1
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Philipp N, Gratton E, Estrada LC. Measuring protein-membrane interaction through radial fluorescence correlation in 2 dimensions. Methods Appl Fluoresc 2023; 11:045009. [PMID: 37586380 DOI: 10.1088/2050-6120/acf118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
The cell membrane has a fundamental role in the cell life cycle but there's still much to be learned about its heterogeneous structure, regulation, and protein interaction. Additionally, the protein-membrane interaction is often overlooked when studying specific protein dynamics. In this work, we present a new tool for a better understanding of protein dynamics and membrane function using live cells and fast non-invasive techniques without the need for individual particle tracking. To this end, we used the 2D-pair correlation function (2D-pCF) to study protein interactions across cellular membranes. We performed numerical simulations and confocal experiments using a GAP-mEGFP fusion construct known to interact with the plasmatic membrane. Our results demonstrate that based on a quantitative correlation analysis as the 2D pair correlation of the signal intensities, is possible to characterize protein-membrane interactions in live systems and real-time. Combining experimental and numerical results this work presents a new powerful approach to the study of the dynamic protein-membrane interaction.
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Affiliation(s)
- N Philipp
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA). Buenos Aires, Argentina
| | - E Gratton
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America
| | - L C Estrada
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA). Buenos Aires, Argentina
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2
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Nixdorf D, Sponheimer M, Berghammer D, Engert F, Bader U, Philipp N, Kazerani M, Straub T, Rohrbacher L, Wange L, Dapa S, Atar D, Seitz CM, Brandstetter K, Linder A, von Bergwelt M, Leonhardt H, Mittelstaet J, Kaiser A, Bücklein V, Subklewe M. Adapter CAR T cells to counteract T-cell exhaustion and enable flexible targeting in AML. Leukemia 2023:10.1038/s41375-023-01905-0. [PMID: 37106163 DOI: 10.1038/s41375-023-01905-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Although the landscape for treating acute myeloid leukemia (AML) patients has changed substantially in recent years, the majority of patients will eventually relapse and succumb to their disease. Allogeneic stem cell transplantation provides the best anti-AML treatment strategy, but is only suitable in a minority of patients. In contrast to B-cell neoplasias, chimeric antigen receptor (CAR) T-cell therapy in AML has encountered challenges in target antigen heterogeneity, safety, and T-cell dysfunction. We established a Fab-based adapter CAR (AdCAR) T-cell platform with flexibility of targeting and control of AdCAR T-cell activation. Utilizing AML cell lines and a long-term culture assay for primary AML cells, we were able to demonstrate AML-specific cytotoxicity using anti-CD33, anti-CD123, and anti-CLL1 adapter molecules in vitro and in vivo. Notably, we show for the first time the feasibility of sequential application of adapter molecules of different specificity in primary AML co-cultures. Importantly, using the AML platform, we were able to demonstrate that chronic T-cell stimulation and exhaustion can be counteracted through introduction of treatment-free intervals. As T-cell exhaustion and target antigen heterogeneity are well-known causes of resistance, the AdCAR platform might offer effective strategies to ameliorate these limitations.
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Affiliation(s)
- D Nixdorf
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - M Sponheimer
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - D Berghammer
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - F Engert
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - U Bader
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - N Philipp
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - M Kazerani
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - T Straub
- Core Facility Bioinformatics, Biomedical Center, LMU, Munich, Germany
| | - L Rohrbacher
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - L Wange
- Anthropology and Human Genomics, Faculty of Biology, LMU, Munich, Germany
| | - S Dapa
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - D Atar
- Department of General Pediatrics, Hematology and Oncology, University Children's Hospital Tuebingen, Tuebingen, Germany
| | - C M Seitz
- Department of General Pediatrics, Hematology and Oncology, University Children's Hospital Tuebingen, Tuebingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tuebingen, Tuebingen, Germany
| | | | - A Linder
- Gene Center and Department of Biochemistry, LMU, Munich, Germany
- Department of Medicine II, University Hospital, LMU, Munich, Germany
| | - M von Bergwelt
- Department of Medicine III, University Hospital, LMU, Munich, Germany
| | - H Leonhardt
- Department of Biology II, LMU, Munich, Germany
| | - J Mittelstaet
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - A Kaiser
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - V Bücklein
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - M Subklewe
- Department of Medicine III, University Hospital, LMU, Munich, Germany.
