1
|
Somalraju A, Soto-Cerda B, Ghose K, McCallum J, Knox R, Fofana B. Structure and genetic diversity of Canadian Maritimes wild hops. Genome 2024; 67:24-30. [PMID: 37738664 DOI: 10.1139/gen-2023-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Studies on the northeastern American native hops (Humulus lupulus ssp. lupuloides) from the Canadian Maritimes are scarce. This study aimed to evaluate the genetic structure and diversity among 25 wild-collected hops from three Canadian Maritime provinces using microsatellite (simple sequence repeat (SSR)) markers. Based on 43 SSR markers, four distinct subgroups were found, with a low molecular variance (19%) between subgroups and a high variance (81%) within subgroups. The Nei's unbiased genetic distance between clusters ranged from 0.01 to 0.08, the genetic distance between clusters 2 and 3 being the farthest and that between clusters 1 and 2 the closest. Cluster 2 captured the highest overall diversity. A total of 18 SSR markers clearly discriminated hop clones by detecting putative subspecies-specific haplotypes, differentiating clones of native-wild H. lupulus ssp. lupuloides from the naturalized old and modern hop cultivars. Seven of the 18 SSR markers also differentiated two clones from the same site from one another. The study is the first, using molecular markers, to identify SSR markers with potential for intellectual property protection in Canadian Maritimes hops. The SSR markers herein used can be prime tools for hop breeders and growers in the region.
Collapse
Affiliation(s)
- Ashok Somalraju
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE C1A 4N6, Canada
| | - Braulio Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Temuco, Chile
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Kaushik Ghose
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
| | - Jason McCallum
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE C1A 4N6, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE C1A 4N6, Canada
| |
Collapse
|
2
|
Driskill M, Pardee K, Hummer KE, Zurn JD, Amundsen K, Wiles A, Wiedow C, Patzak J, Henning JA, Bassil NV. Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PLoS One 2022; 17:e0257746. [PMID: 35421090 PMCID: PMC9009645 DOI: 10.1371/journal.pone.0257746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/06/2022] [Indexed: 11/18/2022] Open
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).
Collapse
Affiliation(s)
- Mandie Driskill
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Katie Pardee
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Kim E. Hummer
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Jason D. Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Keenan Amundsen
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Annette Wiles
- Midwest Hops Producers, Plattsmouth, Nebraska, United States of America
| | - Claudia Wiedow
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Josef Patzak
- Hop Research Institute, Co, Ltd., Žatec, Czech Republic
| | - John A. Henning
- USDA-ARS, Forage Seed and Cereal Research Unit, Corvallis, Oregon, United States of America
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
- * E-mail:
| |
Collapse
|
3
|
Čerenak A, Kolenc Z, Sehur P, Whittock SP, Koutoulis A, Beatson R, Buck E, Javornik B, Škof S, Jakše J. New Male Specific Markers for Hop and Application in Breeding Program. Sci Rep 2019; 9:14223. [PMID: 31578340 PMCID: PMC6775077 DOI: 10.1038/s41598-019-50400-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 09/06/2019] [Indexed: 11/26/2022] Open
Abstract
Male specific DNA sequences were selected from a Diversity Arrays Technology (DArT) mapping study to evaluate their suitability for determination of the sex phenotype among young seedlings in a hop (Humulus lupulus L.) breeding program. Ten male specific DArT markers showed complete linkage with male sex phenotype in three crossing families. Following optimization, four were successfully converted into PCR markers and a multiplex PCR approach for their use was developed. Among 197 plants (97 from the world collection; 100 from three segregating families), 94-100% positive correlation with sex phenotypic data was achieved for the single PCR amplification, whereas the multiplex approach showed 100% correlation. To develop a fast and low-cost method, crude sample multiplex PCR was evaluated in 253 progenies from 14 segregating populations without losing accuracy. The study describes, for the first time, the routine application of molecular markers linked to male sex in an intensive Slovenian hop breeding program. The methods described could be employed for screening of sex at the seedling stage in other hop programs worldwide, thereby saving resources for desirable female plants.
