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Clare SJ, King RM, Tawril AL, Havill JS, Muehlbauer GJ, Carey SB, Harkess A, Bassil N, Altendorf KR. An affordable and convenient diagnostic marker to identify male and female hop plants. G3 (BETHESDA, MD.) 2023; 14:jkad216. [PMID: 37963231 PMCID: PMC10755173 DOI: 10.1093/g3journal/jkad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/11/2023] [Indexed: 11/16/2023]
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.
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Affiliation(s)
- Shaun J Clare
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Ryan M King
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Anna L Tawril
- Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA
| | - Joshua S Havill
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St.Paul, MN 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St.Paul, MN 55108, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Nahla Bassil
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Kayla R Altendorf
- Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA
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Havill JS, Richardson BJ, Rohwer CL, Gent DH, Henning JA, Muehlbauer GJ. Identification of quantitative trait loci associated with R1-mediated resistance to powdery mildew and sex determination in hop (Humulus lupulus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:154. [PMID: 37318664 DOI: 10.1007/s00122-023-04399-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
KEY MESSAGE Two QTL were identified using linkage mapping approaches, one on hop linkage group 3 (qHl_Chr3.PMR1) associated with powdery mildew resistance and a second on linkage group 10 (cqHl_ChrX.SDR1) associated with sex determination. Hop (Humulus lupulus L.) is a dioecious species cultivated for use in beer. Hop powdery mildew, caused by Podosphaera macularis, is a constraint in many growing regions. Thus, identifying markers associated with powdery mildew resistance and sex provides the opportunity to pyramid R-genes and select female plants as seedlings, respectively. Our objectives were to characterize the genetic basis of R1-mediated resistance in the cultivar Zenith which provides resistance to pathogen races in the US, identify quantitative trait loci (QTL) associated with R1 and sex, and develop markers for molecular breeding-based approaches. Phenotypic evaluation of the population indicated that R1-based resistance and sex are inherited monogenically. We constructed a genetic map using 1339 single nucleotide polymorphisms (SNPs) based upon genotype-by-sequencing of 128 F1 progeny derived from a Zenith × USDA 21058M biparental population. SNPs were assigned to 10 linkage groups comprising a map length of 1204.97 cM with an average density of 0.94 cM/marker. Quantitative trait locus mapping identified qHl_Chr3.PMR1, associated with R1 on linkage group 3 (LOD = 23.57, R2 = 57.2%), and cqHl_ChrX.SDR1, associated with sex on linkage group 10 (LOD = 5.42, R2 = 25.0%). Kompetitive allele-specific PCR (KASP) assays were developed for both QTL and assessed against diverse germplasm. Our results indicate that KASP markers associated with R1 may be limited to materials that are pedigree-related to Zenith, whereas markers associated with sex may be transferable across populations. The high-density map, QTL, and associated KASP markers will enable selecting for sex and R1-mediated resistance in hop.
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Affiliation(s)
- Joshua S Havill
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Briana J Richardson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Charlie L Rohwer
- Southern Research and Outreach Center, University of Minnesota, Waseca, MN, 56093, USA
| | - David H Gent
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
- Forage Seed and Cereal Research Unit, USA Department of Agriculture - Agricultural Research Service, Corvallis, OR, 97331, USA
| | - John A Henning
- Forage Seed and Cereal Research Unit, USA Department of Agriculture - Agricultural Research Service, Corvallis, OR, 97331, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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