Molecular characterization of caneberries, strawberries, pear, mint and hops at the Corvallis genebank

Authors: Bassil, Nahla; Zurn, Jason; Hummer, Kim; Hardigan, Michael; KNAPP, STEVEN - University Of California, Davis; MONTANARI, SARA - University Of California, Davis; Postman, Joseph; WORTHINGTON, MARGARET - University Of Arkansas; CLARK, JOHN - University Of Arkansas; ASHRAFI, HAMID - North Carolina State University; ARYAL, RISHI - North Carolina State University; DOSSETT, MICHAEL - British Columbia Blueberry Council; Finn, Chad; Driskill, Mandie; MULCH, CHRISTINA - Oregon State University; VINING, KELLY - Oregon State University; RAPP, RYAN - Pairwise; OCHSENFELD, CHERIE - Pairwise; ZHANG, XIAOYU - Pairwise; POORTEN, TOM - Pairwise; PHAM, GINA - Pairwise

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/28/2020
Publication Date: 8/9/2020
Citation: Bassil, N.V., Zurn, J.D., Hummer, K.E., Hardigan, M.A., Knapp, S.J., Montanari, S., Postman, J.D., Worthington, M., Clark, J.R., Ashrafi, H., Aryal, R., Dossett, M., Finn, C.E., Driskill, M.J., Mulch, C., Vining, K.J., Rapp, R., Ochsenfeld, C., Zhang, X., Poorten, T., Pham, G. 2020. Molecular characterization of caneberries, strawberries, pear, mint and hops at the Corvallis genebank. Abstract for American Society for Horticultural Science Conference, August 9-13, 2020, Orlando, FL

Interpretive Summary: The USDA-ARS National Clonal Germplasm Repository preserves genetic resources of many temperate clonal crops. Notable amoung these are strawberries, blackberries, raspberries, pears, mint, and hops. Advancements in molecular tools for these crops have allowed researchers to answer questions surounding diversity and relatedness. Research using these new tools to identify offspring parent relationships, characterize the genetic diversity of the collections, and identify genes for horticulturally important traits are presented.

Technical Abstract: The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, was dedicated in 1981 to preserve genetic resources of temperate clonal crops. The collections are comprised of 13,007 accessions representing 73 genera, including Fragaria, Rubus, Pyrus, Mentha, and Humulus. Fingerprinting panels of multiplexed, long–core simple sequence repeats (SSRs) are typically used for identity confirmation and genebank management in blackberry, strawberry, pear, mint, and hops. Recent advancements in genomic resources and technologies for these genera are currently being applied at the NCGR to better characterize each collection. The objective of this presentation is to provide an overview of our current efforts in molecular characterization of these valuable resources. A 50 K Axiom array that shares single nucleotide polymorphisms (SNPs) with the IStraw35 K was recently developed for strawberries. The 534 F. ×ananassa accessions were genotyped to assess diversity and establish two core collections. The pear collection was genotyped with the 70 K Axiom array, which resulted in identification of 54 sets of previously unknown duplicates, and in inferred parentage in heritage cultivars. The sources of primocane fruiting and thornlessness in eastern blackberries are being sequenced, and 30× sequence coverage was generated from 620 Rubus accessions in a private-public collaboration with Pairwise, the USDA, North Carolina State University, Cornell and University of Arkansas for genome wide association study (GWAS) analysis. In red and black raspberries, a rhAMPSeq panel of 1,000 SNP and SSR targets is being developed for identity confirmation. Additionally, we are focusing on fine-mapping aphid resistance from three black raspberry sources, and we continue to use one high-resolution melting marker annually to identify aphid resistant seedlings in the USDA-Corvallis breeding program. As described, molecular characterization of genetic resources at the NCGR is a collaborative effort with breeders, researchers, and stakeholders and utilizes numerous genomic techniques to enable better characterization and utilization of the collections.