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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #411375
Research Project: Conservation and Utilization of Temperate-Adapted Fruit, Nut, and Other Specialty Crop Genetic Resources

Location: National Clonal Germplasm Repository

Title: Overview of single nucleotide polymorphism markers in blueberry and their uses

Author
item Bassil, Nahla
item ZHAO, DONGYAN - Cornell University
item MUNOZ, PATRICIO - University Of Florida
item SHEEHAN, MOIRA - Cornell University
item IORIZZO, MASSIMO - North Carolina State University

Submitted to: International Vaccinium Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 6/1/2024
Publication Date: 8/24/2024
Citation: Bassil, N.V., Zhao, D., Munoz, P., Sheehan, M., Iorizzo, M. 2024. Overview of single nucleotide polymorphism markers in blueberry and their uses. International Vaccinium Symposium.

Interpretive Summary:

Technical Abstract: DNA-based markers have been used in blueberry since the early nineties. However, they were either dominant, expensive to use, or assayed a single locus or a limited number of regions. Single nucleotide polymorphisms are the most abundant markers in all organisms including blueberry and are amenable to automation. In blueberry, they are available as low, medium, and high-density markers. This review aims to present an overview of the available SNP markers and their uses in blueberry. Since most cultivated blueberries are autotetraploid, estimating allele dosage is needed for accurate genotyping and categorization of the three heterozygous genotypes. Low-density markers are being developed using the kompetitive allele-specific PCR (KASP™) method for cultivar identification and for marker-assisted selection of simple traits. The Breeding Insight initiative recently developed a medium-density 3,000 loci DArTag (Diversity Array Technology – DArT) platform as a targeted amplicon sequence-based approach. It appears to be a cost-effective method for implementing genomic selection in breeding programs. High-density SNP markers were generated through genotyping by sequencing (GBS) and target capture using Capture-Seq (Rapid Genomics LLC) or the 22K Flex-Seq (LGC Genomics). These high-density approaches have been used for the analysis of genetic diversity, linkage mapping, quantitative trait analysis, genome-wide association, and identity confirmation. The formation of a genotyping consortium coordinated through the VacCAP project has decreased the genotyping cost of the Flex-Seq high-density genotyping platform allowing its widespread use in over 10 breeding programs so far. A choice of SNP-based platforms is finally available in blueberry and is expected to provide blueberry industries, scientists, and breeders with tools to assist in advancing genetic discoveries and the development of cultivars with desired traits.