Collapse
Affiliation(s)
- Andreja Čerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310, Žalec, Slovenia.
| | - Zala Kolenc
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310, Žalec, Slovenia
| | - Petra Sehur
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310, Žalec, Slovenia
| | - Simon P Whittock
- Hop Products Australia, 446 Elizabeth Street Hobart, Tasmania & School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, Australia
| | - Anthony Koutoulis
- University of Tasmania, School of Natural Sciences, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Ron Beatson
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Emily Buck
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Branka Javornik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Suzana Škof
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Jernej Jakše
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| |
Collapse
|
4
|
Van Holle A, Muylle H, Ruttink T, Van Landschoot A, Haesaert G, Naudts D, De Keukeleire D, Roldán-Ruiz I. Single Nucleotide Polymorphisms and Biochemical Markers As Complementary Tools To Characterize Hops ( Humulus lupulus L.) in Brewing Practice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3761-3771. [PMID: 30896165 DOI: 10.1021/acs.jafc.9b00816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In brewing practice, the use of the appropriate hop variety is essential to produce consistent and high-quality beers. Yet, hop batches of the same variety cultivated in different geographical regions can display significant biochemical differences, resulting in specific taste- and aroma-related characteristics in beer. In this study, we illustrate the complementarity of genetic and biochemical fingerprinting methods to fully characterize hop batches. Using genotyping-by-sequencing (GBS), a set of 1 830 polymorphic single nucleotide polymorphism (SNP) markers generated 48 unique genetic fingerprints for a collection of 56 commercial hop varieties. Three groups of varieties, consisting of somaclonal variants, could not be further differentiated using this set of markers. Biochemical marker information offered added value to characterize hop samples from a given variety grown at different geographical locations. We demonstrate the power of combining genetic and biochemical fingerprints for quality control of hop batches in the brewing industry.
Collapse
Affiliation(s)
- Ann Van Holle
- Faculty of Bioengineering Sciences, Department of Plants and Crops , Ghent University , Coupure Links 653 , 9000 Ghent , Belgium
- De Proefbrouwerij , Doornzelestraat 20 , 9080 Lochristi , Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) , Caritasstraat 39 , 9090 Melle , Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) , Caritasstraat 39 , 9090 Melle , Belgium
| | - Anita Van Landschoot
- Faculty of Bioengineering Sciences, Department of Biotechnology , Ghent University , Valentin Vaerwyckweg 1 , 9000 Ghent , Belgium
| | - Geert Haesaert
- Faculty of Bioengineering Sciences, Department of Plants and Crops , Ghent University , Coupure Links 653 , 9000 Ghent , Belgium
| | - Dirk Naudts
- De Proefbrouwerij , Doornzelestraat 20 , 9080 Lochristi , Belgium
| | - Denis De Keukeleire
- Faculty of Pharmaceutical Sciences , Ghent University , c/o Gontrode Heirweg 115 , 9090 Melle , Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) , Caritasstraat 39 , 9090 Melle , Belgium
- Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics , Ghent University , Technologiepark Zwijnaarde 71 , 9052 Zwijnaarde , Belgium
| |
Collapse
|
5
|
Yan D, Wong YF, Shellie RA, Marriott PJ, Whittock SP, Koutoulis A. Assessment of the phytochemical profiles of novel hop (Humulus lupulus L.) cultivars: A potential route to beer crafting. Food Chem 2018; 275:15-23. [PMID: 30724181 DOI: 10.1016/j.foodchem.2018.09.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
Abstract
This study investigated the volatile phytochemical diversity of 30 samples obtained from experimental hybrid and commercial H. lupulus L. plants. Essential oils distilled from these samples were analysed by high resolution gas chromatography coupled with accurate mass time-of-flight mass spectrometry (GC-accTOFMS). A total of 58 secondary metabolites, mainly comprising 18 esters, 6 monoterpene hydrocarbons, 2 oxygenated monoterpenes, 20 sesquiterpene hydrocarbons, 7 oxygenated sesquiterpenes, and 4 ketones, were positively or tentatively identified. A total of 24 metabolites were detected in all samples, but commercial cultivars (selected for brewing performance) had fewer compounds identified compared to experimental genotypes. Chemometrics analyses enabled distinct differentiation of experimental hybrids from commercial cultivars, discussed in terms of the different classes of compounds present in different genotypes. Differences among the mono- and sesquiterpenoids, appear to be related to either: i) the genetic origin of the plants; or ii) the processes of bioaccumulation of the identified secondary metabolites.
