used. While the initial material derived from `Lincoln Logan' had some negative traits, within two generations `Columbia Star' was released. In the early 1990s, the USDA breeder naively crossed trailing higher ploidy types such as `Kotata' with eastern US tetraploid erect types such as `Navaho'; while most of the seedlings were largely sterile, a few were fully fertile. Selections from these populations were further backcrossed to erect/semi-erect types to produce `Eclipse' and `Galaxy', which are 1/4 trailing and 3/4 erect/semi-erect blackberry. The USDA-ARS program has used many species over the past 25 years. While many species have been dead-ends in this program (e.g., R. canadensis, R. insularis), some still have promise (e.g., R. glaucus, R. caesius), and some have been highly successful leading to selections that will be released (e.g., R. caucasicus, R. georgicus). Finally, selecting for primocane fruiting in the cool climate Pacific Northwest from crosses among Arkansas and North Carolina genotypes has led to earlier ripening selections with commercial potential. The relationships between the various programs along with a strong belief in the value of new germplasm, has led to blending diverse germplasm that in just a few generations has led to commercially viable blackberry genotypes containing valuable traits not previously present in our USDA breeding material.

Black raspberry (Rubus occidentalis) is a US Pacific Northwest specialty crop prized for its unique flavor profile and nutritional attributes. Market expansion depends on production, which is currently hindered by aphid-vectored viruses, such as Black raspberry necrosis virus. In order to enable dissection of genetic loci controlling aphid resistance, a reliable RNA extraction protocol was necessary to process leaf samples with a range of maturities. We developed and optimized an RNA extraction protocol we refer to as the modified chloroform (MC) method for black raspberry intended for Pacific Biosciences Iso-Seq analysis. Using this method, we were able to produce high quality RNA from mature leaves. Going forward, we will use RNA for identification and fine mapping of quantitative trait loci (QTL) in the black raspberry genome that correlates with the aphid resistance phenotype.

Mutations in MLO genes have been shown to confer durable broad-spectrum resistance to powdery mildew in many plant species. Very little work has been done to characterize the genetics underlying resistance to powdery mildew (PM) in red raspberry (Rubus idaeus L.) caused by Podosphaera aphanis var. aphanis. Powdery mildew of raspberry has the potential to become more of a problem in the Pacific Northwest in the near future. To better characterize red raspberry MLO genes, 95 accessions from the USDA-ARS red raspberry germplasm collection housed at the National Clonal Germplasm Repository in Corvallis, OR were screened for natural genetic variation. MLO candidate genes from the `Heritage' genome assembly thought to be associated with mlo-mediated powdery mildew resistance were identified by comparing red raspberry sequences to known MLO genes from other plant species. Two red raspberry MLO candidate genes, RedRasp_17904t and RedRasp_26700t were identified to potentially be associated with mlo-mediated resistance. Sequencing of the exons in these genes revealed 22 SNPs in RedRasp_17904t that would result in 11 single amino acid substitutions. In RedRasp_26700t, 23 SNPs were found that would result in eight amino acid substitutions. Phylogenetic analysis indicated that accessions with previously reported PM resistance have closely related haplotypes for RedRasp_17904t. Additional work is needed to determine if any of these mutations can result in mlo-mediated powdery mildew resistance.

Black raspberry (Rubus occidentalis L.), is one of a group of economically important members of the genus Rubus. In this paper, we describe a multi-state project to phenotype 43 traits in black raspberry. Two mapping populations that had parental material from multiple sources, including wild germplasm from North Carolina, Ontario, and Maine were used to assess phenotypes in 11 geographically distinct locations. A summary of the means, sample size, and range of traits including important phenological stages, flowering, plant and fruit characteristics, and fruit chemistry traits are provided in this paper. Variation in traits across populations, locations, and years was observed but was trait dependent. This phenotypic data will be included in the Genome Database for Rosaceae (GDR) (http:/www.rosaceae.org/).

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.

The soilborne pathogens Verticillium dahliae, Macrophomina phaseolina, and Fusarium oxysporum f. sp. fragariae are a challenge for strawberry (Fragaria xananassa) growers. The loss of methyl bromide and increasing restrictions on the use of other fumigants due to health and environmental concerns make the development of effective non-fumigant disease control options critical for the future economic survival of the industry. Genetic resistance can be an economical option to manage these diseases. Little is known about the genetics mediating resistance to these pathogens. Thus, there is a great need to identify sources of resistance for these pathogens to assist future breeding efforts. As such, 21 F. xananassa accessions and 30 individuals from the Fragaria Supercore were evaluated for V. dahliae, M. phaseolina, and F. oxysporum f. sp. fragariae resistance. Six plants of each accession were inoculated via root dips prior to planting and percent mortality was recorded. Accessions with less than 33.3% mortality were considered resistant. Of the accessions evaluated, 29 were resistant to V. dahliae, 20 were resistant to M. phaseolina, and 36 were resistant to F. oxysporum f. sp. fragariae. Future work is needed to identify the resistance genes, develop tools for DNA-informed breeding, and introgress resistance from the Supercore into F. xananassa.

The US Department of Agriculture (USDA), National Clonal Germplasm Repository (NCGR) is the genebank for Rubus (blackberries, raspberries, and their crop wild relatives) in the United States. The genebank includes 198 species with 2,180 accessions of plants and seeds from 67 countries. The primary collection of heritage cultivars and selections are maintained clonally as containerized plants in greenhouses and screenhouses. Propagules from foundation material are distributed for research purposes as root cuttings with dormant buds, crown divisions, or tip layers, depending on crop requirements and season. Several projects concerning Rubus genetic and genomic resources are being conducted including 1) determining phylogenetic relationships of 96 Rubus species representatives and cultivars using target capture sequencing; 2) use of a DNA fingerprinting test to establish genetic profiles, confirm identity, and establish parentage in blackberry; 3) determination of sequence variation in genes that control red raspberry resistance to powdery mildew; and 4) identification of the genes responsible for resistance to aphid feeding in black raspberry to reduce the occurrence of the aphid-borne Black raspberry necrosis virus complex in new cultivars. The availability of wide genetic diversity in Rubus at the NCGR demonstrates the usefulness of this collection in advancing research to benefit scientists, plant breeders, growers, and consumers of these berry crops.

fruit breeding, 'Merton Thornless', semierect blackberry, small fruit, thornlessness, trailing blackberry 'Galaxy' is a thornless, semierect highquality blackberry (Rubus subg.Rubus Watson) that has firm, large, dark fruit suited for the fresh market and that ripen in the early season for this type of blackberry.'Galaxy' was released by the U.S.