VacCAP produces a targeted capture genotyping platform for blueberry

Authors: Bassil, Nahla; DRISKILL, MANDIE - University Of Oregon; EDGER, PATRICK - Michigan State University; CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research; MONTANARI, SARA - New Zealand Institute Of Plant & Food Research; THOMPSON, SUSAN - New Zealand Institute Of Plant & Food Research; ESPLEY, RICHARD - New Zealand Institute Of Plant & Food Research; MUNOZ, PATRICIO - University Of Florida; BENEVENUTO, JULIANA - University Of Florida; ZHAO, DONGYAN - Cornell University; SHEEHAN, MOIRA - Cornell University; FENTIE, MOLLA - North Carolina State University; Rowland, Lisa; ASHRAFI, HAMID - North Carolina State University; MELMAIEE, KALPALATHA - Delaware State University; Babiker, Ebrahiem; OLMSTEAD, JAMES - Driscoll'S; GILBERT, JESSICA - Driscoll'S; KNISKERN, JOEL - Driscoll'S; WELLS, MICAH - Rapid Genomics; IORIZZO, MASSIMO - North Carolina State University

Submitted to: Acta Horticulturae
Publication Type: Abstract Only
Publication Acceptance Date: 1/29/2022
Publication Date: 8/15/2022
Citation: Bassil, N.V., Driskill, M., Edger, P., Chagne, D., Montanari, S., Thompson, S., Espley, R., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M., Fentie, M., Rowland, L.J., Ashrafi, H., Melmaiee, K., Babiker, E.M., Olmstead, J., Gilbert, J., Kniskern, J., Wells, M., Iorizzo, M. 2022. VacCAP produces a targeted capture genotyping platform for blueberry. Acta Horticulturae.

Interpretive Summary: The Vaccinium coordinated agricultural project (VacCAP) was funded in 2019 as a multi-institutional transdisciplinary project focused on enabling DNA-assisted breeding in blueberry and cranberry, with an emphasis on fruit quality traits. The objective of this study is to use a community approach to develop a genotyping platform for blueberry. After assessing current technologies, the Vaccinium research community selected a targeted genotyping platform, for cost effectiveness, flexibility, and ability to capture and generate needed DNA markers in the tetraploid blueberry. A set of 192 (156 from the VacCAP project; 36 from 10 community breeders) northern and southern highbush blueberries and breeding founders was chosen. The first phase consisted of genotyping this set with 50,000 markers distributed across the genome. We present the development and evaluation of this platform in the diversity set and the subsequent selection of 20,000 markers as a resource for genetic studies in the cultivated blueberry.

Technical Abstract: The Vaccinium coordinated agricultural project (VacCAP) was funded in 2019 as a multi-institutional transdisciplinary project focused on enabling marker-assisted selection in blueberry and cranberry, with an emphasis on fruit quality traits. The objective of this study is to use a community approach to develop a high throughput genotyping platform for blueberry. After assessing current technologies, the Vaccinium research community selected a targeted genotyping platform, Flex-Seq EX-L, for cost effectiveness, flexibility, ability to capture single nucleotide polymorphisms (SNPs), and generate genotype and haplotype data in the tetraploid blueberry. A diversity set of 192 (156 from the VacCAP project; 36 from 10 community breeders) northern and southern highbush blueberries and breeding founders was chosen. The first phase consisted of genotyping this set with 50,000 SNPs distributed across the genome. Core genes as well as regions associated with quantitative trait loci (QTL) provided by the blueberry community were prioritized. We present the development and evaluation of this 50K Flex Seq EX-L in the diversity set and the subsequent selection of a 20K genotyping platform as a resource for genome-wide association and other genetic studies for the blueberry community.