Location: Horticultural Crops Production and Genetic Improvement Research Unit
2024 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 FY 2024 progress for project 2072-21000-060-000D, “Genetic Improvement of Blackberry, Red and Black Raspberry, Blueberry, and Strawberry", which started February 2023, and continues research from bridging project 2072-21000-058-000D, titled, "Genetic Improvement of Blackberry, Red and Black Raspberry, and Blueberry."
In support of Objective 1, the ARS raspberry and blackberry breeding program scientist has pursued research projects aimed at exploring and mapping the genetic basis of resistance to raspberry bushy dwarf virus (RBDV) and root lesion nematode (RLN) in red raspberry, and resistance to the large raspberry aphid vector of black raspberry necrotic virus (BRNV) in black raspberry. This included inoculation of diverse red raspberry genotypes with RBDV and RLN in both greenhouse and field environments to identify resistance and develop populations to genetically map the basis of resistance. Similarly in black raspberry, genetic mapping populations were developed and germinated as a basis to inoculate with large raspberry aphid, identify resistant phenotypes, and genetically map the source of genetic resistance. The raspberry and blackberry breeding program also performed sequencing of several important raspberry and blackberry genotypes to develop new reference genome assemblies for supporting global caneberry research efforts and to provide a research platform for genetically mapping traits in caneberry. The caneberry breeding program has also begun working with the USDA-funded Breeding Insight initiative to develop new genetic marker screening tools for blackberry, filling a critical need in this crop.
In support of Objective 2, the ARS 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 North Willamette Research and Extension Center (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. In partnership with Oregon State University and Ekland Marketing Company, the raspberry and blackberry breeding program has successfully moved recent cultivar releases including red raspberry 'Finnberry' and blackberries 'Celestial', 'Thunderhead', and 'Zodiac' to multiple new countries, including Egypt, France, Japan, Mexico, and New Zealand. The breeding program has also established new trial partnerships with multiple U.S. based companies for identifying new fresh and processing cultivars, including MBG Marketing (northern region), California Berry Genetics (western region), and Andros Foods. Progress toward research objectives in the blueberry breeding program has not occurred due to a critical vacancy preceding the most recent fiscal year.
Accomplishments
Review Publications
Hardigan, M.A., Feldmann, M.J., Carling, J., Zhu, A., Kilian, A., Famula, R.F., Cole, G.S., Knapp, S.J. 2023. A medium-density genotyping platform for cultivated strawberry using DArTag technology. The Plant Genome. 16(4). Article e20399. https://doi.org/10.1002/tpg2.20399.
Bassil, N.V., King, R., Peterson, M.E., Dossett, M., Hardigan, M.A. 2024. A black raspberry fingerprinting set identifies seedlings in two families. Acta Horticulturae. 1388:115-120. https://doi.org/10.17660/ActaHortic.2024.1388.16.
Clare, S.J., King, R., Hardigan, M.A., Dossett, M., Montanari, S., Chagne, D., Ochsenfeld, C., Britton, C., Rapp, R., Bassil, N.V. 2023. Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.). Plant Breeding. 142(6):798-808. https://doi.org/10.1111/pbr.13141.