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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3
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Schulthess AW, Kale SM, Zhao Y, Gogna A, Rembe M, Philipp N, Liu F, Beukert U, Serfling A, Himmelbach A, Oppermann M, Weise S, Boeven PHG, Schacht J, Longin CFH, Kollers S, Pfeiffer N, Korzun V, Fiebig A, Schüler D, Lange M, Scholz U, Stein N, Mascher M, Reif JC. Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding. Sci Data 2022; 9:784. [PMID: 36572688 PMCID: PMC9792552 DOI: 10.1038/s41597-022-01891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 12/27/2022] Open
Abstract
Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.
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Affiliation(s)
- Albert W. Schulthess
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sandip M. Kale
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.418674.80000 0004 0533 4528Present Address: Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Yusheng Zhao
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Abhishek Gogna
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maximilian Rembe
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Norman Philipp
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Fang Liu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.9227.e0000000119573309Present Address: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Ulrike Beukert
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Albrecht Serfling
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Axel Himmelbach
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | | | - C. Friedrich H. Longin
- grid.9464.f0000 0001 2290 1502State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Sonja Kollers
- grid.425691.dKWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Viktor Korzun
- grid.425691.dKWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Anne Fiebig
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Lange
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jochen C. Reif
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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4
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Rembe M, Reif JC, Ebmeyer E, Thorwarth P, Korzun V, Schacht J, Boeven PHG, Varenne P, Kazman E, Philipp N, Kollers S, Pfeiffer N, Longin CFH, Hartwig N, Gils M, Zhao Y. Reciprocal Recurrent Genomic Selection Is Impacted by Genotype-by-Environment Interactions. Front Plant Sci 2021; 12:703419. [PMID: 34630453 PMCID: PMC8498042 DOI: 10.3389/fpls.2021.703419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Reciprocal recurrent genomic selection is a breeding strategy aimed at improving the hybrid performance of two base populations. It promises to significantly advance hybrid breeding in wheat. Against this backdrop, the main objective of this study was to empirically investigate the potential and limitations of reciprocal recurrent genomic selection. Genome-wide predictive equations were developed using genomic and phenotypic data from a comprehensive population of 1,604 single crosses between 120 female and 15 male wheat lines. Twenty superior female lines were selected for initiation of the reciprocal recurrent genomic selection program. Focusing on the female pool, one cycle was performed with genomic selection steps at the F2 (60 out of 629 plants) and the F5 stage (49 out of 382 plants). Selection gain for grain yield was evaluated at six locations. Analyses of the phenotypic data showed pronounced genotype-by-environment interactions with two environments that formed an outgroup compared to the environments used for the genome-wide prediction equations. Removing these two environments for further analysis resulted in a selection gain of 1.0 dt ha-1 compared to the hybrids of the original 20 parental lines. This underscores the potential of reciprocal recurrent genomic selection to promote hybrid wheat breeding, but also highlights the need to develop robust genome-wide predictive equations.
