The evolutionary histories of many polyploid plant species are difficult to resolve due to a complex interplay of hybridization, incomplete lineage sorting, and missing diploid progenitors. In the case of octoploid strawberry with four subgenomes designated ABCD, the identities of the diploid progenitors for subgenomes C and D have been subject to much debate. By integrating new sequencing data from North American diploids with reticulate phylogeny and admixture analyses, we uncovered introgression from an extinct or unsampled species in the clade of Fragaria viridis, Fragaria nipponica, and Fragaria nilgerrensis into the donor of subgenome A of octoploid Fragaria prior to its divergence from F. vesca subsp. bracteata. We also detected an introgression event from F. iinumae into an ancestor of F. nipponica and F. nilgerrensis. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of F. viridis and F. nipponica as donors of the C and D subgenomes and suggest a greater role than previously thought for homoploid hybridization in the diploid progenitors of octoploid strawberry. The integrated set of approaches used here can help advance polyploid genome analysis in other species where hybridization and incomplete lineage sorting obscure evolutionary relationships.

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.

The identity of the diploid progenitors of octoploid cultivated strawberry ( Fragaria × ananassa ) has been subject to much debate. Past work identified four subgenomes and consistent evidence for F. californica (previously named F. vesca subsp. bracteata ) and F. iinumae as donors for subgenomes A and B, respectively, with conflicting results for the origins of subgenomes C and D. Here, reticulate phylogeny and admixture analysis support hybridization between F. viridis and F. vesca in the ancestry of subgenome A, and between F. nipponica and F. iinumae in the ancestry of subgenome B. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of F. viridis and F. nipponica as donors of the C and D subgenomes and unify conflicting hypotheses about the evolutionary origin of octoploid Fragaria . ### Competing Interest Statement The authors have declared no competing interest.

Societal Impact statement To secure a stable, safe food supply, the future of humanity depends on the conservation and application of cultivated and wild plant diversity. Strawberries are globally important. They are widely produced and provide significant human health benefits. In 2019, annual world production was 14.5 MT (FAOSTAT, 2022). This report characterizes agricultural traits of diverse heritage strawberries. The gene pool of breeding programs has traditionally included a reliable but limited set of cultivars. The traits of lesser known heritage strawberry cultivars and selections examined by our study could be of value in expanding gene pools by tapping into existing cultivated genetic diversity. Summary Strawberries are a berry crop of global significance. We present a comprehensive evaluation of strawberry diversity through phenotyping 284 strawberry cultivars from the U.S. Department of Agriculture, National Clonal Germplasm Repository Corvallis, Oregon, USA. We assessed 284 cultivars in 2019 and 2020 for quantified variation across 16 traits, including phenology, plant morphology, and fruit quality traits at full ripeness. Through cluster analysis, we determined groups of accessions that had desirable traits, including quality fruits, earliest fruit ripening, or high numbers of daughter plant production. We observed that this strawberry diversity panel displayed a wide range of phenotypic variation that could prove useful for future strawberry improvement. ORUS 2427‐1, NW 90054‐37, and “Independence,” each developed by the Oregon USDA breeding program, displayed a combination of the highest fruit quality traits. “Independence” also had the longest runner length and the highest number of daughter plants. Two California cultivars, Oso Grande and Cuesta, and the Oregon cultivar Pinnacle had a short ripening time, on average 32 days between flowering and harvest, with the range for the study group of 25–41 days. Our data provide insight for breeders to expand gene pools, producers who choose cultivars for green‐wall production, or geneticists who need data to prepare genome‐wide association studies.

