AFLP fingerprinting in hop: analysis of the genetic variability of the Tettnang variety

Fleischer, Robert C.; Horlemann, C.; Schwekendiek, A.; Kling, C. I.; Weber, G.

doi:10.1023/b:gres.0000027052.72343.2d

Cited by 16 publications

(8 citation statements)

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“…Previous work in hop have focused upon the identification of male plants from a population of offspring [ 16 ] or genetic diversity and DNA fingerprinting using older marker technology such as STS, SSR, AFLP, RAPD and DArT [ 7 , 17 – 19 ]. In all publications, differentiation of accessions required the full compliment of markers used for defining genetic diversity in hop populations.…”

Section: Resultsmentioning

confidence: 99%

Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation

Henning¹,

Coggins²,

Peterson

2015

BMC Res Notes

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BackgroundHop is an economically important crop for the Pacific Northwest USA as well as other regions of the world. It is a perennial crop with rhizomatous or clonal propagation system for varietal distribution. A big concern for growers as well as brewers is variety purity and questions are regularly posed to public agencies concerning the availability of genotype testing. Current means for genotyping are based upon 25 microsatellites that provides relatively accurate genotyping but cannot always differentiate sister-lines. In addition, numerous PCR runs (25) are required to complete this process and only a few laboratories exist that perform this service. A genotyping protocol based upon SNPs would enable rapid accurate genotyping that can be assayed at any laboratory facility set up for SNP-based genotyping. The results of this study arose from a larger project designed for whole genome association studies upon the USDA-ARS hop germplasm collection consisting of approximately 116 distinct hop varieties and germplasm (female lines) from around the world.ResultsThe original dataset that arose from partial sequencing of 121 genotypes resulted in the identification of 374,829 SNPs using TASSEL-UNEAK pipeline. After filtering out genotypes with more than 50 % missing data (5 genotypes) and SNP markers with more than 20 % missing data, 32,206 highly filtered SNP markers across 116 genotypes were identified and considered for this study. Minor allele frequency (MAF) was calculated for each SNP and ranked according to the most informative to least informative. Only those markers without missing data across genotypes as well as 60 % or less heterozygous gamete calls were considered for further analysis. Genetic distances among individuals in the study were calculated using the marker with the highest MAF value, then by using a combination of the two markers with highest MAF values and so on. This process was reiterated until a set of markers was identified that allowed for all genotypes in the study to be genetically differentiated from each other. Next, we compared genetic matrices calculated from the minimal marker sets [(Table 2; 6-, 7-, 8-, 10- and 12-marker set matrices] and that of a matrix calculated from a set of markers with no missing data across all 116 samples (1006 SNP markers). The minimum number of markers required to meet both specifications was a set of 7-markers (Table 3). These seven SNPs were then aligned with a genome assembly, and DNA sequence both upstream and downstream were used to identify primer sequences that can be used to develop seven amplicons for high resolution melting curve PCR detection or other SNP-based PCR detection methods.ConclusionsThis study identifies a set of 7 SNP markers that may prove useful for the identification and validation of hop varieties and accessions. Variety validation of unknown samples assumes that the variety under question has been included a priori in a discovery panel. These results are based upon in silica studies and markers need to be validated using ...

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Section: Resultsmentioning

confidence: 99%

Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation

Henning¹,

Coggins²,

Peterson

2015

BMC Res Notes

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“…Only 3 out of 279 hop plants cvs. 'Tettnang' were found to be polymorphic using AFLPs (Fleischer et al, 2004) and only one presented variation that could be related to a somaclonal variation process. Despite the differences between asexual propagation in the field and in vitro conditions, the results presented in our work, together with data from field behavior, point to relatively high genetic stability of the asexually propagated hop.…”

