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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #403358

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

Location: National Clonal Germplasm Repository

Title: A breeder-friendly PACE assay to identify male and female hops

item Clare, Shaun
item King, Ryan
item Tawril, Anna
item Olatoye, Olalere
item Bassil, Nahla
item Altendorf, Kayla

Submitted to: HortScience
Publication Type: Abstract Only
Publication Acceptance Date: 5/3/2023
Publication Date: 8/3/2023
Citation: Clare, S.J., King, R., Tawril, A., Olatoye, O.M., Bassil, N.V., Altendorf, K.R. 2023. A breeder-friendly PACE assay to identify male and female hops. HortScience.

Interpretive Summary:

Technical Abstract: Hop (Humulus lupulus L.) is a dioecious species where the female plant is cultivated for its cones that provide bitterness, flavor, and aroma for the brewing industry. Male plants only serve to generate new crosses within breeding programs. Breeding programs are interested in a fast and cost-effective DNA assay that can identify male and female seedlings to prevent subsequent time-consuming and resource-intensive evaluations. The objective of this study was to identify single nucleotide polymorphism(s) (SNPs) associated with sex in hops and develop a breeder-friendly assay that can be used in marker assisted selection (MAS). Association mapping was conducted in 855 individuals consisting of 632 females and 223 males, using 20,861 bi-allelic SNPs obtained through genotyping by sequencing. The BLINK model identified a single SNP marker at LOD score of 174.26 on the sex chromosome of hops after alignment to the ‘Cascade’ reference genome. A PCR Allele Competitive Extension (PACE) assay was developed and resulted in clearly defined clusters for 30 males and 64 females from 15 independent breeding populations. This PACE marker had an accuracy of 96% correctly identifying 80/83 samples that were amplified. A rapid DNA extraction protocol that generates crude DNA in less than an hour was subsequently developed, and resulted in accurate clustering of males and females. This diagnostic marker is an excellent tool for MAS that is accurate, affordable, convenient and highly scalable to the size of any breeding program.