Collapse
Affiliation(s)
- DanDan Yan
- Australian Centre for Research on Separation Science, School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia; Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Yong Foo Wong
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Present address: School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| | - Robert A Shellie
- Australian Centre for Research on Separation Science, School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia; Trajan Scientific and Medical, 7 Argent Place, Ringwood, VIC 3134, Australia; Centre for Advanced Sensory Science, School of Exercise and Nutrition Sciences, Deakin University, 221 Burwood Highway, Burwood, VIC 3125, Australia.
| | - Philip J Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Simon P Whittock
- Australian Centre for Research on Separation Science, School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia; Hop Products Australia, 446 Elizabeth St, Hobart, TAS 7000, Australia.
| | - Anthony Koutoulis
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia.
| |
Collapse
|
6
|
Yamauchi H, Mukouzaka Y, Taniguchi T, Nakashima K, Furukubo S, Harada M. Newly Developed SNP-Based Identification Method of Hop Varieties. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2014-1006-01] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Yuri Mukouzaka
- Suntory Business Expert Limited, Safety Science Institute, Japan
| | | | | | - Susumu Furukubo
- Suntory Business Expert Limited, Quality Assurance and Regulatory Affairs Department, Japan
| | - Masami Harada
- Suntory Business Expert Limited, Quality Assurance and Regulatory Affairs Department, Japan
| |
Collapse
|
7
|
Machado JC, Faria MA, Ferreira IMPLVO, Páscoa RNMJ, Lopes JA. Varietal discrimination of hop pellets by near and mid infrared spectroscopy. Talanta 2017; 180:69-75. [PMID: 29332835 DOI: 10.1016/j.talanta.2017.12.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 01/19/2023]
Abstract
Hop is one of the most important ingredients of beer production and several varieties are commercialized. Therefore, it is important to find an eco-real-time-friendly-low-cost technique to distinguish and discriminate hop varieties. This paper describes the development of a method based on vibrational spectroscopy techniques, namely near- and mid-infrared spectroscopy, for the discrimination of 33 commercial hop varieties. A total of 165 samples (five for each hop variety) were analysed by both techniques. Principal component analysis, hierarchical cluster analysis and partial least squares discrimination analysis were the chemometric tools used to discriminate positively the hop varieties. After optimizing the spectral regions and pre-processing methods a total of 94.2% and 96.6% correct hop varieties discrimination were obtained for near- and mid-infrared spectroscopy, respectively. The results obtained demonstrate the suitability of these vibrational spectroscopy techniques to discriminate different hop varieties and consequently their potential to be used as an authenticity tool. Compared with the reference procedures normally used for hops variety discrimination these techniques are quicker, cost-effective, non-destructive and eco-friendly.
Collapse
Affiliation(s)
- Julio C Machado
- LAQV/REQUIMTE/ Departamento de Ciências Químicas, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Miguel A Faria
- LAQV/REQUIMTE/ Departamento de Ciências Químicas, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Isabel M P L V O Ferreira
- LAQV/REQUIMTE/ Departamento de Ciências Químicas, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Ricardo N M J Páscoa
- LAQV/REQUIMTE, Laboratório de Química Aplicada, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - João A Lopes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| |
Collapse
|
8
|
Yan D, Wong YF, Tedone L, Shellie RA, Marriott PJ, Whittock SP, Koutoulis A. Chemotyping of new hop (Humulus lupulus L.) genotypes using comprehensive two-dimensional gas chromatography with quadrupole accurate mass time-of-flight mass spectrometry. J Chromatogr A 2017; 1536:110-121. [PMID: 28830588 DOI: 10.1016/j.chroma.2017.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/28/2017] [Accepted: 08/07/2017] [Indexed: 02/03/2023]
Abstract
Comprehensive two-dimensional gas chromatography with quadrupole accurate mass time-of-flight mass spectrometry (GC×GC-Q-TOFMS) is employed to profile Humulus lupulus L. (hop) essential oils. Comparison of characterised essential oils allows discrimination among chemotypes. Experimental and commercial hop genotypes displayed distinguishable chemotypic patterns among the volatile secondary metabolites making up their essential oils. In total, 210-306 unique compounds were detected (depending on specific genotype), with 99 of these compounds either positively or tentatively identified. Identified volatile secondary metabolites were grouped into esters, monoterpene hydrocarbons, oxygenated monoterpenes, sesquiterpene hydrocarbons, oxygenated sesquiterpenes and ketones. Terpenoids were the dominant chemical families across all hop genotypes analysed, representing between 67% and 90% of the total ion count. The multidimensional chromatographic profiles of hop essential oils are extremely information-rich, making GC×GC-Q-TOFMS useful for fast screening of new hybrid hop genotypes, and therefore informing breeding strategies to derive new commercial hop cultivars for the development of distinctive and desirable beers.
