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United States Department of Agriculture

Agricultural Research Service

Research Project: Physiology and Genetic Improvement of Small Fruit Crops

Location: Horticultural Crops Research

2013 Annual Report

1a. Objectives (from AD-416):
Objective 1: Enhance genetic resources for small fruit crops via germplasm acquisition, evaluation, and breeding. Objective 2: Working with plant breeders of berry crops, develop plants free of known viruses for field evaluation and release of enhanced germplasm. Objective 3: Sequence viruses associated with blueberry necrotic ringblotch and blueberry mosaic diseases for use in the development of diagnostic tools. Objective 4: Determine the utility of the recently discovered aphid resistance in black raspberry for reducing virus spread in the field.

1b. Approach (from AD-416):
Studies will be conducted to collect and evaluate germplasm from wild and domesticated small fruits and incorporate it into advanced breeding material for development of new cultivars with traits ideally adapted for commercial production. Key determinants of resistance, tolerance, and susceptibility to environmental constraints will also be ascertained and utilized for selection of new genotypes and for development of new cultural practices better suited to production of the crops. Anticipated products of the research will include: new cultivars of blackberry, blueberry, raspberry, and strawberry; new small fruit germplasm with improved and novel traits; knowledge of the availability and distribution of genetic variability in small fruit species; greater understanding of physiological mechanisms governing the response of small fruit crops to various abiotic and biotic stresses; and new cultural practices and management systems for small fruit crops that result in higher yield and fruit quality, efficient water and nutrient use, and lower environmental impact. Formerly 5358-21000-036-00D (3/08).

3. Progress Report:
This is the final report for this project which was terminated on March 20, 2013 and replaced by the new project, 5358-21220-002-00D, "Genetic Improvement and Virus Management of Small Fruit Crops". For additional information, see the new project report. We successfully conducted a breeding program in blackberry, red and black raspberry, strawberry, and blueberry. Patent applications were prepared and submitted for 'Charm' and 'Sweet Sunrise' strawberries and 'Columbia Star' blackberry. Our ongoing germplasm project with black raspberry (Rubus occidentalis) that began with the collection of germplasm in the Midwestern and southern U.S. has led to the identification of sources of aphid resistance that should impart resistance to Black raspberry necrosis virus. Anthocyanins and phenolics were determined for this germplasm in collaboration with an ARS scientist in Parma, Idaho. In an SCRI blueberry project coordinated by the USDA-ARS, PSI, we phenotyped a population that will be genotyped for developing marker assisted breeding in blueberry. In our SCRI funded RosBreed project, we are working on the potential for marker assisted breeding in strawberry by merging phenotyping and genotyping information. We developed a phenotyping protocol for 37 fruiting and vegetative traits to be measured at 5 locations across the US. We used this protocol to evaluate 800+ genotypes at our location for two years. A virus associated with Blueberry necrotic blotch disease in southern highbush blueberry in Georgia was characterized. Determine the role of several viruses on plant growth, fruit yield and quality of berry crops.

4. Accomplishments
1. Sequenced genome of Blueberry necrotic ring blotch virus. A new disease developed in the southeastern U.S. since 2006, initially in one location in Georgia and by the end of 2011, blueberries in the entire southeast quadrant of the U.S. were exhibiting symptoms. The symptoms start out as necrotic rings with green centers that expand and can coalesce such that much of the leaf becomes necrotic and eventually can lead to defoliation. ARS scientists in Corvallis, Oregon, with collaborators in North Carolina, Georgia, Florida, Mississippi and Arkansas collected diseased tissue, extracted double-stranded RNA and used it as a template to clone and sequence the virus. The genome has been compared to other viruses in the GenBank database and proposed to represent a new virus genus. Primers specific to the virus were developed, screened against an array of 60 isolates and used in development of plant material so that nurseries can provide plants free of this virus.

2. Sequenced virus associated with Blueberry mosaic disease. Blueberry mosaic, a well known disease of blueberry with unknown etiology, has been characterized by isolating double-stranded RNA from diseased plants. ARS scientist in Corvallis, Oregon in collaboration with colleagues in Arkansas, Michigan, New Jersey, Slovenia and Japan, have reverse transcribed the dsRNA to cDNA; amplified and then subjected to high throughput sequencing, we obtained the genomes of two viruses. One, Blueberry latent virus, had been characterized previously, whereas the second represented a new type of virus infecting blueberry, an Ophiovirus. The coat protein and RNA dependent RNA polymerase were amplified by RT-PCR from 25 isolates, then cloned and sequenced. Additional isolates from the northeastern and Midwestern U.S., Europe and Japan are being analyzed to examine virus diversity. Detection primers based on 20 isolates are being used to ensure this virus is not present in material for certification programs.

3. New thornless blackberry. ARS researchers at Corvallis, Oregon, developed submitted for patent (S.N. 13/815,074) and released 'Columbia Star' thornless trailing blackberry for the commercial blackberry industry. The industry standard 'Black Diamond' is outstanding for the growers but lacks outstanding fruit quality and the second industry standard 'Marion' is thorny and soft, but has excellent flavor and processing quality. 'Columbia Star' is thornless, high yielding and has superior fruit quality as a processed and fresh marketed fruit. Every plant that was available (over 40,000) this past spring were purchased and the nurseries are working hard to meet next years demands.

4. Root rot in strawberry. ARS Researchers in Corvallis, Oregon, determined that the marker-trait association between an identified genetic marker for strawberry root rot resistance and actual root rot resistance was 84%. Genetic markers for root rot tolerance had been identified but they had not been validated in populations of plants exposed to phytophthora root rot. Genotypes that are part of the USDA-NIFA, SCRI RosBREED project were screened by collaborators with Agriculture and Agrifoods Canada (NS) for their response to the disease and each was screened for the presence of the marker. The marker should have an excellent ability to identify resistance to phytophthora root rot without having to use the time consuming and labor intensive bench screening trials to identify strawberries that are resistant.

Review Publications
Martin, R.R., Polashock, J.J., Tzanetakis, I.E. 2012. New and emerging viruses of blueberry and cranberry. Viruses. 4(11):2831-2852.

Finn, C.E., Retamales, J.B., Lobos, G.A., Hancock, J. 2013. The Chilean strawberry (Fragaria chiloensis): Over 1000 years of domestication. HortScience. 48:418-421.

Last Modified: 06/27/2017
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