An affordable and convenient diagnostic marker to identify male and female hop plants

Shaun J. Clare, Ryan M. King, Anna L. Tawril, Joshua S. Havill, Gary J. Muehlbauer, Sarah B. Carey, Alex Harkess, Nahla Bassil, Kayla R. Altendorf

Research output: Contribution to journalArticlepeer-review

Abstract

Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.

Original languageEnglish (US)
Article numberjkad216
JournalG3: Genes, Genomes, Genetics
Volume14
Issue number1
DOIs
StatePublished - Jan 2024

Bibliographical note

Publisher Copyright:
© The Author(s) 2023.

Keywords

  • Humulus lupulus
  • association mapping
  • diagnostic marker
  • hops
  • sex determination

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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