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Affiliation(s)
- Maximilian Rembe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | | | | | | | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, Kazan, Russia
| | - Johannes Schacht
- Limagrain Europe, Ferme de l'Etang – BP3−77390, Verneuil-l'Ètang, France
| | | | - Pierrick Varenne
- Limagrain Europe, Ferme de l'Etang – BP3−77390, Verneuil-l'Ètang, France
| | | | | | | | | | | | | | - Mario Gils
- Nordsaat Saatzucht GmbH, Langenstein, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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5
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Schneider J, Berkner MO, Philipp N, Schulthess AW, Reif JC. Assessing the Suitability of Elite Lines for Hybrid Seed Production and as Testers in Wide Crosses With Wheat Genetic Resources. Front Plant Sci 2021; 12:689825. [PMID: 34194460 PMCID: PMC8236896 DOI: 10.3389/fpls.2021.689825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The use of genetic resources in breeding is considered critical to ensure future selection gain, but the absence of important adaptation genes often masks the breeding value of genetic resources for grain yield. Testing genetic resources in a hybrid background has been proposed as a solution to obtain unbiased estimates of breeding values for grain yield. In our study, we evaluated the suitability of European wheat elite lines for implementing this hybrid strategy, focusing on maximizing seed yield in hybrid production and reducing masking effects due to susceptibility to lodging, yellow rust, and leaf rust of genetic resources. Over a 3-year period, 63 wheat elite female lines were crossed with eight male plant genetic resources in a multi-environment field experiment to evaluate seed yield on the female side. Then, the resulting hybrids and their parents were tested for plant height, lodging, and susceptibility to yellow rust and leaf rust in a further field experiment at multiple locations. We found that seed yield was strongly influenced by the elite wheat line choice in addition to environment and observed substantial differences among elite tester lines in their ability to reduce susceptibility to lodging, yellow rust, and leaf rust when the hybrid strategy was implemented. Consequently, breeders can significantly increase the amount of hybrid seed produced in wide crosses through appropriate tester choice and adapt genetic resources of wheat with the hybrid strategy to the modern cropping system.
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6
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Zhao Y, Thorwarth P, Jiang Y, Philipp N, Schulthess AW, Gils M, Boeven PHG, Longin CFH, Schacht J, Ebmeyer E, Korzun V, Mirdita V, Dörnte J, Avenhaus U, Horbach R, Cöster H, Holzapfel J, Ramgraber L, Kühnle S, Varenne P, Starke A, Schürmann F, Beier S, Scholz U, Liu F, Schmidt RH, Reif JC. Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat. Sci Adv 2021; 7:7/24/eabf9106. [PMID: 34117061 PMCID: PMC8195483 DOI: 10.1126/sciadv.abf9106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/28/2021] [Indexed: 05/07/2023]
Abstract
The potential of big data to support businesses has been demonstrated in financial services, manufacturing, and telecommunications. Here, we report on efforts to enter a new data era in plant breeding by collecting genomic and phenotypic information from 12,858 wheat genotypes representing 6575 single-cross hybrids and 6283 inbred lines that were evaluated in six experimental series for yield in field trials encompassing ~125,000 plots. Integrating data resulted in twofold higher prediction ability compared with cases in which hybrid performance was predicted across individual experimental series. Our results suggest that combining data across breeding programs is a particularly appropriate strategy to exploit the potential of big data for predictive plant breeding. This paradigm shift can contribute to increasing yield and resilience, which is needed to feed the growing world population.
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Affiliation(s)
- Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70593 Stuttgart, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Norman Philipp
- Syngenta Seeds GmbH, Kroppenstedterstr. 4, 39398 Hadmersleben, Germany
| | - Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Mario Gils
- Nordsaat Saatzucht GmbH, , Böhnshauserstr. 1, 38895 Langenstein, Germany
| | | | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70593 Stuttgart, Germany
| | | | - Erhard Ebmeyer
- KWS LOCHOW GmbH, Ferdinand-von-Lochow-Str. 5, 29303 Bergen, Germany
| | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37574 Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center, "Kazan Scientific Center of Russian Academy of Sciences," ul. Lobachevskogo, 2/31, Kazan, 420111 Tatarstan, Russian Federation
| | - Vilson Mirdita
- BASF Agricultural Solutions Seed GmbH, OT Gatersleben, Am Schwabeplan 8, 06466 Seeland, Germany
| | - Jost Dörnte
- Deutsche Saatveredelung AG, Leutewitz 26, 01665 Käbschütztal, Germany
| | - Ulrike Avenhaus
- W. von Borries-Eckendorf GmbH & Co. KG, Hovedisserstr. 92, 33818 Leopoldshöhe, Germany
| | - Ralf Horbach
- Saatzucht Bauer GmbH & Co. KG, Hofmarkstr.1, 93083 Niederträubling, Germany
| | | | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg, Germany
| | - Ludwig Ramgraber
- Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Simon Kühnle
- Pflanzenzucht Oberlimpurg, Oberlimpurg 2, 74523 Schwäbisch Hall, Germany
| | - Pierrick Varenne
- Limagrain Europe, Ferme de l'Etang BP3, 77390 Verneuil l'Etang, France
| | - Anne Starke
- Limagrain GmbH, Salderstr. 4, 31226 Peine-Rosenthal, Germany
| | | | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Renate H Schmidt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany.