Rubus (Rosaceae), one of the most complicated angiosperm genera, contains about 863 species, and is notorious for its taxonomic difficulty. The most recent (1910-1914) global taxonomic treatment of the genus was conducted by Focke, who defined 12 subgenera. Phylogenetic results over the past 25 years suggest that Focke's subdivisions of Rubus are not monophyletic, and large-scale taxonomic revisions are necessary. Our objective was to provide a comprehensive phylogenetic analysis of the genus based on an integrative evidence approach. Morphological characters, obtained from our own investigation of living plants and examination of herbarium specimens are combined with chloroplast genomic data. Our dataset comprised 196 accessions representing 145 Rubus species (including cultivars and hybrids) and all of Focke's subgenera, including 60 endemic Chinese species. Maximum likelihood analyses inferred phylogenetic relationships. Our analyses concur with previous molecular studies, but with modifications. Our data strongly support the reclassification of several subgenera within Rubus. Our molecular analyses agree with others that only R. subg. Anoplobatus forms a monophyletic group. Other subgenera are para- or polyphyletic. We suggest a revised subgeneric framework to accommodate monophyletic groups. Character evolution is reconstructed, and diagnostic morphological characters for different clades are identified and discussed. Based on morphological and molecular evidence, we propose a new classification system with 10 subgenera: R. subg. Anoplobatus, R. subg. Batothamnus, R. subg. Chamaerubus, R. subg. Cylactis, R. subg. Dalibarda, R. subg. Idaeobatus, R. subg. Lineati, R. subg. Malachobatus, R. subg. Melanobatus, and R. subg. Rubus. The revised infrageneric nomenclature inferred from our analyses is provided along with synonymy and type citations. Our new taxonomic backbone is the first systematic and complete global revision of Rubus since Focke's treatment. It offers new insights into deep phylogenetic relationships of Rubus and has important theoretical and practical significance for the development and utilization of these important agronomic crops.

Control of spotted-wing Drosophila, Drosophila suzukii, in small fruits emphasizes biological, cultural, and chemical approaches, whereas studies of host plant resistance as a form of genetic control are just getting underway. The identification of resistance patterns among genotypes of host plants whose fruit, leaves, roots, stems, or seeds are specifically targeted by an invasive pest is the first step in the development of an effective genetic control. Therefore, a detached fruit bioassay was developed to screen for D. suzukii oviposition and larval infestation within berries from 25 representative species and hybrids of wild and cultivated Vaccinium. Ten Vaccinium species showed strong resistance; among them, two wild diploids originating from within the fly's native range: V. myrtoides and V. bracteatum. Other resistant species came from the sections Pyxothamnus and Conchophyllum. They included New World V. consanguineum and V. floribundum. Large-cluster blueberry, V. amoenum, and three Floridian genotypes of related rabbiteye blueberry, V. virgatum, were the only hexaploids expressing strong resistance against D. suzukii. Most screened blueberry genotypes from managed lowbush and cultivated highbush types were susceptible to the flies' attacks (i.e., oviposition). Tetraploid blueberries tended to host the most eggs, whereas diploids and hexaploids harbored 50%-60% fewer eggs, on average. D. suzukii cannot lay eggs or complete development in the smallest, sweetest, and firmest diploid fruits. Likewise, certain genotypes of large-fruited tetraploid and hexaploid blueberry strongly curbed D. suzukii egg-laying and larval growth, indicating the possibility of heritable resistance operating against this invasive fly species.

