Stem and bud tissues of promocanes from more than 260 Rubus genotypes were evaluated for mid-winter cold hardiness after laboratory freezing in January 1990. T50 values were calculated for cane samples of red, yellow, black and purple raspberry, and blackberry cultivars, hybrids and species. Red raspberries exhibited the hardiest stem tissue, although several purple raspberries (Rubus sp. cvs. Brandywine, Royalty) survived as low as -33 C. Fall fruiting red raspberries, such as R. idaeus L. cvs. Zeva Remontante, Indian Summer, St. Regis, and Fallred, survived from -23 to -25 C. Summer-bearing cultivars, Canby and Puyallup, survived to -30 C. Stems of several black raspberries (R. occidentalis L. cvs. New Logan, Bristol) survived to -27 C. Stems of the hardiest blackberry cultivars, (R. sp. cvs. Black Satin, Smoothstem) survived to -22 C. In most genotypes the region of the bud at the axis of the stem was less hardy than tissues within the bud scales. Buds tissue was 2 to 10 C less hardy than stem tissue. Field plants were also visually rated for cold injury following record low temperatures occurring in 1989, 1990, and 1991.
Microsatellite markers for blueberry (Vaccinium L.) were created from a preexisting blueberry expressed sequence tag (EST) library of 1305 sequences and a microsatellite-enriched genomic library of 136 clones.
Microsatellite primers for 65 EST-containing simple sequence repeats (SSRs) and 29 genomic SSR were initially tested for amplification and polymorphism on agarose gels. Potential usefulness of these SSRs for estimating species relationships in the genus was assessed through cross-species transference of 45 SSR loci and cluster analysis using genetic distance values from five highly polymorphic EST-SSR loci. Cross-species amplification for 45 SSR loci ranged from 17% to 100%, and was 83% on average in nine sections. Cluster analysis of 59 Vaccinium species based on genetic distance measures obtained from 5 EST-SSR loci supported the concept of V. elliotii Chapm. as a genetically distinct diploid highbush species and indicated that V. ashei Reade is of hybrid origin. Twenty EST-SSR and 10 genomic microsatellite loci were used to determine genetic diversity in 72 tetraploid V. corymbosum L. accessions consisting mostly of common cultivars. Unique fingerprints were obtained for all accessions analyzed. Genetic relationships, based on microsatellites, corresponded well with known pedigree information. Most modern cultivars clustered closely together, but southern highbush and northern highbush cultivars were sufficiently differentiated to form distinct clusters. Future use of microsatellites in Vaccinium will help resolve species relationships in the genus, estimate genetic diversity in the National Clonal Germplasm Repository (NCGR) collection, and confirm the identity of clonal germplasm accessions.
Genetic resources of temperate berry crops were collected 7 to 27 July 2004 in Hokkaido, Japan, under a bilateral agreement between the United States and Japan. This expedition was a collaborative effort between the United States Department of Agriculture (USDA), the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF), the University of New Hampshire, and Akita Prefectural College of Agriculture, Japan. Additional assistance was provided by the Hokkaido Governmental Plant Genetic Resources Center, several Forest Research Stations of the Hokkaido University, and private botanists. The expedition obtained 100 accessions encompassing eight genera and 29 species. In all, 84 seedlots, and 23 plants were obtained. The genera collected included: Actinidia, Fragaria, Lonicera, Morus, Ribes, Rubus, Sambucus, and Vaccinium. Plant and seed accessions from this trip are preserved and distributed from the USDA ARS National Clonal Germplasm Repository in Corvallis, Ore., and from MAFF. The target genus for this expedition was Fragaria, so the trip was planned for July. Multiple samples of the two Japanese diploid strawberry species, Fragaria iinumae Makino and F. nipponica Makino (synonym = F. yezoensis H. Hara) were obtained during their prime ripening time. Ribes, Rubus, and Vaccinium fruits ripened later in the summer, but were collected when fruit were observed. Unfortunately, seeds of some of these accessions proved to be immature or nonviable upon extraction. We suggest that expeditions to collect these genera should be planned for late August. Morphological and molecular evaluation of collected germplasm is underway at the USDA ARS Corvallis Repository and at the University of New Hampshire.
