USDA-ARS National Clonal Germplasm Research Articles

GENETIC CONTROL OF PHYLLOTAXY PHASE SHIFT IN JUVENILE VINES IN A ROOTSTOCK HYBRID POPULATION

Grapevine seedlings initially display spiral phyllotaxy of true leaves, then undergo a shift to alternate phyllotaxy with the production of the first lateral meristems (typically tendrils). The node at which the shift from spiral to alternate phyllotaxy occurs varies from about the 4th to about the 12th node on the vine. To investigate the genetic control of the transition from spiral phyllotaxy to alternate phyllotaxy, a population segregating for this trait was developed and screened. The population derived from four female parents and six male parents crossed in a Design 2 mating array (all female parents crossed to all male parents). The female parents were the pistillate flowered rootstock varieties 1613 Couderc, 93-5 Couderc (California clone), Vitis rupestris 187G, and Fercal. The male parents were staminate flowered grape rootstock germplasm, species, and species hybrid selections with diverse backgrounds, including accessions from the USDA ARS National Clonal Germplasm Repository, Davis, California (denoted with DVIT accession numbers): IAC 572, Vitis labrusca Y137 DVIT 1392, Vitis hybrid Y93 DVIT 1519, Vitis hybrid Q126 DVIT 1456, Vitis hybrid Q130 DVIT 1466, and Vitis hybrid R127 DVIT 1490. The species background of the male parents includes V. labrusca, V. mustangensis, V. riparia, V. tiliifolia, and V. rupestris. Seedlings from controlled crosses were grown in individual pots in a greenhouse with artificial illumination to provide 24 h day length. The node number of the first observed lateral meristem was recorded; the goal was 50 seedlings per population for each of 24 populations, although some populations showed poor seed germination. Male and female parents differ from one another at P =0.01, with male parents falling into three groups and female parents into two groups based on the mean node of phyllotaxy shift in their seedlings. Narrow sense heritability of the first tendril bearing node is estimated at 0.23 based on breeding value of male parents and at 0.45 based on breeding value of female parents.

ANALYSIS OF GENETIC DIVERSITY AND STRUCTURE OF SOME HISTORIC OLIVE (OLEA EUROPAEA L.) GERMPLASM IN THE UNITED STATES USING MICROSATELLITE MARKERS

Fifteen microsatellite simple-sequence repeat (SSR) loci were used to genotype 58 accessions of cultivated olive, Olea europaea L. ssp. europaea var. europaea, from two collections of 19th to 20th century plantings in Arizona and California, in order to examine genetic diversity and structure within and among collections. These collections are Lotusland Gardens in Santa Barbara, CA, and the Arboretum of the University of Arizona, Tucson. Genotypes in the olive collection at the USDA-ARS National Clonal Germplasm Repository for Fruit & Nut Crops (NCGR) in Davis, California were compared with the historic collections to potentially establish cultivar identity. Mean number of alleles per locus was 5.0 for Lotusland and 3.5 for the University of Arizona. Mean observed heterozygosity per collection was 0.650 for Lotusland and 0.598 for the University of Arizona. Up to 90% of the samples per collection were found to be synonymous with named, primarily Spanish or Italian, cultivars, yet these historic collections also contain significant genetic diversity, including genotypes and alleles not present in the NCGR germplasm collection. The cluster analysis placed the unknown genotypes within clades containing cultivars from the Eastern Mediterranean or from throughout the Mediterranean region, and in some cases produced relatively distinct branches.

