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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #403367

Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: VacCAP develops high throughput genotyping platforms for blueberry and cranberry

item Bassil, Nahla
item Clare, Shaun
item DRISKILL, MANDIE - Fall Creek Farm And Nursery
item ZHENG, PING - Washington State University
item CHAGNE, DAVID - Plant And Food Research
item MONTANARI, SARA - Plant And Food Research
item THOMPSON, SUSAN - Plant And Food Research
item ESPLEY, RICHARD - Plant And Food Research
item MUNOZ, PATRICIO - University Of Florida
item BENEVENUTO, JULIANA - University Of Florida
item ZHAO, DONGYAN - Cornell University
item SHEEHAN, MOIRA - Cornell University
item MENGIST, MOLLA - North Carolina State University
item Rowland, Lisa
item ASHRAFI, HAMID - North Carolina State University
item MELMAIEE, KALPALATHA - Delaware State University
item Babiker, Ebrahiem
item OLMSTEAD, JAMES - Driscolls
item GILBERT, JESSICA - Driscolls
item KNISKERN, JOEL - Driscolls
item MAIN, DORRIE - Washington State University
item Zalapa, Juan
item Polashock, James
item EDGER, PATRICK - Michigan State University
item IORIZZO, MASSIMO - North Carolina State University

Submitted to: HortScience
Publication Type: Abstract Only
Publication Acceptance Date: 5/3/2023
Publication Date: 8/3/2023
Citation: Bassil, N.V., Clare, S.J., Driskill, M., Zheng, P., Chagne, D., Montanari, S., Thompson, S., Espley, R., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M., Mengist, M., Rowland, L.J., Ashrafi, H., Melmaiee, K., Babiker, E.M., Olmstead, J., Gilbert, J., Kniskern, J., Main, D., Zalapa, J.E., Polashock, J.J., Edger, P., Iorizzo, M. 2023. VacCAP develops high throughput genotyping platforms for blueberry and cranberry. HortScience.

Interpretive Summary:

Technical Abstract: The Vaccinium Coordinated Agricultural Project (VacCAP) was funded in 2018 as a multi-institutional transdisciplinary project focused on advancing genomic resources and breeding tools for blueberry and cranberry, emphasizing fruit quality traits. One objective of the project is to leverage newly developed pangenomes of both blueberry and cranberry to design high-throughput genotyping platforms for these two crops that are optimized for high-resolution genetic studies. After assessing current technologies, the Vaccinium research and breeding community selected a targeted genotyping platform, Flex-Seq EX-L, for its cost-effectiveness, flexibility, efficiency to capture single nucleotide polymorphisms (SNPs), and ability to generate genotype and haplotype data in the tetraploid blueberry and diploid cranberry. A diverse set of 192 cultivars, wild accessions, and breeding founders was chosen for each of these two crops. Following SNP detection, 50,000 genome-distributed loci were screened in these diversity sets. Conserved core genes identified in the pangenomes, as well as regions associated with quantitative trait loci (QTL) provided by each crop community, were prioritized. We will present the development and evaluation of these Flex Seq EX-L (22K in blueberry and 17K in cranberry) in the diversity set. These high throughput platforms are valuable resources for genome-wide association and other genetic studies for the blueberry and cranberry communities.