SNP Genotyping pushes modern breeding of hops for brewing and beyond
In hop cultivation, identifying female plants is crucial for efficient production. Traditionally, determining a plant’s sex has been a time consuming, extending breeding program by 1-2 years. A recent breakthrough from researchers from the National Clonal Germplasm Repository, OR and Forage Seed and Cereal Research Unit, WA of the USDA-ARS, in collaboration with the University of Minnesota and Hudson Alpha Institute for Biotechnology has generated a cost-effective and convenient SNP genotyping marker using PACE technology.
To develop this, Dr Shaun Clare, Dr Kayla Altendorf and colleagues collaborated to assemble a diverse collection of 765 hop genotypes and conducted Genome-Wide Association Studies (GWAS) on 20,681 bi-allelic SNPs. A highly significant SNP marker on the sex chromosome, accurately predicting sex with 96% accuracy, was discovered.
High-throughput SNP genotyping workflow
The teams combined a PACE SNP genotyping assay with targeted allele-specific primers, and a quick DNA extraction methodology for a rapid, high-throughput SNP genotyping workflow. Validation in a separate population achieved 96% accuracy in identifying male and female seedlings. Applied in the USDA-ARS hop breeding program, this marker increased the female-to-male seedling ratio by 25%, resulting in a 97.4% female yard in 2023.
This marker and methodology is widely applicable, requiring only standard molecular laboratory equipment, affordable reagents and saves time, labour, and space, enhancing breeding program planning and efficiency.
This new diagnostic, accurate, affordable, and scalable SNP genotyping marker, applied using PACE technology is a boost for hop breeding and showcases the efficacy of Marker-Assisted-Selection (MAS) techniques for hop breeding.
