Two DNA-based fingerprinting sets for hops

Authors: Driskill, Mandie; Hummer, Kim; ZURN, JASON - Kansas State University; AMUNDSEN, KEENAN - University Of Nebraska; WILES, ANNETTE - Midwest Hop Producers; WIEDOW, CLAUDIA - Plant And Food Research; JAKSE, JERNEJ - University Of Ljubljana; Henning, John; Bassil, Nahla

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/12/2021
Publication Date: 1/18/2022
Citation: Driskill, M.J., Hummer, K.E., Zurn, J., Amundsen, K., Wiles, A., Wiedow, C., Jakse, J., Henning, J.A., Bassil, N.V. 2022. Two DNA-based fingerprinting sets for hops. Abstract for 65th Annual American Hop Convention; 1/18/21-1/22/21; Virtual.

Interpretive Summary: Cultivated hops are derived from the European hop, though other subspecies have contributed to breeding genepools. Breeding programs at the USDA-ARS Forage Seed and Cereal Research Unit as well as the USDA-ARS National Clonal Germplasm Repository maintain hop collections that are vegetatively propagated and used to create new varieties that meet industry needs. Accurate and economic DNA-based tools to confirm cultivar identity are needed for breeding and germplasm management and for hop identification in nurseries or grower fields. Our objective was to develop two fingerprinting sets from different marker systems: one based on tandemly repeated DNA sequences (referred to as simple sequence repeat, SSR); and the other one based on variations at a single nucleotide base (referred to as single nucleotide polymorphism, SNP). The 9-SSR set was used to genotype 629 hop samples that included cultivated and wild accessions. Parentage and sibling relationship analyses were used to identify true-to-type cultivars. One of the 9-SSRs generated two male- and eight female- specific alleles among cultivated and wild North American (WNA) samples, possibly enabling marker assisted selection for gender. The SNP assay consisted of 25 markers. Comparison of marker assays across 190 hop accessions demonstrated that both systems distinguished unique genotypes of the cultivated European hop accessions while only the 25 SNP assay was unable to differentiate WNA accessions. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the SNP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96). Both sets are useful tools for identity certification in hops.

Technical Abstract: Cultivated hops are derived from the European hop, Humulus lupulus L., though other subspecies have contributed to breeding genepools. Breeding programs at the USDA-ARS Forage Seed and Cereal Research Unit as well as the USDA-ARS National Clonal Germplasm Repository maintain hop collections that are vegetatively propagated and used to create new varieties that meet industry needs. Accurate and economic DNA-based tools to confirm cultivar identity are needed for breeding and germplasm management and for hop identification in nurseries or grower fields. Our objective was to develop two fingerprinting sets: a simple sequence repeat (SSR)-based one; and a kompetitive allele specific PCR (KASP) assay of single nucleotide polymorphisms (SNPs). The 9-SSR set was used to genotype 629 hop samples that included cultivated and wild accessions. Parentage and sibship analyses were used to identify true-to-type cultivars. One SSR, HI-AGA7, generated two male and eight female specific alleles among cultivated and wild North American (WNA) samples. Clustering separated accessions into WNA and cultivated groups. The KASP assay consisted of 25 marker loci. Comparison of marker assays across 190 hop accessions demonstrated that both systems distinguished unique genotypes of the cultivated European hop accessions while KASP was unable to differentiate WNA accessions. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96). Both sets are useful tools for identity certification in hops.