Collapse
Affiliation(s)
- DanDan Yan
- Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Hobart, TAS 7001, Australia; Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, VIC 3800, Australia
| | - Yong Foo Wong
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, VIC 3800, Australia
| | - Laura Tedone
- Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Robert A Shellie
- Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Hobart, TAS 7001, Australia; Trajan Scientific and Medical, 7 Argent Place Ringwood 3154 VIC, Australia
| | - Philip J Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, VIC 3800, Australia.
| | - Simon P Whittock
- Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Hobart, TAS 7001, Australia; Hop Products Australia, 446 Elizabeth St, Hobart, TAS 7000, Australia
| | - Anthony Koutoulis
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia.
| |
Collapse
|
9
|
Methods for verifying the authenticity of hops - an effective tool against falsification. KVASNY PRUMYSL 2016. [DOI: 10.18832/kp2016030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
10
|
Henning JA, Coggins J, Peterson M. Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation. BMC Res Notes 2015; 8:542. [PMID: 26438052 PMCID: PMC4595125 DOI: 10.1186/s13104-015-1492-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 09/21/2015] [Indexed: 12/31/2022] Open
Abstract
Background Hop 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. Results The 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. Conclusions This 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 different SNP marker technology upon a differential set of hop genotypes. The marker sequence data and suggested primer sets provide potential means to fingerprint hop varieties in most genetic laboratories utilizing SNP-marker technology. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1492-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- John A Henning
- USDA-ARS, 3450 SW Campus Way, Corvallis, OR, 97331, USA.
| | - Jamie Coggins
- ROY FARMS, INC., 401 Walters Road, Moxee, WA, 98936, USA.
| | - Matthew Peterson
- CGRB, ALS Building, Oregon State University, Corvallis, OR, 97331, USA.
| |
Collapse
|
11
|
McAdam EL, Vaillancourt RE, Koutoulis A, Whittock SP. Quantitative genetic parameters for yield, plant growth and cone chemical traits in hop (Humulus lupulus L.). BMC Genet 2014; 15:22. [PMID: 24524684 PMCID: PMC3927220 DOI: 10.1186/1471-2156-15-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most traits targeted in the genetic improvement of hop are quantitative in nature. Improvement based on selection of these traits requires a comprehensive understanding of their inheritance. This study estimated quantitative genetic parameters for 20 traits related to three key objectives for the genetic improvement of hop: cone chemistry, cone yield and agronomic characteristics. RESULTS Significant heritable genetic variation was identified for α-acid and β-acid, as well as their components and relative proportions. Estimates of narrow-sense heritability for these traits (h2 = 0.15 to 0.29) were lower than those reported in previous hop studies, but were based on a broader suite of families (108 from European, North American and hybrid origins). Narrow-sense heritabilities are reported for hop growth traits for the first time (h2 = 0.04 to 0.20), relating to important agronomic characteristics such as emergence, height and lateral morphology. Cone chemistry and growth traits were significantly genetically correlated, such that families with more vigorous vegetative growth were associated with lower α-acid and β-acid levels. This trend may reflect the underlying population structure of founder genotypes (European and North American origins) as well as past selection in the Australian environment. Although male and female hop plants are thought to be indistinguishable until flowering, sex was found to influence variation in many growth traits, with male and female plants displaying differences in vegetative morphology from emergence to cone maturity. CONCLUSIONS This study reveals important insights into the genetic control of quantitative hop traits. The information gained will provide hop breeders with a greater understanding of the additive genetic factors which affect selection of cone chemistry, yield and agronomic characteristics in hop, aiding in the future development of improved cultivars.
