Project : USDA ARS

ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Research Project #434229

Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

2021 Annual Report

Accomplishments
1. Anthocyanins in wild relatives of strawberry (Fragaria L.). ARS scientists in Corvallis, Oregon, worked with researchers at Oregon State University and Plant Resources Center in Hanoi, Vietnam, to determine the total anthocyanin content and profiles in ripe fruit of nine strawberry species and one out-group, Potentilla indica L. Anthocyanin profiles were obtained using high-performance liquid chromatograph (HPLC). Red-fruited samples had varying amounts of typical strawberry anthocyanins but in varying proportions. White-fruited types contained the three compounds in much lower quantities and different proportions. Evaluation of anthocyanins in wild species will inform breeders of fruit quality for broadening crosses to increase the gene pool. In 2017, the United States produced 1.6 billion pounds of strawberries valued at nearly $4.5 billion.

2. Genetic diversity in the cultivated strawberry (Fragaria ×ananassa) collection at the NCGR. ARS scientists in Corvallis, Oregon, genotyped 539 of 560 cultivated strawberry accessions in the national USDA collection. Clustering analysis using 4,033 markers revealed eight sub-populations associated with different geographic breeding centers. Two 100 accession core collections were determined: one represented a uniform distribution of the gene space, and the other its maximum genetic diversity. Pedigree linkages were also confirmed in the collection. Accessions containing disease resistance associated genes for anthracnose fruit rot, Colletotrichum crown rot, charcoal rot, and Phytophthora crown rot were also identified. These new core collections will allow for breeders and researchers to more efficiently utilize the F. ×ananassa collection in developing new cultivars with desired traits.

3. Evaluated genotype x environment interactions for predicting sweetness in strawberry. Strawberry fruit flavor is due to a complex mix of sugars, acids, and aromatic compounds. The majority of strawberry soluble solids are sugars, and soluble solid content (SSC) is used as a proxy to determine sweetness and has been a target for breeders. A strong genotype × environment (G × E) interaction has been observed for SSC, causing difficulties when studying the genetics underlying SSC in individual environments. In this study, ARS scientists in Corvallis, Oregon, collected genotypic and SSC phenotypic data for 2,064 individuals from seven breeding programs (located in the United States, Spain, United Kingdom, and Australia). Population structure analysis of the 2,064 accessions revealed that populations were clustered into two large groups consisting primarily of subtropical or temperate strawberry accessions. Three models for these subpopulation categories were developed and assessed for their ability to improve prediction accuracy in the presence of population structure. Of the approaches investigated, two were found to have the highest prediction accuracy for SSC. The approaches investigated in this study will provide new insights for the practical implementation of genomic selection in strawberry improvement programs.

4. Berberis hypoxantha C.Y. Wu ex S.Y. Bao (Berberidaceae), a new record for Vietnamese flora. ARS scientists from Corvallis, Oregon, collaborated with scientists in Vietnam and the United Kingdom concerning the identification of a unique barberry species (Berberis hypoxantha) in Lao Cai, Vietnam. This shrub was first observed on Fansipan Mountain during a USDA-sponsored plant exploration expedition in 2015. This high elevation evergreen species has yellow flowers and reduced prickles as compared with other species of the genus. Barberry, known as a hardy garden shrub in the United States, has about 500 species distributed throughout the world. Some species are also valued for their edible berries for culinary and traditional medicinal applications. This is the first report for this endemic species in Vietnam.

5. Developed two hop fingerprinting sets and used them to genotype hop collections. ARS scientists from Corvallis, Oregon, developed two fingerprinting sets for hop: a 9-SSR fingerprinting set and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set was used to genotype 629 hop accessions from collections kept by USDA and University of Nebraska-Lincoln. It identified unique genotypes except for 89 sets of synonymous samples. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Parentage and sibship analyses were used to identify true-to-type cultivars. The SSR fingerprinting set distinguished cultivars, selections, and WNA accessions, while the KASP assays were unable to distinguish the WNA samples. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop.

U.S. DEPARTMENT OF AGRICULTURE

National Clonal Germplasm Repository: Corvallis, OR