Location: Horticultural Crops Production and Genetic Improvement Research Unit
2022 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.
Objective 2: Breed improved blueberry, blackberry, and raspberry cultivars for the commercial fruit industry including high yielding, virus tolerant, high-quality fruits for the fresh and processing markets.
Approach
For each crop, a modified recurrent mass selection system will be used. Individuals that are selected in a given generation will be intercrossed to produce the next generation. For Rubus spp. and strawberry 4000-6000 seedlings, and 2500-4000 blueberry seedlings from 30-100 crosses will be evaluated annually. Approximately 0.5 to 1.0% of the seedlings are selected based on subjectively evaluated fruit quality, plant performance, ripening period, and yield. Frozen samples will be evaluated for processing characteristics. Selections identified as being superior will be propagated for commercial trial and release. For nursery production, the ARS virology program in Corvallis, OR will help produce virus-tested propagation material. To broaden the germplasm base, superior individuals or representatives of superior populations of small fruit species will be crossed among themselves or with advanced selections or cultivars. Selections from these crosses will be used in our breeding program and distributed to other breeders. Emphasis will be on aphid resistance, disease resistance, fruit quality, thornlessness and tolerance to abiotic stresses associated with growing these crops in regions with more diverse climates.
This program collaborates with molecular geneticists in efforts to bridge the gap between genomics and applied plant breeding in berry crops. Our program helps to determine the mapping populations to develop or genotypes to include and how the various phenotypic traits (phenological, reproductive, and vegetative) will be evaluated. The phenotyping for each project is being coordinated across multiple locations with different climatic conditions. For raspberry leaf curl disease, suspect raspberry samples will be collected and their virome analyzed using Next Generation Sequencing. This approach will also be used to examine two novel diseases of grapevines in Oregon. Diagnostic assays will be developed and used for epidemiology studies, certification and quarantine purposes. Virus vectors will be identified and strategies for vector control developed as a means to manage virus diseases. Total genomic sequencing of five Rubus cultivars will be used to determine if the inserted RYNV sequences represent full-length or partial RYNV and if all insertions are at the same site. If the RYNV insertions are at the same site in each of these cultivars it would indicate that the insertion may have happened once and been passed on in breeding programs. Several approaches will be tested for applying gene silencing as a tool to eliminate viruses from growing points of plants (meristematic dome and several leaf primordia): 1. Virus specific dsRNA will be produced and provided to plants in tissue culture as an additive to the media; 2. dsRNA will be attached to positively charged clay nanoparticles and sprayed on plants in tissue culture or growth chambers; and 3. RBDV infected plants will be grafted onto transgenic plants (already developed red raspberry) that are producing RNAi silencing of RBDV. Meristems will be collected at various times after treatments, plants regenerated and tested for RBDV.
Progress Report
Breeding program activity was somewhat below typical levels leading into fiscal year (FY) 2022 due to COVID-19, the departure of the former plant breeder, and both new scientists (plant breeders) being hired shortly before FY22. Virology research did not continue in FY22 due to the retirement of the former virologist and transfer of the new virologist from this project to project 2072-22000-043-000D due to a Program Adjustment Decision Item (PADI). In FY22, the ARS scientists focused heavily on outreach, germplasm maintenance, and restoring breeding program activity to its previous operational capacity.
In support of Objective 1, the breeding programs resumed pre-COVID-19 operations in FY22 that included making new plant crosses, germinating new seedling populations, and evaluating advanced selections for commercially important horticultural and fruit quality traits. The breeding programs are now operating again at full capacity, are continuing to engage with stakeholders through commission meetings and industry reports and are continuing to distribute clean plant material of cultivars and promising new advanced selections to nurseries and grower-cooperators by working with the National Clean Plant Network. The breeding program continued its historic cooperation with Oregon State University (OSU) to host on-farm trials of advanced breeding lines at the OSU North Willamette Research and Extension Center (OSU-NWREC). The breeders established multiple new Material Transfer Agreements (MTAs) to support propagation of advanced breeding lines in U.S. nurseries and subsequent commercial trials to identify new potential cultivars. Substantial commercial plantings of the most recent trailing blackberry release, ‘Columbia Star’, have recently been established in Oregon over the last several years. Invention disclosures and patent applications were submitted for four new Rubus cultivars in FY22, with patents currently pending for a new thornless trailing blackberry for the Pacific Northwest (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’).