Collapse
Affiliation(s)
- Erin L McAdam
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, TAS 7001, Australia
| | - René E Vaillancourt
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, TAS 7001, Australia
| | - Anthony Koutoulis
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, TAS 7001, Australia
| | - Simon P Whittock
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, TAS 7001, Australia
- Hop Products Australia, 26 Cambridge Road, Bellerive, TAS 7018, Australia
| |
Collapse
|
12
|
Castillo A, Ramírez MC, Martín AC, Kilian A, Martín A, Atienza SG. High-throughput genotyping of wheat-barley amphiploids utilising diversity array technology (DArT). BMC PLANT BIOLOGY 2013; 13:87. [PMID: 23725040 PMCID: PMC3679790 DOI: 10.1186/1471-2229-13-87] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/27/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Hordeum chilense, a native South American diploid wild barley, is one of the species of the genus Hordeum with a high potential for cereal breeding purposes, given its high crossability with other members of the Triticeae tribe. Hexaploid tritordeum (×Tritordeum Ascherson et Graebner, 2n=6×=42, AABBH(ch)H(ch)) is the fertile amphiploid obtained after chromosome doubling of hybrids between Hordeum chilense and durum wheat. Approaches used in the improvement of this crop have included crosses with hexaploid wheat to promote D/H(ch) chromosome substitutions. While this approach has been successful as was the case with triticale, it has also complicated the genetic composition of the breeding materials. Until now tritordeum lines were analyzed based on molecular cytogenetic techniques and screening with a small set of DNA markers. However, the recent development of DArT markers in H. chilense offers new possibilities to screen large number of accessions more efficiently. RESULTS Here, we have applied DArT markers to genotype composition in forty-six accessions of hexaploid tritordeum originating from different stages of tritordeum breeding program and to H. chilense-wheat chromosome addition lines to allow their physical mapping. Diversity analyses were conducted including dendrogram construction, principal component analysis and structure inference. Euploid and substituted tritordeums were clearly discriminated independently of the method used. However, dendrogram and Structure analyses allowed the clearest discrimination among substituted tritordeums. The physically mapped markers allowed identifying these groups as substituted tritordeums carrying the following disomic substitutions (DS): DS1D (1H(ch)), DS2D (2H(ch)), DS5D (5H(ch)), DS6D (6H(ch)) and the double substitution DS2D (2H(ch)), DS5D (5H(ch)). These results were validated using chromosome specific EST and SSR markers and GISH analysis. CONCLUSION In conclusion, DArT markers have proved to be very useful to detect chromosome substitutions in the tritordeum breeding program and thus they are expected to be equally useful to detect translocations both in the tritordeum breeding program and in the transference of H. chilense genetic material in wheat breeding programs.
Collapse
Affiliation(s)
- Almudena Castillo
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| | - María C Ramírez
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| | - Azahara C Martín
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla, ACT 2600, Australia
| | - Antonio Martín
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| | - Sergio G Atienza
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| |
Collapse
|
13
|
McAdam EL, Freeman JS, Whittock SP, Buck EJ, Jakse J, Cerenak A, Javornik B, Kilian A, Wang CH, Andersen D, Vaillancourt RE, Carling J, Beatson R, Graham L, Graham D, Darby P, Koutoulis A. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry. BMC Genomics 2013; 14:360. [PMID: 23718194 PMCID: PMC3680207 DOI: 10.1186/1471-2164-14-360] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. RESULTS QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. CONCLUSIONS Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS.