Polyphenolic and Antioxidant Properties of Elderberry (Sambucus) Fruits

Elderberries (Sambucus sp.) are rich in phenolics which could provide protection of LDL against oxidation. S. Canadensis (S.c.) and S. nigra (S.n.) are native to N American and Europe, respectively. The antioxidant and phenolic properties of their water soluble phenolic extracts could be important for human nutritional health. S.c. cultivars (Johns, CSAM72, Adams II, Brush Hill 2, Maxima, Scotia, Eridu 1, and York) and S.n. (Albo‐variegata, Purpurea, Samdal, and Guincho Purple) were cultivated at the USDA ARS National Clonal Germplasm Repository, Corvallis, Oregon. Ripe fruits were harvested, frozen at −80C, and aqueous extracts prepared/pasteurized. Phenolic content (gallic acid equivalence mg/L; GAE) for S.n. (6751 ± 528) was significantly (P=0.004) greater than S.c. (5271 ± 806). Effects of elderberry antioxidants on human LDL oxidation (5μM Cu++) lag‐time (A234nm) was examined at extract dilutions of 1:10,000, 1:50,000 and 1:100,000. At the 1:10,000 dilution, antioxidant activity for S.n. (201±12 min) was significantly higher than S.c. (138±12 min), 1:50,000 and 1:100,000 dilutions were not associated with significant antioxidant activity. Higher GAE was correlated with increased lag‐time (R2= 0.55). Understanding differences in elderberry antioxidant activity may be important for development of elderberry nutritional health applications and cultivar selection.

A UNIVERSAL FINGERPRINTING SET FOR RED RASPBERRY

Red raspberry, Rubus idaeus L., is the most economically important fruit crop in the highly diverse Rubus subgenus Idaeobatus. This subgenus also includes black raspberry R. occidentalis L. The USDA-ARS National Clonal Germplasm Repository (Corvallis, Ore.), is responsible for preserving a Rubus collection of 1940 accessions that includes 370 red raspberry genotypes originating from 26 countries. These red raspberry clones are maintained as potted plants in screenhouses. Microsatellite or simple sequence repeat (SSR) markers can be used for rapid identity verification. The objective of this study was to develop a universal SSR fingerprinting set for establishing genetic profiles for red raspberry accessions and enabling comparison of genotypes between collections. We tested 24 SSRs for ease of scoring and polymorphism in 35 red raspberry accessions common to both the NCGR and the James Hutton Institute. Ten additional species genotypes with edible berries, including Rubus subsp. Rubus and R. trivialis Mich., the American black raspberry (R. occidentalis), purple raspberry (R. ×neglectus Peck) and two Asian black raspberry species (R. biflorus Buch.-Ham. ex Sm. and R. niveus Thunb.) were also examined. Six SSRs were easy to score, polymorphic, and mapped to five of the seven red raspberry linkage groups. They were amplified in two multiplexes and were successful in comparing fingerprints from eight red raspberry accessions at both genebanks. The fingerprinting set differentiated between the unique accessions. This protocol is recommended for scientists and industry for raspberry identity verification.

SSR FINGERPRINTING OF BLACK RASPBERRY CULTIVARS SHOWS DISCREPANCIES IN IDENTIFICATION

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars are noted for showing very few differences, and seedlings for a lack of segregation for important traits. Genetic fingerprinting using microsatellite, or simple sequence repeat (SSR) markers, can reliably identify unique clones and evaluate diversity in black raspberry cultivars. Twenty-one black raspberry cultivars were sampled from the USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. Black raspberry clones were also sampled from nurseries, grower’s fields, and other black raspberry breeding programs for comparison. These genotypes were compared using 18 polymorphic SSR primer pairs. The black raspberries 'Bristol,' 'Jewel,' and 'Mac Black' had consistent SSR fingerprints between sources. However, plants being sold as 'Black Hawk' and 'Cumberland' had the same fingerprint as 'Jewel'. Plants of 'Bristol', 'Cumberland', 'Munger', 'New Logan', 'Plum Farmer' and 'Shuttleworth' in the NCGR collection had identical fingerprints. Eleven unique SSR fingerprints were found among plants being grown or sold as ‘Munger’, though there was one predominant fingerprint for this cultivar. 'Allen' and 'John Robertson' were each represented by three different fingerprints from three different sources, and 'Earlysweet' and 'Jewel' had SSR alleles at multiple loci that cannot be explained by their reported pedigrees. While overall genetic diversity in black raspberry cultivars is low, discrepancies in the naming of clones appear to be widespread in commercial and research plantings. Future work in this area should focus on sampling additional independent sources of plant material and evaluating clones to determine the extent of performance differences. Further SSR development in black raspberry may be needed to fingerprint some unique clones.