VacciniumL., a globally distributed genus, encompasses economically and nutritionally valuable species such as blueberry ( V. corymbosumL. and its hybrids), cranberry ( V. macrocarponA.), bilberry ( V. myrtillusL.), and lingonberry ( V. vitis-ideaL.). There has been a robust growth of blueberry cultivation in the tropical and subtropical regions of the world, such as Central and South America, the Southern United States, Australia, and the Mediterranean. This growth has been enabled by the integration of various wild species such as northern lowbush blueberry V. angustifolium(Aiton), evergreen blueberry V. darrowii(Camp), and rabbiteye blueberry V. virgatum(Aiton) into highbush blueberry breeding programs. Still, numerous under-studied wild Vacciniumspecies have untapped potential for breeding use and local cultivation in diverse climates. The harvest of wild Vacciniumfruit has long contributed to the nutrition of local communities throughout Southeast Asia and the Americas. Our objective was to conduct preliminary investigations into the fruit qualities and anthocyanin profiles of two such under-studied species, V. myrtoides(Blume) and V. floribundum(Kunth), and compare their characteristics to that of the southern highbush blueberry cultivar ‘O’Neal’ ( V. corymbosumhybrid). Over the spring and summer of 2021, we determined fruit size, percent soluble solids, pH, total anthocyanin concentration, and anthocyanin aglycons profiles. The fruit was sourced from the US Department of Agriculture (USDA), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. The wild species’ fruit size, soluble solids, and pH were not significantly different from those of ‘O’Neal.’ The total anthocyanin levels for V. floribundum(87.4 mg anthocyanin/100 g frozen fruit) and V. myrtoides(80.4 mg/100 g frozen fruit) were significantly higher than those for ‘O’Neal’ (32 mg/100 g frozen fruit). Anthocyanin profiles were also unique to each species. V. myrtoideshad the most complex profile with eight anthocyanin peaks; V. floribundumhad four peaks ‘O’Neal’ had three. One of the most prominent anthocyanins in blueberries, petunidin-3- galactoside, occurred in ‘O’Neal’ and V. myrtoidesbut was absent from V. floribundum. Del-3-arabinoside was present in both V. myrtoidesand V. floribundumyet absent in ‘O’Neal’. The unique anthocyanin profiles of the two wild species could have value in diversifying the anthocyanins available in cultivated blueberries and deserve further investigation.

Abstract The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops’ relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.

Abstract The cultivated strawberry (Fragaria ×ananassa) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750s. Since then, breeders have developed improved cultivars adapted to different growing regions. Diverse germplasm is crucial to meet the challenges strawberry breeders will continue to address. The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon maintains the U.S. strawberry collection. Recent developments in high-throughput genotyping for strawberry can provide new insights about the diversity and structure of the collection, germplasm management, and future breeding strategies. Genotyping was conducted on 539 F. ×ananassa accessions using either the iStraw35 or FanaSNP 50 K Axiom array. Data for markers shared by the two arrays were curated for call quality, missing data, and minor allele frequency resulting in 4033 markers for structure assessment, diversity analysis, pedigree confirmation, core collection development, and the identification of haplotypes associated with desirable traits. The F. ×ananassa collection was equally diverse across the different geographic regions represented. K-means clustering, sNMF, and UPGMA hierarchal clustering revealed seven to nine sub-populations associated with different geographic breeding centers. Two 100 accession core collections were created. Pedigree linkages within the collection were confirmed. Finally, accessions containing disease resistance-associated haplotypes for FaRCa1, FaRCg1, FaRMp1, and FaRPc2 were identified. These new core collections will allow breeders and researchers to more efficiently utilize the F. ×ananassa collection. The core collections and other accessions of interest can be requested for research from the USDA-ARS NCGR via the Germplasm Resources Information Network (https://www.ars-grin.gov/).

