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 Horticultural Crops Production and Genetic Improvement Research Unit: Corvallis, OR
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ARS Home Pacific West Area Corvallis, Oregon Horticultural Crops Production and Genetic Improvement Research Unit Research





- Hardigan, Michael
- 2023
- Publications
- Plant Genetic Resources, Genomics and Genetic Improvement (301)
- Plant Diseases (303)

Research Project: Genetic Improvement of Blackberry, Red and Black Raspberry, and Blueberry **Location:
                            Horticultural Crops Production and Genetic Improvement Research Unit** 2023 Annual Report **Objectives**
                                

Objective 1: Characterize important genetic traits in blueberry, blackberry, and raspberry to improve selection efficiency and identify novel sources of genetic resistance to disease.
Sub-objective 1.A: Screen germplasm for useful horticultural traits, climate adaptation, and disease resistance and incorporate into breeding populations. 

Sub-objective 1.B: Develop and implement molecular breeding tools for genetic mapping, DNA fingerprinting, genome-wide association studies, and assessment of population genetic diversity. 

Objective 2: Breed improved blueberry, blackberry, and raspberry cultivars for the commercial small fruit industry including high yielding, virus tolerant, high-quality fruits for the fresh and processing markets. **Approach**
                                

Objective 1: Blueberry Shock Virus & Luteovirus – We will test 139 advanced breeding lines from our breeding program, 19 check cultivars at OSU-NWREC & 301 Vaccinium accessions at the NCGR in Corvallis, OR. We will perform phenotypic evaluation of shock by counting the number of canes per blueberry plant showing the characteristic symptoms of defoliation, flower necrosis, & cane die-back.  
Blueberry Genomic Prediction using the Breeding Insight Platform – We will screen PNW highbush blueberry populations housed in the USDA-ARS breeding program for fruit quality related traits including size, firmness, sugars, acidity, & seasonality-related traits including bloom & ripening dates. We will use genetic marker platforms developed by the Breeding Insight project to test accuracy of genomic prediction of quality & seasonality traits. 
Red Raspberry Resistance to Raspberry Bushy Dwarf Virus – We will assemble a diversity panel of 50 historic wild & cultivated red raspberry accessions at NCGR to screen for RBDV resistance. The accessions used for RBDV screening will support a bulk-segregant analysis approach for physical mapping based on SNP frequencies in resistant & susceptible bulk pools. The NCGR accessions will be sequenced to 30x coverage on an Illumina HiSeq & sequences will be used to perform alignments & variant calling against the R. occidentalis V3 genome assembly. The bi-parental mapping population used for RBDV screening will be used for genetic mapping to validate the locus identified by bulk-segregant analysis. 
Genomic Prediction of Red Raspberry Resistance to Root Lesion Nematode (RLN) – We will clonally replicate a population of 275 raspberry genotypes from various breeding programs. Nematode resistance will be measured as the difference between sample means for biomass accumulation & RLN density in non-inoculated & inoculated replicates. We will implement GWAS & genomic prediction using phenotype data from the RLN experiment. 
Black Raspberry Resistance to Large Raspberry Aphid – We will generate black raspberry mapping populations consisting of full-sib families segregating for sources of A. agathonica resistance. We will physically map the sources of aphid resistance & develop source-specific DNA markers. 
Linkage Mapping of Hexaploid Blackberry – We will attempt genetic mapping of a hexaploid blackberry using a ‘Columbia Star’ x ‘Black Pearl’ F1 population segregating for the ‘Lincoln Logan’ source of thornlessness. 

Objective 2: We will use conventional & marker-assisted breeding strategies to increase beneficial alleles & reduce the frequency of wild or deleterious alleles in the various outcrossing, clonally propagated small fruit crops. New hybrid families are tested annually & stepwise evaluations will be used to cull thousands of seedlings down to a handful. We employ a form of phenotypic recurrent selection in which selections from one generation serve as the parents for the next generation & elite individuals with valuable traits demonstrated combining ability may be used again in subsequent years. We will build on conventional breeding approaches by implementing marker-assisted selection & genomic prediction. **Progress Report**
                                

This report documents fiscal year (FY) 2023 progress for project 2072-21000-060-000D, “Genetic Improvement of Blackberry, Red and Black Raspberry, and Blueberry”, which started February 11, 2023, and continues research from project 2072-21000-058-000D.

In support of Objective 1, the breeding programs initiated and continued ongoing projects aimed at screening diverse germplasm for sources of commercial traits, climate adaptation, and pest resistance, while generating molecular marker data to investigate the underlying genetics of these traits. The caneberry breeding program developed new black raspberry populations segregating for resistance to the large raspberry aphid vector of black raspberry necrotic virus (BRNV). The caneberry program assembled and propagated over 50 diverse red raspberry accessions to screen for resistance to raspberry bushy dwarf virus (RBDV). The caneberry program also generated the first set of genomic single nucleotide polymorphisms (SNPs) for a trailing blackberry breeding population and used these to design a marker genotyping panel for blackberries while assisting in the development and validation of a set of molecular markers for DNA fingerprinting of red raspberry germplasm housed in ARS genebanks. The blueberry breeding program continued its ongoing collaborations with the Vaccinium Coordinated Agriculture Project (VacCAP) and Breeding Insights working groups to collect phenotype data related to plant development and fruit quality and generated molecular marker datasets to support genome-wide association studies (GWAS) and genomic prediction for these traits. The blueberry program screened diverse breeding material for susceptibility to shock virus and the new luteovirus, as well as heat tolerance traits for climate resilience. New 3K and 5K strawberry genetic marker panels were developed with Diversity Arrays Technology (DArT) for the USDA-ARS Breeding Insight initiative and were validated and submitted for publication to support future USDA-ARS as well as public and private breeding research for implementing genomic prediction in strawberry.