Collapse
Affiliation(s)
- Erin L McAdam
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
| | - Jules S Freeman
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore 4558 QLD, Australia
| | - Simon P Whittock
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
- Hop Products Australia, 26 Cambridge Road, Bellerive 7018 TAS, Australia
| | - Emily J Buck
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11 600, Palmerston North 4442, New Zealand
| | - Jernej Jakse
- Agronomy Department, Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana 1000, Slovenia
| | - Andreja Cerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, Zalec 3310, Slovenia
| | - Branka Javornik
- Agronomy Department, Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana 1000, Slovenia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla 2600ACT, Australia
| | - Cai-Hong Wang
- Department of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Dave Andersen
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - René E Vaillancourt
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla 2600ACT, Australia
| | - Ron Beatson
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - Lawrence Graham
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - Donna Graham
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - Peter Darby
- Wye Hops Ltd., China Farm, Upper Harbledown, Canterbury, Kent CT2 9AR, UK
| | - Anthony Koutoulis
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
| |
Collapse
|
14
|
Cruz VMV, Kilian A, Dierig DA. Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop lesquerella and related species. PLoS One 2013; 8:e64062. [PMID: 23724020 PMCID: PMC3665832 DOI: 10.1371/journal.pone.0064062] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 04/08/2013] [Indexed: 02/05/2023] Open
Abstract
The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa.
Collapse
Affiliation(s)
- Von Mark V. Cruz
- USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, Colorado, United States of America
- Department of Bioagricultural Sciences and Pest Mgt., Colorado State University, Fort Collins, Colorado, United States of America
| | - Andrzej Kilian
- Diversity Arrays Technology Pty. Ltd., Yarralumla, ACT, Australia
| | - David A. Dierig
- USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, Colorado, United States of America
- * E-mail:
| |
Collapse
|
15
|
Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 2012; 7:e44684. [PMID: 22984541 PMCID: PMC3439404 DOI: 10.1371/journal.pone.0044684] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
Collapse
|
16
|
Patzak J, Paprštein F, Henychová A, Sedlák J. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources. Genome 2012; 55:647-65. [PMID: 22954156 DOI: 10.1139/g2012-054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes.
Collapse
Affiliation(s)
- Josef Patzak
- Hop Research Institute Co. Ltd., Kadaňská 2525, 438 46 Žatec, Czech Republic.
| | | | | | | |
Collapse
|
17
|
Sohail Q, Shehzad T, Kilian A, Eltayeb AE, Tanaka H, Tsujimoto H. Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii. BREEDING SCIENCE 2012; 62:38-45. [PMID: 23136512 PMCID: PMC3405951 DOI: 10.1270/jsbbs.62.38] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 12/03/2011] [Indexed: 05/18/2023]
Abstract
Aegilops tauschii Coss. is the D-genome donor to hexaploid bread wheat (Triticum aestivum) and is the most promising wild species as a genetic resource for wheat breeding. To study the population structure and diversity of 81 Ae. tauschii accessions collected from various regions of its geographical distribution, the genomic representation of these lines were used to develop a diversity array technology (DArT) marker array. This Ae. tauschii array and a previously developed DArT wheat array were used to scan the genomes of the 81 accessions. Out of 7500 markers (5500 wheat and 2000 Ae. tauschii), 4449 were polymorphic (3776 wheat and 673 Ae. tauschii). Phylogenetic and population structure studies revealed that the accessions could be divided into three groups. The two Ae. tauschii subspecies could also be separately clustered, suggesting that the current taxonomy might be valid. DArT markers are effective to detect very small polymorphisms. The information obtained about Ae. tauschii in the current study could be useful for wheat breeding. In addition, the new DArT array from this Ae. tauschii population is expected to be an effective tool for hexaploid wheat studies.
Collapse
Affiliation(s)
- Quahir Sohail
- Laboratory of Molecular Breeding, Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Tariq Shehzad
- Laboratory of Plant Genetics and Breeding Science, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Andrezj Kilian
- Diversity Array Technology Pty. Ltd., P.O. Box 7141 Yarralumla, ACT 2006, Australia
| | - Amin Elsadig Eltayeb
- Laboratory of Molecular Breeding, Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Hiroyuki Tanaka
- Laboratory of Plant Genetics, Faculty of Agriculture, Tottori University, 4-101 Minami, Koyama, Tottori 680-8553, Japan
| | - Hisashi Tsujimoto
- Laboratory of Molecular Breeding, Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
- Corresponding author (e-mail: )
| |
Collapse
|