Breeding strategies for improving blueberry (Vaccinium corymbosum and V. virgatum) cultivars often include introgressing regionally adapted species into the cultivated gene pools through interspecific hybridization. However, these approaches are complicated by variation in ploidy, triploid blocks and infertility, production of unreduced gametes, and aneuploidy. The objective of this study was to use flow cytometry, k-mer distribution analysis, and known pedigree information to evaluate genome sizes (2C nuclear and 1Cx monoploid), and ploidy of diverse accessions from Vaccinium sections and species. A total of 369 accessions, including a diversity panel (DP) of 251 inter- and intra-specific hybrid Vaccinium accessions, as well as 118 non-hybrid Vaccinium species across multiple sections, were sampled from the North Carolina State University blueberry breeding program and the National Clonal Germplasm Repository. The nuclear DNA content was analyzed via flow cytometry. The mean (range) DNA content of diploid, tetraploid, and hexaploid reference species were 1.20 pg (0.99 pg in V. crassifolium 'Well's Delight' to 1.41 pg in V. caesariense NC79–24), 2.37 pg (2.11 pg in V. corymbosum 'Concord' to 3.01 pg in V. corymbosum DE599), and 3.64 pg (3.24 in V. constablaei NC83–21–2 to 3.80 in V. virgatum 'Premier' and NC4790), respectively. Of the 369 unique accessions analyzed for ploidy, 259 were tetraploid, 46 were diploid, one was triploid, 51 were pentaploid or aneuploid with 2C values between tetraploid and hexaploid values, and 12 were hexaploid. Tetraploid hybrid pedigrees, which involved hexaploid crosses within three prior generations, had a 2C value range between 2.22 pg and 2.59 pg. Interspecific pentaploid and aneuploid progeny 2C DNA content ranged from 2.61 pg to 3.15 pg. We speculate some of these progeny to be near tetraploids with extra chromosomes from hexaploid progenitors. Further karyotyping of these individuals is necessary to ascertain aneuploidy anomalies. This research provides an expanded knowledge base of genome sizes, ploidy, and reproductive pathways for diverse species and hybrids to enhance future breeding, improvement, and the genomic study of blueberry.

Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96).

Worldwide, hazelnut (Corylus spp.) (Family Betulaceae) is one of the most economically important nut crops cultivated in the northern hemisphere. With its tasty nuts valued on the global market, emerging discovery of the plant pharmaceutical properties, and its role in sustainable agroecosystems, there is a quest to find and develop cultivars suitable for new growing areas. In a 2-yr study, 53 hazelnut accessions from the Corvallis germplasm collection were evaluated for nut yield, kernel percentage, weight, and shape in the San Joaquin Valley (SJV) of California. The best traits were observed for 'Lewis' (PI 617210) and 'Ennis' (PI 557045); however, a few other accessions showed characteristics supporting cultivation in the SJV growing conditions. These findings might serve as a guidance for cultivar selection for farming in that region. The evaluation also contributed to the characterization of the USDA-ARS germplasm collection of Corylus.

Currant and gooseberry plants (Ribes L.) are native to the temperate regions of the Northern hemisphere through high elevations in Mexico and Central America to the mountainous regions of South America. Annually, the global production is about 838 MT. The fruits are used for cassis, juice preserves, in bakery, dairy products and pharmaceuticals. Some species such as black currant (Ribes nigrum) have antimicrobial, antitumor and immunostimulatory qualities; hence, interest is growing in crop improvement using a diversity of plant genetic resources. Active germplasm collections preserve Ribes cultivars as clonal plantations in the field or under protected cultivation, and species as plants in the field or seeds in cold storage. Long-term preservation of Ribes germplasm may be accomplished by various methods, one of them is cryopreservation of dormant winter buds (DB). This method is reported for preservation of R. nigrum. We have investigated the possibility of applying DBs for cryopreservation of other Ribes species. Eleven accessions in seven species (R. aureum var. aureum, R. aureum var. villosum, R. cereum, R. erythrocarpum, R. mascalerium, R. turbinatum and R. uva-crispa) were cryopreserved over two winter seasons without a pretreatment (standard), with a cryoprotectant (0.75 M sucrose) or a cryoprotectant with an antioxidant (0.75 M sucrose with 0.75 mM vitamin C). A 2-year average viability varied significantly among the accessions processed with the standard method (10 to 87.5%) and among accessions processed with the pretreatments (32.5 to 97.5%); however, the difference between the standard and treatment procedures was not significant. A significant difference in viability between the processing years was observed and there was an interaction between accession, year and treatments for seven accessions processed in three treatments but not in the four accessions processed in the two treatments. Cryopreservation of the broad species in the Ribes germplasm collection may be supported by identifying modifications of the standard cryopreservation procedure.