In support of Objective 2, the breeding programs resumed pre-COVID-19 breeding activities in FY22 that included screening small fruit germplasm with genetic diversity incorporated from diverse wild species materials, development of genetic markers to study important horticultural traits in these crops, and application of genetic marker technologies. The raspberry breeding program made selections and evaluated germplasm containing wild introgressions from native Rubus idaeus, R. parvifolius, R. coreanus, and R. innominatus. The blackberry breeding program made selections and evaluated germplasm containing wild introgressions from R. georgicus or R. caucasicus. The blueberry breeding program made selections and evaluated germplasm based on crosses using parents that showed greater resistance to infection from blueberry shock virus (BlShV). The strawberry breeding program made selections and evaluated germplasm containing introgressions from day-neutral California varieties to introduce the day-neutral flowering trait into Oregon varieties. Prior to FY22, the previous plant breeder actively mined wild germplasm diversity, both housed at the ARS Corvallis, Oregon, germplasm repository, and from germplasm collection expeditions to broaden the genetic diversity and adaptive potential of the small fruit breeding programs. During FY22, the new plant breeders actively engaged in collaborative research projects involving the development and deployment of genetic marker technologies for small fruit crops. These activities included: developing 3K and 5K genetic marker panels with Diversity Arrays Technology (DArT) for the USDA-ARS Breeding Insight initiative that are suitable for performance in octoploid strawberries; participating in the testing of database tools, phenotype collection software, and genetic marker technologies developed for blueberry and strawberry by the Breeding Insight team; collaborating with the Vaccinium Coordinated Agriculture Project (VacCAP) team for blueberry; developing genetic markers for polyploid blackberries; and developing a genetic marker fingerprinting panel for red raspberry. Prior to FY22, the previous plant breeder worked with geneticists at ARS Corvallis, Oregon, to develop genetic markers for black raspberry that are capable of prediction for aphid resistance, and these markers were deployed for making aphid-resistant black raspberry seedling selections in FY22.
Accomplishments
1. Development of FaRR1, a gold-standard, chromosome-scale reference genome of a day-neutral octoploid strawberry. Molecular breeding and genetics research in strawberry (Fragaria x ananassa) was historically hampered by the complex allo-octoploid genome of this important horticultural crop species. This prevented the accurate design and development of subgenome-targeting molecular markers, analysis of underlying gene content and functions, and assessment of haplotype structure, all of which are core aspects of modern plant genetics. In collaboration with the public strawberry breeding program at the University of California, Davis, an ARS researcher at Corvallis, Oregon, used cutting edge sequencing and assembly tools to develop a new, "gold-standard" genome assembly of the day-neutral strawberry cultivar, 'UCD Royal Royce', called FaRR1. As demonstration of the achievement and the dramatically improved quality of the FaRR1 assembly over previous octoploid genomes, FaRR1 contains multiple pseudomolecules representing entire chromosomes in a single contiguous sequence without gaps of sequence information, and each of the pseudomolecules is 100% phased to represent the complete haplotype diversity of both parental chromosome complements. The FaRR1 assembly represents the closest approximation of octoploid strawberry chromosomes as they exist in an actual plant cell nucleus to-date, has been made publicly available, and has already been used for development of new molecular marker platforms to support public strawberry research.
2. Release of new and improved blackberry and raspberry cultivars for the Pacific Northwest processing industry and global fresh market. The Pacific Northwest and broader global fresh markets require improved small fruit cultivars to support the nutritional needs of consumers, as well as for processed food products. ARS researchers at Corvallis, Oregon, and collaborators from Oregon State University and Washington State University, have patents pending for four new cultivars of blackberry and raspberry. 'Zodiac' is a thornless trailing blackberry for the Pacific Northwest processing market that is machine harvestable and produces highly uniform and attractive berries with excellent shape, color, firmness, and a pleasant sweet and aromatic flavor. 'Celestial' is a thornless semi-erect blackberry for the U.S. and global fresh markets that contains a combination of Pacific Northwest and eastern species genetics, produces tremendous yields of fruit with excellent flavor and post-harvest quality, and is expected to eventually replace current semi-erect blackberry yield standards such as ‘Chester’. 'Thunderhead' is the first-ever primocane-fruiting blackberry variety to be released by the USDA, with yields that easily exceed currently available primocane-fruiting blackberry varieties, as well as superior flavor and fruit quality with smaller seeds and reduced bitterness. 'Finnberry' is a primocane-fruiting raspberry and is a highly unique cultivar that produces tremendous yields of bright-colored fruit with excellent tart flavor and good firmness to support shipping to fresh markets.