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7
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Chu J, Zhao Y, Beier S, Schulthess AW, Stein N, Philipp N, Röder MS, Reif JC. Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat. Front Plant Sci 2020; 11:42. [PMID: 32117381 PMCID: PMC7033508 DOI: 10.3389/fpls.2020.00042] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 05/20/2023]
Abstract
Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel of 378 winter wheat genotypes including 190 elite lines and 188 plant genetic resources (PGR), which were phenotyped in multi-environmental trials for grain yield and plant height. We observed an ascertainment bias for the array-based SNP markers, which led to an underestimation of the molecular diversity within the population of PGR. In contrast, the marker system played only a minor role for the overall picture of the population structure and precision of genome-wide predictions. Interestingly, we found that rare markers contributed substantially to the prediction ability. This combined with the expectation that valuable novel diversity is most likely rare suggests that markers with minor allele frequency deserve careful consideration in the design of a pre-breeding program.
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Affiliation(s)
- Jianting Chu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sebastian Beier
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Albert W. Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Marion S. Röder
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Faculty of Sciences III - Agricultural and Nutritional Sciences, Earth Sciences and Computer Science, Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
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8
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Longin F, Beck H, Gütler H, Heilig W, Kleinert M, Rapp M, Philipp N, Erban A, Brilhaus D, Mettler-Altmann T, Stich B. Aroma and quality of breads baked from old and modern wheat varieties and their prediction from genomic and flour-based metabolite profiles. Food Res Int 2020; 129:108748. [PMID: 32036907 DOI: 10.1016/j.foodres.2019.108748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022]
Abstract
Bread aroma is the principal characteristic perceived by the consumer yet it is mostly disregarded in the product chain. The main aim of this study was to evaluate the potential to include bread aroma as a new target criterion into the wheat product chain. The objectives of our study were to (i) quantify the influence of genetic versus environmental factors on the bread aroma and quality characteristics, (ii) evaluate whether bread baked from modern wheat varieties differ in terms of aroma from those baked from old varieties, and (iii) compare genomic and metabolomic approaches for their efficiency to predict bread aroma and quality characteristics in a wheat breeding program. Agronomic characters as well as bread aroma and quality traits were assessed for 18 old and 22 modern winter wheat varieties evaluated at up to three locations in Germany. Metabolite profiles of all 120 flour samples were collected using a 7200 GC-QTOF. Considerable differences in the adjusted entry means for all examined bread aroma and quality characters were observed. For aroma, which was rated on a scale from 1 to 9, the adjusted entry means varied for the 40 wheat varieties between 3 and 8. In contrast, the aroma of bread prepared from old and modern wheat varieties did not differ significantly (P < 0.05). Bread aroma was not significantly (P < 0.05) correlated with grain yield, which suggested that it is possible to select for the former character in wheat breeding programs without reducing the gain of selection for the latter. Finally, we have shown that bread aroma can be better predicted using a combination of metabolite and SNP genotyping profiles instead of the SNP genotyping profile only. In conclusion, we have illustrated possibilities to increase the quality of wheat for consumers in the product chain.
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Affiliation(s)
- Friedrich Longin
- State Plant Breeding Institute, Univ. of Hohenheim, 70599 Stuttgart, Germany
| | | | | | | | - Michael Kleinert
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Matthias Rapp
- State Plant Breeding Institute, Univ. of Hohenheim, 70599 Stuttgart, Germany
| | - Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research(IPK), 06466 Gatersleben, Germany
| | - Alexander Erban
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, 14476 Golm, Germany
| | - Dominik Brilhaus
- Institute of Plant Biochemistry, Heinrich Heine University, 40225 Düsseldorf, Germany; Plant Metabolism and Metabolomics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Heinrich Heine University, 40225 Düsseldorf, Germany; Plant Metabolism and Metabolomics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Benjamin Stich
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany.
