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- Title
An affordable and convenient diagnostic marker to identify male and female hop plants.
- Authors
Clare, Shaun J; King, Ryan M; Tawril, Anna L; Havill, Joshua S; Muehlbauer, Gary J; Carey, Sarah B; Harkess, Alex; Bassil, Nahla; Altendorf, Kayla R
- 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.
- Subjects
WESTERN Australia; UNITED States. Dept. of Agriculture; HOPS; MALE sterility in plants; SEX chromosomes; GENOME-wide association studies; GENETIC markers; SEX determination
- Publication
G3: Genes | Genomes | Genetics, 2024, Vol 14, Issue 1, p1
- ISSN
2160-1836
- Publication type
Article
- DOI
10.1093/g3journal/jkad216