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(Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within . Subgenus and Subg. were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. (blackberries) × Subg. (raspberries) and Subg. × Subg. (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. species diversified greatly in Asia during the Miocene. taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.

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).

Mentha is a strongly scented herb of the Lamiaceae (formerly Labiatae ) and includes about 30 species and hybrid species that are distributed or introduced throughout the globe. These fragrant plants have been selected throughout millennia for use by humans as herbs, spices, and pharmaceutical needs. The distilling of essential oils from mint began in Japan and England but has become a significant industrial product for the US, China, India, and other countries. The US Department of Agriculture (USDA), Agricultural Research Service, National Clonal Germplasm Repository (NCGR) maintains a mint genebank in Corvallis, Oregon. This facility preserves and distributes about 450 clones representing 34 taxa, hybrid species, advanced breeder selections, and F1 hybrids. Mint crop wild relatives are included in this unique resource. The majority of mint accessions and hybrids in this collection were initially donated in the 1970s by the A.M. Todd Company, located in Kalamazoo, Michigan. Other representatives of diverse mint taxa and crop wild relatives have since been obtained from collaborators in Australia, New Zealand, Europe, and Vietnam. These mints have been evaluated for cytology, oil components, verticillium wilt resistance, and key morphological characters. Pressed voucher specimens have been prepared for morphological identity verification. An initial set of microsatellite markers has been developed to determine clonal identity and assess genetic diversity. Plant breeders at private and public institutions are using molecular analysis to determine identity and diversity of the USDA mint collection. Evaluation and characterization includes essential oil content, disease resistance, male sterility, and other traits for potential breeding use. These accessions can be a source for parental genes for enhancement efforts to produce hybrids, or for breeding new cultivars for agricultural production. Propagules of Mentha are available for distribution to international researchers as stem cuttings, rhizome cuttings, or seed, which can be requested through the GRIN-Global database of the US National Plant Germplasm System, subject to international treaty and quarantine regulations.

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. Summary Pour garantir un approvisionnement alimentaire stable et sûr, l'avenir de l'humanité dépendsur la conservation et l'utilisation de la diversité des plantes cultivées et sauvages. Les fraises sont d'importance au niveau mondial. Elles sont largement cultivées et offrent des avantages conséquents pour la santé humaine. En 2019, la production mondiale annuelle était de 14,5 MT. Ce rapport caractérise les traits agronomiques de variétés de fraisier patrimoiniales. Les ressources génétiques des programmes de sélection comprennent traditionnellement un ensemble cohérent mais limité de variétés. Les caractères des variétés et des sélections de fraises patrimoniales moins connues décrits dans notre étude pourraient être utiles pour élargir les ressouces génétiques en exploitant la diversité génétique cultivée existante. 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. 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. Photo credits to Dr. Beatrice Amyotte.

The strawberry genus, Fragaria (Rosaceae), has a base chromosome number of x = 7. Cultivated strawberries (F. xananassa nothosubsp. ananassa) are octoploid (2n = 8x = 56) and first hybridized from F. chiloensis subsp. chiloensis forma chiloensis x F. virginiana subsp. virginiana. Europe has no known native octoploid species, and only one Asian octoploid species has been reported: F. iturupensis, from Iturup Island. Our objective was to examine the chromosomes of F. iturupensis. Ploidy levels of wild strawberry species, include diploid (2n = 2x = 14), tetraploid (2n = 4x = 28), pentaploid (2n = 5x = 35), hexaploid (2n = 6x = 42), octoploid (2n = 8x = 56), and nonaploid (2n = 9x = 63). Artificial triploid (2n = 3x = 21), tetraploid, pentaploid, octoploid, decaploid (2n = 10x = 70), 16-ploid, and 32-ploid plants have been constructed and cultivated. Surprisingly, chromosome counts and flow cytometry revealed that F. iturupensis includes natural decaploid genotypes with 2n = 10x = 70 chromosomes. This report is the first of a naturally occurring decaploid strawberry species. Further research on F. iturupensis and exploration on northern Pacific islands is warranted to ascertain the phylogeny and development of American octoploid species.