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9
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Philipp N, Weise S, Oppermann M, Börner A, Keilwagen J, Kilian B, Arend D, Zhao Y, Graner A, Reif JC, Schulthess AW. Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection. Sci Data 2019; 6:137. [PMID: 31358775 PMCID: PMC6662709 DOI: 10.1038/s41597-019-0146-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022] Open
Abstract
Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warrant the seed integrity of individual accessions during periodical regeneration cycles in the field phenotypic characterizations are performed. This study provides non-orthogonal historical data of 12,754 spring and winter wheat accessions characterized for flowering time, plant height, and thousand grain weight during 70 years of seed regeneration at the German genebank. Supported by historical weather observations outliers were removed following a previously described quality assessment pipeline. In this way, ready-to-use processed phenotypic data across regeneration years were generated and further validated. We encourage international and national genebanks to increase their efforts to transform into bio-digital resource centers. A first important step could consist in unlocking their historical data treasures that allows an educated choice of accessions by scientists and breeders.
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Affiliation(s)
- Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Daniel Arend
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany.
| | - Albert W Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
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Gonzalez MY, Weise S, Zhao Y, Philipp N, Arend D, Börner A, Oppermann M, Graner A, Reif JC, Schulthess AW. Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection. Sci Data 2018; 5:180278. [PMID: 30512010 PMCID: PMC6278694 DOI: 10.1038/sdata.2018.278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/15/2018] [Indexed: 01/21/2023] Open
Abstract
The scarce knowledge on phenotypic characterization restricts the usage of genetic diversity of plant genetic resources in research and breeding. We describe original and ready-to-use processed data for approximately 60% of ~22,000 barley accessions hosted at the Federal ex situ Genebank for Agricultural and Horticultural Plant Species. The dataset gathers records for three traits with agronomic relevance: flowering time, plant height and thousand grain weight. This information was collected for seven decades for winter and spring barley during the seed regeneration routine. The curated data represent a source for research on genetics and genomics of adaptive and yield related traits in cereals due to the importance of barley as model organism. This data could be used to predict the performance of non-phenotyped individuals in other collections through genomic prediction. Moreover, the dataset empowers the utilization of phenotypic diversity of genetic resources for crop improvement.
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Affiliation(s)
- Maria Y Gonzalez
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Daniel Arend
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Albert W Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
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Philipp N, Weichert H, Bohra U, Weschke W, Schulthess AW, Weber H. Grain number and grain yield distribution along the spike remain stable despite breeding for high yield in winter wheat. PLoS One 2018; 13:e0205452. [PMID: 30304020 PMCID: PMC6179273 DOI: 10.1371/journal.pone.0205452] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022] Open
Abstract
Two winter wheat (Triticum aestivum L.) populations, i.e. 180 genetic resources and 210 elite varieties, were compared in a field trial to analyse how grain number and grain yield distribution along the spike changed during the breeding process and how this associates to yield-related traits. Elites showed in average 38% more yield compared to resources. This breeding improvement mainly derived from an increase in grains and yield per spike in addition to grains and yield per spikelet. These increments corresponded to 19, 23, 21 and 25%, respectively. Not much gain in thousand grain weight (4%) was observed in elites as compared to resources. The number of spikelets per spike was not, or even negatively, correlated with most traits, except of grains per spike, which suggests that this trait was not favoured during breeding. The grain number and grain yield distributions along the spike (GDAS and GYDAS) were measured and compared by using a novel mathematical tool. GDAS and GYDAS measure the deviation of a spike of interest from the architecture of a model spike with even grain and yield distribution along all spikelets, respectively. Both traits were positively correlated. Elites showed in average only a 1% improvement in GDAS and GYDAS values compared to resources. This comparison revealed that breeding increased grain number and yield uniformly along the spike without changing relative yield input of individual spikelets, thereby, maintaining the general spike architecture.
