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Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers
Mandie Driskill1, Katie Pardee1, Kim E Hummer1
1USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America.
Plos One
|April 14, 2022
Summary
Developing DNA fingerprinting tools like SSR and KASP assays is crucial for verifying hop (Humulus lupulus L.) clonal identity and conserving genetic resources. These methods accurately confirm identity and parentage, essential for hop breeding programs.
Area of Science:
- Plant genetics
- Horticultural science
- Molecular biology
Background:
- Clonal identity verification is vital for conserving hop (Humulus lupulus L.) genetic resources.
- Morphological observations are insufficient for reliable identity and parentage determination in dioecious hop.
- Accurate and economical DNA-based tools are needed for hop germplasm management.
Purpose of the Study:
- To develop and compare two DNA fingerprinting sets for hop: a 9-SSR assay and a 25-SNP KASP assay.
- To assess the utility of these assays for clonal identity confirmation, parentage analysis, and population structure studies in hop.
- To evaluate the cost-efficiency and applicability of each assay for different genotyping scales.
Main Methods:
- Development of a 9-locus Simple Sequence Repeat (SSR) fingerprinting set with a sex-linked marker (HI-AGA7).
- Development of a 25-Single Nucleotide Polymorphism (SNP) Kompetitive Allele Specific PCR (KASP) assay.
- Genotyping of 629 hop accessions from diverse US collections using the SSR set.
- Comparative analysis of SSR and KASP assays on 190 accessions for identity, diversity, and population structure.
Main Results:
- The 9-SSR set identified unique genotypes for most accessions, revealing 89 sets of synonyms (e.g., different cultivar names for the same clone).
- SSR and KASP assays confirmed clonal identity and parentage, with SSRs distinguishing wild North American (WNA) and cultivated groups.
- The HI-AGA7 marker identified sex-specific alleles, aiding in genetic analysis.
- KASP assays were less effective in distinguishing WNA samples and showed lower diversity estimates compared to SSRs.
Conclusions:
- Both 9-SSR and KASP fingerprinting sets are valuable tools for hop identity confirmation and parentage analysis.
- The 9-SSR assay is cost-effective for smaller-scale genotyping (<96 samples) of wild and cultivated hop.
- The KASP assay is suitable for large-scale genotyping (multiples of 96) of cultivated hop due to its ease of interpretation and cost-efficiency.