DESICCATION TOLERANCE AND CRYOPRESERVATION OF IN VITRO GROWN BLUEBERRY AND CRANBERRY SHOOT TIPS

vitro grown shoot tips of two cranberry (Vaccinium macrocarpon) cultivars, Wilcox (PI 614079) and Franklin (PI 554998) and three blueberry (Vaccinium corymbosum) cultivars, Berkeley (PI 554883), O'Neal (PI 554944) and Brigitta Blue (PI 618166) from the tissue culture collections of the USDA-ARS National Clonal Germplasm Repository (NCGR), Corvallis, were tested for recovery from desiccation and following cryopreservation using three protocols. Cold acclimated, encapsulated and sucrose-pretreated blueberry cultivars were tolerant of desiccation under laminar flow of up to 7h while cranberry cultivars were very sensitive to drying by 3h. Cryopreservation screening followed 2 weeks of alternating-temperature cold acclimation. The three blueberry cultivars cryopreserved with the encapsulation-dehydration technique (ED) produced 83% to 92% regrowth. PVS2 vitrification (VIT) (33% to 87%) and controlled rate cooling (CC) (50% to 67%) were also successful for some blueberries. The cranberry cultivars had poor (5% to 37%) recovery with all three techniques and will require further study to improve recovery after desiccation and cryopreservation.

Microsatellites are Used to Examine Apple and Pear Identities and Genetic Relationships

Simple Sequence Repeat (SSR) markers developed in apple and pear were used to determine genetic relationships among heritage apple and pear cultivars from Portugal's Azore Islands, and to develop identity fingerprints for European and Asian pear accessions at the USDA–ARS National Clonal Germplasm Repository (NCGR). We used 11 SSR markers (six from apple and five from pear) to examine 18 heritage apple and 9 heritage pear cultivars from the Azores. Eight additional Portuguese and economically important cultivars of apple and eight of pear were used as standards. Cluster analysis separated the apple and pear accessions into two distinct groups. Among apple genotypes, 12 unique accessions and five groups of synonyms were identified, while, in pear, seven unique genotypes and three pairs of synonyms were found. None of the accessions obtained from the Azores corresponded to widely grown standard Portuguese apple or pear cultivars. To examine 144 NCGR pear accessions, we used nine polymorphic SSR loci that were developed from GenBank sequences. Cluster analysis identified five sets of synonyms (four in P. communis L. and one in P. ussuriensis Maxim.) and four pairs of homonyms (three in P. communis and one in P. pyrifolia Burm. f. Nakai), and confirmed three clonal sets. Morphological evaluations and additional SSR markers will be used to confirm these results, and to genetically document the identities of pear genotypes. SSR markers will greatly assist the management of ex situ pome fruit germplasm collections by helping to eliminate duplicate accessions and expanding the genetic diversity represented.

Chromosome counts in the Mentha collection at the USDA‐ARS National Clonal Germplasm Repository

SummaryChambers, H. L. & Hummer, K. E.: Chromosome counts in the Mentha collection at the USDA–ARS National Clonal Germplasm Repository. – Taxon 43: 423‐432. 1994. – ISSN 0040‐0262.The present chromosome number survey is based on the holdings of the National Clonal Germplasm Repository in Corvallis, which houses a world Mentha collection which includes most of the known taxa. The survey complements previously published counts and provides information about 73 accessions that are available to researchers. It includes chromosome counts for two accessions of M. australis, a previously uncounted Australian endemic, and accessions of M. japonica, M. diemenica, and M. cunninghamii, taxa with but one or a few published previous counts.