In support of Objective 2, the breeding programs continued efforts toward development of new and improved small fruit cultivars for the Pacific Northwest (PNW) and broader U.S. industry. This included making new plant crosses, germinating new seedling populations, and evaluating advanced selections for commercially important horticultural and fruit quality traits in trials at the Oregon State University (OSU) North Willamette Research and Extension Center (OSU-NWREC). The breeding programs engaged with stakeholders through commission meetings, field days, and industry reports and continued distributing clean plant material of cultivars and promising new advanced selections to nurseries and grower-cooperators by working with the National Clean Plant Network. The breeders established multiple new Material Transfer Agreements (MTAs) to support propagation of advanced breeding lines in U.S. nurseries and commercial grower trials to identify new potential cultivars. The most recent trailing blackberry release, ‘Columbia Star’, continues to see significant acreage planted in the PNW. The four new caneberry cultivars for which patent applications were submitted in FY 2022 have each received patent approval in FY 2023 and licensing agreements were established between the USDA and Oregon State University for each cultivar. These included a thornless trailing blackberry for the PNW processing industry (tent. ‘Zodiac’), a thornless semi-erect blackberry for the U.S. and global fresh market (tent. ‘Celestial’), a primocane-fruiting blackberry for the U.S. and global fresh market (tent. ‘Thunderhead’), and a primocane-fruiting red raspberry for the U.S. and global fresh market (tent. ‘Finnberry’). Each of the new cultivars has been sub-licensed for propagation by at least one domestic nursery and they are being planted into commercial trials in the United States and abroad. ‘Finnberry’ and ‘Thunderhead’ are being licensed for international propagation and commercial production. **Accomplishments**
                                

1. Four new caneberry cultivars released. ARS researchers in Corvallis, Oregon, developed new and improved cultivars of blackberry and raspberry for commercialization. ‘Zodiac’ is a thornless and machine harvestable trailing blackberry for the Pacific Northwest (PNW) processing industry. ‘Celestial’ is the first thornless and machine harvestable semi-erect blackberry with good fruit quality for both the fresh and processed markets. ‘Thunderhead’ is the first-ever primocane-fruiting blackberry released by the USDA for the fresh market. ‘Finnberry’ is a primocane-fruiting red raspberry with improved yields and shipping traits for the U.S. and global fresh market. The cultivars have been licensed for commercialization in the United States and abroad and will support the commercial small fruit industry with higher yielding varieties with better fruit quality. 2. Low-cost molecular marker panels for strawberry breeding released. Molecular breeding of strawberry is difficult due to its octoploid genome. Developing a low-cost and scalable marker genotyping solution for strawberry is an objective of the USDA Breeding Insights initiative and research community. ARS researchers in Corvallis, Oregon, designed molecular marker assays to target specific strawberry subgenomes for better ease of use by breeders. The markers have since been validated, submitted for publication, and the ARS researchers and collaborators at University of California, Davis, have made the platforms available for use by USDA, public, and private researchers through Diversity Arrays Technology (DArT). The platforms will make genomic prediction and DNA fingerprinting significantly more affordable for small fruit research programs. 3. Low-cost DNA fingerprinting panels for verification of plant identities released. Validation of genetic identity and parentage is a major challenge for clonally propagated small fruit crops, including red raspberry. A low-cost and reproducible panel of molecular markers was needed to support validation of identities for USDA gene banks and breeding programs. ARS researchers in Corvallis, Oregon, used sequencing data to identify candidate single nucleotide polymorphisms capturing the genomic diversity of raspberry germplasm. These were converted to a panel of Kompetitive Allele Specific polymerase chain reaction assays. The assays were validated for their ability to establish unique fingerprints for a wide range of accessions and selections found in USDA gene banks and the breeding program in Corvallis, Oregon, and will give both scientists and nurseries confidence in the identities of the plants they request. 4. Unique anthocyanins from subtropical Vaccinium. Anthocyanins are natural pigments found in blueberries which may contain health benefits. Concentrations of different anthocyanins may differ among cultivars and wild populations. ARS researchers in Corvallis, Oregon, and researchers at Oregon State University analyzed anthocyanins in domesticated blueberry and subtropical Vaccinium species that have not been used in breeding. They showed the subtropical species contain unique anthocyanin profiles that were not present in domesticated North American germplasm. This finding highlighted new potential uses of untapped blueberry species for breeding programs and could lead to new cultivars with improved health benefits. This paper was given the UP Hedrick Journal of American Pomological Society 2023 best paper award.


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