Core Ideas Genetic restructuring yielded distinct temperate and coastal‐adapted subpopulations. Ancestral species selection bias was discovered in temperate and coastal octoploids. Flowering and fruit development genes targeted during strawberry domestication were identified. Garden strawberry (Fragaria × ananassa Duchesne ex Rozier) arose from spontaneous hybridization of distinct octoploid species 300 yr ago. Since its discovery in the 1700s, migration and selection restructured the genetic diversity of early hybrids to produce elite fruit‐bearing groups. Breeders’ understanding of the genetic architecture of domesticated populations is incomplete. To resolve the impacts of domestication on strawberry genetic diversity, we analyzed genome‐wide DNA profiles of 1300 octoploid individuals (1814–present), including wild species, historic varieties, and the University of California germplasm collection. Commercially important California genotypes, adapted to mild coastal climates and accounting for a large fraction of global production, have diverged from temperate cultivars originating in eastern North America and Europe. Whereas temperate cultivars were shown to have selected North American Fragaria virginiana Miller ssp. virginiana ancestral diversity at higher frequencies, coastal breeding increased selection of Fragaria chiloensis (L.) Miller (beach strawberry) alleles in F. × ananassa, in addition to photoperiod‐insensitive flowering alleles from nonancestral F. virginiana (S.Watson) Staudt ssp. glauca, underscoring the role of continued adaptive introgressions in the domestication of artificial hybrids. Selection for mass production traits in coastal climates over the last 20 to 30 yr has restructured domesticated strawberry diversity on a scale similar to the first 200 yr of breeding; coastal F. × ananassa has diverged further from temperate F. × ananassa than the latter from their wild progenitors. Selection signatures indicate that strawberry domestication targeted genes regulating hormone‐mediated fruit expansion, providing a blueprint for genetic factors underlying elite phenotypes.

Fragaria cascadensis K.E. Hummer, sp. nov. is endemic to the western high Cascade Mountain Range in Oregon, United States. This decaploid species can be distinguished by adaxial leaf hairs, distal tooth of the terminal leaflet always smaller than adjacent teeth, and commashaped achenes. Its known range is in the western Cascade Mountains from the Columbia River in the north, to the vicinity of Crater Lake in the south, at elevations of 1,000 to 3,800 m, in sandy-clay loams of volcanic origin, in forest clearings and open meadows. Fragaria cascadensis K.E. Hummer, sp. nov. es endémica de la Cordillera de las Cascadas en Oregón, Estados Unidos. Esta especie decaploide puede diferenciarse por los pelos del envés de las hojas, diente distal del foliólo terminal siempre más pequeño que los dientes adyacentes, y los aquenios en forma de coma. Su rango conocido va del oeste de la Cordillera de las Cascadas desde el río Columbia en el norte, a las proximidades del Crater Lake en el sur, a elevaciones de 1,000 a 3,800 m, en margas arenoso-calcáreas de origen volcánico, en claros de bosque y en parados abiertos.

