Two new Flex-Seq-EX-L high throughput genotyping platforms for blueberry and cranberry

Authors: Bassil, Nahla; Clare, Shaun

Submitted to: World Wide Web
Publication Type: Other
Publication Acceptance Date: 1/3/2023
Publication Date: 1/26/2023
Citation: Bassil, N.V., Clare, S.J. 2023. Two new Flex-Seq-EX-L high throughput genotyping platforms for blueberry and cranberry. World Wide Web.

Interpretive Summary: The Vaccinium coordinated agricultural project (VacCAP) was funded in 2018 as a multi-institutional transdisciplinary project focused on advancing genomic resources and breeding tools in blueberry and cranberry, with an emphasis on fruit quality traits. One objective of the project is to leverage newly developed pangenomes of both blueberry and cranberry to design high-throughput genotyping tools for these two crops. After assessing current technologies, the Vaccinium research and breeding community selected a targeted genotyping platform, for cost effectiveness, flexibility, ability to capture genetic variant markers in the tetraploid blueberry and diploid cranberry. In each of these two crops, a diversity set of 192 cultivars, wild accessions, and breeding founders was chosen. Following SNP detection, 50,000 genome-distributed loci were screened in this diversity set. Conserved core genes identified in the pangenomes, as well as regions associated with traits of economic importance by each crop community were prioritized. We will present the development and evaluation of these tools (22K in blueberry and 17K in cranberry) in their respective 192-member diversity set. These two high throughput platforms are valuable resources for genetic studies for the blueberry and cranberry communities.

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 in blueberry and cranberry, with an emphasis on 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. The pangenome consists of core genes, those shared by all cultivars, and auxiliary genes, genes unique to only a subset of cultivars. Auxiliary genes are highly enriched with functions associated with important adaptive traits (e.g. disease resistance, abiotic stress tolerance, etc) and superior fruit quality characteristics (e.g. metabolites associated with aroma and taste). After assessing current technologies, the Vaccinium research and breeding 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 and diploid cranberry. In each of these two crops, a diversity set of 192 cultivars, wild accessions, and breeding founders was chosen. Following SNP detection, 50,000 genome-distributed loci were screened in this diversity set. 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 their respective 192-member diversity set. These two high throughput platforms are valuable resources for genome-wide association and other genetic studies for the blueberry and cranberry communities.