Open-pollinated hop seeds (Humulus lupulus var. lupuloides E. Small, H. l. var. pubescensE. Small, H.l. var. neomexicanusNelson and Cockerell, and H.l. var. lupulusL.) were collected from the United States, Canada, and Kazakhstan and screened for resistance to hop powdery mildew (Podosphaeramacularis Braun & Takamatus). A total of 2108 seedlings were repeatedly inoculated with high levels of P. macularis. Under greenhouse conditions, most seedlings exhibited a compatible disease response typical of susceptible hosts with sporulating colonies covering both leaf surfaces. Three genotypes from hop seed native to Emba, Kazakhstan, remained uninfected in greenhouse assays. Further experimentation of those genotypes in growth chambers at 18 °C revealed that they demonstrated an atypical disease response. Six days after inoculation, necrotic lesions on the adaxial leaf surfaces were visually apparent. Microscopic examination showed areas of collapsed epidermal cells, collapsed hyphae, and golden-brown discolorations extending out from the center of the infection. These symptoms contrasted those of a hypersensitive response in which fungal growth is restricted by the collapse of epidermal cells in advance of the fungus. The infection frequency of Kazakhstani genotypes was intermediate compared to H.l. cultivars Symphony (susceptible) and Nugget (resistant) after exposure to three preinoculation temperature regimes. These genotypes could represent a new source of polygenic resistance to hop powdery mildew, and could broaden hop germplasm available to global breeding programs.
A pawpaw (Asimina triloba) regional variety trial (PRVT) was established at the U.S. Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository (NCGR), Corvallis, Ore., in Fall 1995. This orchard was a replicated planting of 28 commercially available varieties or advanced selections from the PawPaw Foundation (PPF; Frankfort, Ky.), with eight replicate trees of each selection grafted onto seedling rootstocks and planted in a randomized block design. Two years after planting, 32 trees had either failed to establish or had died after an initial healthy start. By July 1999, 25% of grafted trees had died due to a vascular wilt-like disease, and 2 years later mortality exceeded 50%. Grafted selections with the lowest symptom severity include 1-7-2, 2-54, 7-90, 8-58, 9-58, `Mitchell', `PA-Golden #1', `Taylor' and `Wilson'. Seedling guard trees were unaffected until July 2000, when six guard trees of 76 died and 10 more were declining. By July 2001, 14 guard trees were dead. No fungi were consistently isolated from declining trees. A number of bacteria were isolated from infected trees, but no specific pathogen has been confirmed as the causal agent. Polymerase chain reaction (PCR) tests for phytoplasmas and for the bacterium Xylella fastidiosa were also negative. Research is ongoing to determine if a bacterial pathogen was the cause of the pawpaw decline in the Oregon PRVT.
Stem sections of 31 filbert genotypes were collected, artificially frozen, and evaluated by visual browning of cambium and other tissues to determine cold hardiness during 5 sample dates in 1984 and 1985. Corylus heterophylla Fish. ex. Trau. was the most cold-hardy filbert tested, but it deacclimated sharply before the end of February. The tested filberts were divided into 3 temporal groups of acclimation to maximum cold hardiness—early, midwinter, and late. C. avellana L. ‘Butler’, ‘Tombul’, ‘Barcelona’, ‘Ennis’, and ‘Casina’ acclimated early; ‘Gasaway’, acclimated in midwinter season; ‘Daviana’ and ‘Hall’s Giant’ acclimated late. The genotypes tested also were separated into very hardy, hardy, and least hardy groups for cortex-cambium, pistillate bud, and staminate bud tissues. The general order of tissue hardiness from least to most was pith, xylem, cambium, and cortex. Vegetative buds in midwinter were as hardy or hardier than the cambium. Staminate flowers were hardier than pistillate in October, but most pistillate flowers were hardier than staminate by January. Several filberts had fully blooming pistillate flowers that were uninjured at −30°C in December and −40° in January. Filbert flower buds demonstrated maximum cold hardiness during nondormancy.