Section: Article In Pressmentioning

confidence: 99%

Epigenetic changes detected in micropropagated hop plants

Peredo

Arroyo-García

Revilla

2009

Journal of Plant Physiology

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“…Další metodou, využívající neznámé sekvence, byl amplifikovaný délkový polymorfi smus fragmentů (AFLP), který kombinuje RFLP a PCR. 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).…”

Section: ■ 3 Genetické Metodyunclassified

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

Olšovská¹,

Krofta²,

Jandovská³

et al. 2016

Kvasny Prum

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■ 1 ÚVODAutenticita potravin je termín, který jednoduše označuje, zda potraviny nakupované spotřebitelem odpovídají jejich popisu, a je aktuálním tématem v nejrůznějších potravinářských komoditách. Proto je v současné době věnováno mnoho pozornosti a jsou vynakládány nemalé fi nanční prostředky na vývoj analytických metod pro ověřo-vání autenticity potravin, nápojů a jejich surovin.Také chmel je komodita, ve které dochází k falzifi kaci původu a odrůd, což může ve velké míře ovlivnit senzorický profi l piva z něho vyrobeného. Žatecký poloraný červeňák (ŽPČ) je na trhu všeobec-ně považován za světový standard kvality v kategorii aromatických chmelů. Prvotřídní kvalitě odpovídá i vyšší cena. V uplynulých letech bylo zaznamenáno několik opakovaných případů jeho falzifi kace. Falzifi kace Žateckého poloraného červeňáku ve formě granulí byla Recenzovaný článek / Reviewed Paper Olšovská, J., Krofta, K., Jandovská, V., Patzak, J., Štěrba, K., 2016: Metody pro ověřování autenticity chmele -účinný nástroj proti falzifi kaci. Kvasny Prum. 62, č. 10, s. 294-305 K pokusům o falzifi kaci dochází téměř u všech komodit a výjimkou není ani chmel. Je proto nezbytné hledat způsoby, jak ověřovat jeho autenticitu. Přehledový článek shrnuje moderní metody pro ověřování autenticity chmele a uvádí rovněž nejnovější výsledky spolupráce Výzkumného ústavu pivovarského a sladařského, a.s. a Chmelařského institutu, s.r.o., v Žatci. K ověřování autenticity chmele se používají metody chemotaxonomické a genetické. V roce 2015 byly provedeny chemické analýzy novošlechtěných hybridů pro České pivo (obsah a složení alfa a beta kyselin, obsah a složení chmelových silic, obsah celkových polyfenolů) a byly provedeny molekulárně-genetické analýzy 150 vybraných genotypů chmele ze světového sortimentu a šlechtitelského materiálu. Pomocí výsledků byl z testovaných genotypů sestaven přehledný dendrogram. Autoři se dále zabývali profi lováním českých odrůd chmele na základě chemických profi lů proanthokyanidinů a podařilo se jim pomocí klastrové analýzy jasně odlišit odrůdy chmele včetně jejich genetické příbuznosti.Olšovská, J., Krofta, K., Jandovská, V., Patzak, J., Štěrba, K., 2016: Methods for verifying the authenticity of hops -an effective tool against falsifi cation. Kvasny Prum. 62, No. 10, pp. 294-305Falsifi cation attempts occur in almost all commodities and hops is no exception. It is therefore necessary to look for ways to verify its authenticity. This review summarizes modern methods for verifying the authenticity of hops and also provides the latest results of the collaboration of the Research Institute of Brewing and Malting, PLC. and the Hop Research Institute, Ltd., in Žatec. Chemotaxonomic and genetic methods are used to verify the authenticity of hops. Chemical analyzes of newly bred hybrids potentially suitable for Czech beer focused on the content and composition of alpha and beta acids, content and composition of hop oils, and content of total polyphenols were performed and molecular genetic analyses of 150 selected hop genotypes in...

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AFLP fingerprinting in hop: analysis of the genetic variability of the Tettnang variety

Cited by 16 publications

References 16 publications

Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation

Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation

Epigenetic changes detected in micropropagated hop plants

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

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