High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

Abstract

Implementation of molecular methods in hop (Humulus lupulus L.) breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. However, use of molecular marker technology is limited due to expense, time inefficiency, laborious methodology and dependence on DNA sequence information. Diversity arrays technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of quality polymorphic markers without reliance on DNA sequence information. This study is the first to utilise DArT for hop genotyping, identifying 730 polymorphic markers from 92 hop accessions. The marker quality was high and similar to the quality of DArT markers previously generated for other species; although percentage polymorphism and polymorphism information content (PIC) were lower than in previous studies deploying other marker systems in hop. Genetic relationships in hop illustrated by DArT in this study coincide with knowledge generated using alternate methods. Several statistical analyses separated the hop accessions into genetically differentiated North American and European groupings, with hybrids between the two groups clearly distinguishable. Levels of genetic diversity were similar in the North American and European groups, but higher in the hybrid group. The markers produced from this time and cost-efficient genotyping tool will be a valuable resource for numerous applications in hop breeding and genetics studies, such as mapping, marker-assisted selection, genetic identity testing, guidance in the maintenance of genetic diversity and the directed breeding of superior cultivars.

Construction of integrated linkage map of a recombinant inbred line population of white lupin (<i>Lupinus albus</i> L.)

“…The average reproducibility of all the DArT markers was 98.6% which was similar to that obtained in barley (99.8%) (Wenzl et al 2004), hop (100%) (Howard et al 2011) and pigeonpea (99.7%). Call rate being 90.9% and which expresses the reliability of the final scores versus the maximum number of potential scores, was similar to sugarcane (92.5%) (Heller-Uszynska et al 2010) and banana (91.6%) (Risterucci et al 2009) was slightly lower than barley (95.0%) (Wenzl et al 2004), wheat (99.2%) (Akbari et al 2006), pigeonpea (96.0%) (Yang et al 2006) and hop (97.6%) (Howard et al 2011).…”

“…Call rate being 90.9% and which expresses the reliability of the final scores versus the maximum number of potential scores, was similar to sugarcane (92.5%) (Heller-Uszynska et al 2010) and banana (91.6%) (Risterucci et al 2009) was slightly lower than barley (95.0%) (Wenzl et al 2004), wheat (99.2%) (Akbari et al 2006), pigeonpea (96.0%) (Yang et al 2006) and hop (97.6%) (Howard et al 2011). The P value here was 86.8%, which agreed with the values obtained in hop (89.9%) (Howard et al 2011) and was slightly higher compared to banana (81.4%) and sugarcane (80.7%) (Heller-Uszynska et al 2010). …”

Quantitative genetic parameters for yield, plant growth and cone chemical traits in hop (Humulus lupulus L.)

“…Studies which have examined the genetic diversity of hop have determined two primary genetic groupings: European and North American [53-61]. The genotypes used in previous hop studies [24,26,27,31] were largely of European genetic origin and from a relatively narrow genetic base.…”

Methods for verifying the authenticity of hops - an effective tool against falsification

“…It was found to be more sensitive for genotyping of hops (Hartl and Seefelder, 1998;Seefelder et al, 2000;Townsend et al, 2000;Jakše et al, 2001;Patzak, 2001;2002;Fleisher et al, 2004;Townsend and Henning, 2009;Reeves and Richards, 2011;Solberg et al, 2014) and could detect also somaclonal variability (Patzak, 2003;Peredo et al, 2006;. Unknown sequences in molecular hybridization system have also been used in Diversity Arrays Technology (DArT) method (Howard et al, 2011) but better identifi cation and determination of hop cultivars is achieved when using DNA sequence specifi c methods such as the previously mentioned STS methods in structural genes (Patzak et al, 2007;Bassil et al, 2008;Castro et al, 2008;Venger et al, 2015). Microsatellite nucleotide (di-or tri-) repeats are the most useful for molecular genetic analysis of variability and evaluation of biodiversity in different plant zeny nové molekulární markery typu jednoduchých sekvenčních repetic v exprimovaných sekvenčních úsecích (EST-SSR) (Patzak a Matoušek, 2011;Jakše et al, 2011;Koelling et al, 2012;Singh et al, 2012) a jedno-nukleotidového polymorfi smu (SNP) (Matthews et al, 2013;Yamauchi et al, 2014;Henning et al, 2015).…”

“…Je citlivější pro genotypizaci chmele (Hartl a Seefelder, 1998;Seefelder et al, 2000;Townsend et al, 2000;Jakše et al, 2001;Patzak, 2001;2002;Fleischer et al, 2004;Townsend a Henning, 2009;Reeves a Richards, 2011;Solberg et al, 2014) a dokáže detekovat též somaklonální variabilitu (Patzak, 2003;Peredo et al, 2006;. Neznámé sekvence v systému molekulární hybridizace byly využity v technologii rozlišovacích čipů (DArT) (Howard et al, 2011). Ale lepší pro identifi kaci a determinaci chmelových odrůd je využít DNA specifi cké sekvenční metody, jako již zmíněnou metodu STS pro strukturní geny (Patzak et al, 2007;Bassil et al, 2008;Castro et al, 2008;Venger et al, 2015).…”