3. Development of 3K and 5K high-throughput, low-cost genetic marker panels for strawberry and Breeding Insight initiative. The USDA-ARS funded Breeding Insight initiative and public strawberry breeding programs in the United States and worldwide have been searching for a low-cost, high-throughput and turn-key solution for genotyping in octoploid strawberry. This has been a major hurdle for the implementation of new molecular breeding methods such as genomic selection and prediction. Development of genetic and genomic tools for strawberry is particularly difficult due to its highly complex polyploid genome, which contains four ancestrally-related subgenomes in a single crop. Leveraging polyploid bioinformatics expertise and prior collaborations with the public breeding program at the University of California, Davis, ARS researchers in Corvallis, Oregon, developed new 3K and 5K panels of genetic markers able to target the specific subgenomes in octoploid strawberry, and which can be accessed by any public research program through the company, Diversity Arrays Technology. These genetic marker panels suit the requirements of the Breeding Insight group in seeking to bring access to genetic tools to underserved ARS crops and will help make low-cost and high-accuracy DNA marker screening in strawberry a reality.
Review Publications
Petrasch, S., Mesquida-Pesci, S.D., Pincot, D.D., Feldmann, M.J., Lopez, C.M., Famula, R., Hardigan, M.A., Cole, G.S., Knapp, S.J., Blanco-Ulate, B. 2021. Genomic prediction of strawberry resistance to post-harvest fruit decay caused by the fungal pathogen Botrytis cinerea. G3, Genes/Genomes/Genetics. 12(1). Article jkab378. https://doi.org/10.1093/g3journal/jkab378.
Bird, K.A., Hardigan, M.A., Ragsdale, A.P., Knapp, S.J., VanBuren, R., Edger, P.P. 2021. Diversification, spread, and admixture of octoploid strawberry in the western hemisphere. American Journal of Botany. 108(11):2269-2281. https://doi.org/10.1002/ajb2.1776.
Stockwell, V.O., Shaffer, B.T., McGhee, G., Hardigan, M.A. 2022. First report of Gnomoniopsis idaeicola causing cane wilt and canker in commercial blackberry fields in Oregon. Plant Disease. 106(7):1980. https://doi.org/10.1094/PDIS-11-21-2397-PDN.
Edger, P.P., Iorizzo, M., Bassil, N.V., Benevenuto, J., Ferrao, L.F., Giongo, L., Hummer, K.E., Lawas, L.F., Leisner, C.P., Li, C., Munoz, P., Ashrafi, H., Atucha, A., Babiker, E.M., Canales, E., Chagne, D., DeVetter, L., Ehlenfeldt, M.K., Espley, R.V., Gallardo, K., Gunther, C.S., Hardigan, M.A., Hulse-Kemp, A.M., Jacobs, M.L., Lila, M., Luby, C.H., Main, D., Mengist, M.F., Owens, G.L., Perkins-Veazie, P., Polashock, J.J., Pottorff, M., Rowland, L.J., Sims, C.A., Song, G., Spencer, J., Vorsa, N., Yocca, A.E., Zalapa, J.E. 2022. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Horticulture Research. 9. Article uhac083. https://doi.org/10.1093/hr/uhac083.
Pincot, D.D., Feldmann, M.J., Hardigan, M.A., Vachev, M.V., Henry, P.M., Gordon, T.R., Bjornson, M., Rodriguez, A., Cobo, N., Famula, R., Cole, G.S., Coaker, G.L., Knapp, S.J. 2022. Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. Theoretical and Applied Genetics. 135:2121-2145. https://doi.org/10.1007/s00122-022-04102-2.