Heritage apple ( Malus domestica Borkh. hybrids) and pear ( Pyrus communis L. hybrid) trees grow in villages throughout Terceira Island, Azores, Portugal. Some of these pears have different names but similar morphology. The objective of this study was to determine synonymy, homology, and phylogeny of apples and pears from Terceira and to examine potential relationships of the island pears with standard apples and pears of Portuguese or American descent. Nine apple microsatellite markers were used to determine genetic relationships. Distance- and parsimony-based cluster analysis grouped these genotypes into separate apple and pear clades. The Terceira apples were divided into two clades: the maçā and the reineta-reinette. Among the 17 heritage apple genotypes, seven unique accessions were identified and four groups of synonyms, or possibly clones, were detected including: ‘Reineta Agosto’ and ‘Reineta Verde’ from Altares; ‘Reineta Castanha’ and ‘Reineta Verde Miuda’; ‘Maçā Pêra,’ ‘Maçā Calhau’, ‘Pêro Branco’ from Salga and from Terra-Chā and ‘Maçā Marmelo’; and the five genotypes ‘Maçā Sao Joao’, ‘Malápio Rosa’, ‘Maçā Gaspar’, ‘Maçā Branca’ and ‘Maçā Pato’. In addition, two homonyms were detected. ‘Pêro Vermelho’ from Terra Chā was a separate genotype from a tree from Doze Ribeiras of the same name, but Pêro Branco from Terra Chā appears to be a clone that can be distinguished by an additional allele at CH1F07a from a tree with that name from Salga. One pair of apple clones, ‘Reineta Agosto’ and ‘Reineta Verde’ from Altares appear to be derived from an unreduced gamete of ‘Golden Delicious.’ Another apple genotype ‘Maçā Acida’ could be a sibling of the ‘Maçā Pêra’ clonal group. Other tested standard apples from the US genebank were unrelated to Terceira genotypes. Of the seven heritage pears, five unique genotypes and one pair of synonyms were detected. ‘Pêra Papo Pintassilgo’ from Raminho and ‘Pêra Vermelha’ from the nursery of Serviço de Desenvolvimento Agario da Terceira (SDAT) were synonyms. ‘Passans du Portugal’ was related to ‘Pêra Cabaca’ but other standard pears from the US genebank were unrelated to Terceira genotypes. Future studies will include additional apple and pear cultivars from other Islands of the Azores and continental Portugal, and wild Asian species to further explore genetic relationships.

The United States Department of Agriculture (USDA)—Agricultural Research Service (ARS)—National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, is a genebank that preserves strawberry genetic resources. Representatives of two Japanese diploid species, Fragaria iinumae Makino and F. nipponica Makino were collected for conservation by the NCGR during an expedition to Hokkaido, Japan. Fragaria iinumae may be a genome contributor to the cultivated octoploid strawberries. The objective of this study was to evaluate the genetic diversity of these two species by using simple sequence repeat (SSR) markers. Twenty of 82 Fragaria-derived SSRs, polymorphic among and within the two species, were selected for genetic analysis of 137 accessions. Genetic diversity, based on the proportion of shared alleles between the two species, in F. nipponica (0.4542) and F. iinumae (0.1808) was significantly different. Three wild interspecific hybrids were identified from intermediate memberships in the two diploid species groups revealed by using the clustering program, Structure. Principal coordinate analysis followed by non-parametric modal clustering (PCO-MC) grouped accessions into two clusters representing the two diploid species. Further clustering within the species groups generated with the program, STRUCTURAMAᵀᴹ, resulted in seven subclusters in F. iinumae and three in F. nipponica, which may represent breeding populations appropriate for clonal conservation. Long-term preservation of the species populations and the limited number of hybrids on the island is discussed relative to their geographical distribution and the geological history of Hokkaido Island.

Cultivars of blue honeysuckle, Lonicera caeruleaL., have been recently introduced into North America from Russia. In addition, wild material has been collected from Russia, Japan and China and is now preserved at the United States Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. Blue honeysuckle has potential as a commercial berry crop for northern latitudes. Russian cultivars were released in the 1980’s and 1990’s and are now available in North America. These cultivars bloom and ripen early in the season, and can yield between 2 and 3 kg/plant. The berry shape is similar to an elongated or cylindrical blueberry and the fruit flavor ranges from tart sugar/acid to bland. The fruit varies from about 1 to 2 g/berry, has high Vitamin C levels, and high antioxidant content. This crop could provide an additional opportunity for small fruit growers in high latitudes and colder climates to diversify their production for high-end specialty crop markets.