Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers

Abstract

Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. 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).

Revealing the genetic diversity of Sumbawa endemic horse using microsatellite-based DNA fingerprint

“…Similarity value was essential for clustering analysis for dendrogram construction (Wangiyana et al 2022). This systematic step has been used recently for genetic diversity studies based on microsatellite DNA fingerprinting (Driskill et al 2022;Fiore et al 2022). This research also applied microsatellite DNA fingerprinting to study horse population genetic diversity.…”

Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.)

“…It is imperative that farmers grow varieties that are true to type to maximize their economic value. However, as with several other clonally propagated crops (Akpertey et al, 2021; Bassil et al, 2020; de Wever et al, 2019; Dossett et al, 2012; Driskill et al, 2022; Durán et al, 2018; Montanari et al, 2020; Oraguzie et al, 2005; Zhang et al, 2006; Zurn et al, 2018), red raspberry suffers from clonal misidentification. Initially, red raspberry clonal identification was performed using morphological characteristics (Laurentin, 2009).…”

Diversity in genetic and downy mildew resistance among wild and mutagenized hops as revealed by single nucleotide polymorphisms and disease rating

“…The disease pressure in these humid climates, mainly by downy and powdery mildew diseases, decimated local hop production in eastern north America in the early 20th century (Morton 2013;Nova Scotia Hops Growers' Guide 2013), shifting the hop production to the pacific northwest of America (Hoerner 1933;Skotland and Johnson 1983). According to available literature, most of the current commercial hop cultivars in North America can be traced back to common ancestries involving Brewers Gold and Northern Brewers (Hampton et al 2001;Driskill et al 2022) and are mostly susceptible to common diseases of hops (Salmon and Ware 1931), highlighting their narrow genetic diversity (Patzak et al 2010). In the past decades, the genetic diversity of many crops have been broadened through artificially-induced mutagenesis, as performed in flax (Chantreau et al 2013;Fofana et al 2017), potato (Muth et al 2008;Somalraju et al 2018), tomato (Shikata et al 2015), and eggplant (Xi-ou et al 2017).…”

“…We anticipate that new induced allelic variants in some of these genes will lead to broader genetic diversity and DM-resistant phenotypes in hops. Whereas hop diversity using morpho-physiological characteristics (Small 1978;Hampton et al 2001), molecular phylogeny (Murakami et al 2006a(Murakami et al , 2006bBassil et al 2008;Howard et al 2011;Driskill et al 2022), and chemotaxonomy (Hampton et al 2002;McCallum et al 2019;Riccioni et al 2021) has been investigated at regional and global levels, to our current knowledge, no recent study addressed DM resistance in wild hops from the Canadian Maritimes, nor has an induced mutagenesis approach for increased genetic diversity been attempted. The objectives of the current study were to (i) generate EMS-mutagenized hops for increased genetic diversity and (ii) evaluate a subset of the mutagenized hop clones for DM resistance.…”