Peonies (Paeonia), the grand garden perennial of spring and early summer, are economically important to the international cut flower market. Herbaceous peonies (Paeonia section Paeonia), tree peonies (Paeonia section Moutan), and intersectional crosses between the two types (Itoh Paeonia hybrids) are of interest to gardeners, growers, and nursery producers. Thousands of peony cultivars exist and identity is traditionally determined by experienced horticulturists knowledgeable in plant and bloom characteristics. With DNA extraction possible during any time of the year, molecular markers can provide genotype identity confirmation for dormant roots or mature post-bloom plants. The primary objective of our research was to rapidly and inexpensively develop microsatellite markers in a range of Paeonia species using barcoded Illumina libraries. A secondary objective was to apply these simple sequence repeat (SSR) markers to fingerprint 93 accessions that include tree, intersectional, and herbaceous peonies. We used 21 primers to distinguish cultivars and their close relatives. Also from our sequence information, greater than 9000 primers were designed and are made available.
Identifying and evaluating genetic diversity of culinary rhubarb (Rheum ×rhababarum) cultivars using morphological characteristics is challenging given the existence of synonyms and nomenclatural inconsistencies. Some cultivars with similar names are morphologically different, and seedlings may grow and become associated with the parental name. Morphological traits of one cultivar may vary when measured under different environmental conditions. Molecular markers are consistent for unique genotypes across environments and provide genetic fingerprints to assist in resolving identity issues. Microsatellite repeats, also called simple sequence repeats (SSRs), are commonly used for fingerprinting fruit and nut crops, but only 10 SSRs have previously been reported in rhubarb. The objectives of this study were to use short-read DNA sequences to develop new di-nucleotide-containing SSR markers for rhubarb and to determine if the markers were useful for cultivar identification. A total of 97 new SSR primer pairs were designed from the short-read DNA sequences. The amplification success rate of these SSRs was 77%, whereas polymorphism of those reached 76% in a test panel of four or eight rhubarb individuals. From the 57 potentially polymorphic primer pairs obtained, 25 SSRs were evaluated in 58 Rheum accessions preserved in the U.S. Department of Agriculture, National Plant Germplasm System. The primer pairs generated 314 fragments with an average of 12.6 fragments per pair. The clustering of many accessions in well-supported groups supported previous findings based on amplified fragment length polymorphisms (AFLPs). Cluster analysis, using the proportion of shared allele distance among the 25 SSRs, distinguished each of the 58 accessions including individuals that had similar names or the same name. Accessions that grouped in well-supported clusters previously belonged to similar clusters with high bootstrap support based on AFLP. In summary, our technique of mining short-read sequencing data was successful in identifying 97 di-nucleotide-containing SSR sequences. Of those tested, the 25 most polymorphic and easy-to-score primer pairs proved useful in fingerprinting rhubarb cultivars. We recommend the use of short-read sequencing for the development of SSR markers in the identification of horticultural crops.
The genetic control of flowering habit in many species of Fragaria has not been well studied. Identification of flowering traits and patterns for these taxa could be used in the quest for perpetual flowering (PF) genes and for the octoploids, broaden the genepool of available PF parents for breeding programs. As such, clones from the Fragaria germplasm collection housed at the USDA-ARS National Clonal Germplasm Repository in Corvallis, OR, were evaluated to describe flowering habits in various taxa and identify PF clones. Flower presence was recorded monthly for 962 clones of 36 taxa from the first of May through October in 2015 and 2016 to determine flowering habit and pairwise comparisons between taxa were examined using Pearson’s Chi-squared test. Taxa with the largest percent of PF accessions were F. vesca subsp. vesca f. semperflorens, F. vesca subsp. vesca f. alba, F. vesca subsp. americana, and F. virginiana subsp. glauca. These taxa had similar flowering habits to each other but were significantly different (α = 0.05) from most other taxa in which the seasonal flowering (SF) trait was predominant. Fifteen clones that demonstrated the PF phenotype in both 2015 and 2016 were identified. Differing genetic controls have been observed for flowering habit in F. ×ananassa and F. vesca. Additional studies are needed to determine genetic control of flowering in other Fragaria taxa.