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Affiliation(s)
- Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben, Germany
- * E-mail:
| | - Heiko Weichert
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben, Germany
| | - Utkarsh Bohra
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben, Germany
| | - Winfriede Weschke
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben, Germany
| | - Albert Wilhelm Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben, Germany
| | - Hans Weber
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben, Germany
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González MY, Philipp N, Schulthess AW, Weise S, Zhao Y, Börner A, Oppermann M, Graner A, Reif JC. Unlocking historical phenotypic data from an ex situ collection to enhance the informed utilization of genetic resources of barley (Hordeum sp.). Theor Appl Genet 2018; 131:2009-2019. [PMID: 29959470 DOI: 10.1007/s00122-018-3129-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/17/2018] [Indexed: 05/11/2023]
Abstract
Key message Historical data generated during seed regeneration are valuable to populate a bio-digital resource center for barley (Hordeum sp.). Precise estimates of trait performance of genetic resources are considered as an intellectually challenging, complex, costly and time-consuming step needed to exploit the phenotypic and genetic diversity maintained in genebanks for breeding and research. Using barley (Hordeum sp.) as a model, we examine strategies to tap into historical data available from regeneration trials. This is a first step toward extending the Federal ex situ Genebank into a bio-digital resource center facilitating an informed choice of barley accessions for research and breeding. Our study is based on historical data of seven decades collected for flowering time, plant height, and thousand grain weight during the regeneration of 12,872 spring and winter barley accessions. Linear mixed models were implemented in conjunction with routines for assessment of data quality. A resampling study highlights the potential risk of biased estimates in second-order statistics when grouping accessions for regeneration according to the year of collection or geographic origin. Based on rigorous quality assessment, we obtained high heritability estimates for the traits under consideration exceeding 0.8. Thus, the best linear unbiased estimations for the three traits are a valuable source to populate a bio-digital resource center for the IPK barley collection. The proposed strategy to leverage historical data from regeneration trials is not crop specific and can be used as a blueprint for other ex situ collections.
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Affiliation(s)
- Maria Y González
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Albert W Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
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Philipp N, Weise S, Oppermann M, Börner A, Graner A, Keilwagen J, Kilian B, Zhao Y, Reif JC, Schulthess AW. Leveraging the Use of Historical Data Gathered During Seed Regeneration of an ex Situ Genebank Collection of Wheat. Front Plant Sci 2018; 9:609. [PMID: 29868066 PMCID: PMC5953327 DOI: 10.3389/fpls.2018.00609] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/17/2018] [Indexed: 05/20/2023]
Abstract
Genebanks are a rich source of genetic variation. Most of this variation is absent in breeding programs but may be useful for further crop plant improvement. However, the lack of phenotypic information forms a major obstacle for the educated choice of genebank accessions for research and breeding. A promising approach to fill this information gap is to exploit historical information gathered routinely during seed regeneration cycles. Still, this data is characterized by a high non-orthogonality hampering their analysis. By examining historical data records for flowering time, plant height, and thousand grain weight collected during 70 years of regeneration of 6,207 winter wheat (Triticum aestivum L.) accessions at the German Federal ex situ Genebank, we aimed to elaborate a strategy to analyze and validate non-orthogonal historical data in order to charge genebank information platforms with high quality ready-to-use phenotypic information. First, a three-step quality control assessment considering the plausibility of trait values and a standard as well as a weather parameter index based outlier detection was implemented, resulting in heritability estimates above 0.90 for all three traits. Then, the data was analyzed by estimating best linear unbiased estimations (BLUEs) applying a linear mixed-model approach. An in silico resampling study mimicking different missing data patterns revealed that accessions should be regenerated in a random fashion and not blocked by origin or acquisition date in order to minimize estimation biases in historical data sets. Validation data was obtained from multi-environmental orthogonal field trials considering a random subsample of 3,083 accessions. Correlations above 0.84 between BLUEs estimated for historical data and validation trials outperformed previous approaches and confirmed the robustness of our strategy as well as the high quality of the historical data. The results indicate that the IPK winter wheat collection reveals an extraordinary high phenotypic diversity compared to other collections. The quality checked ready-to-use phenotypic information resulting from this study is the first brick to extend traditional, conservation driven genebanks into bio-digital resource centers.
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Affiliation(s)
- Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | | | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Albert W. Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Abstract
Predicting the grain yield performance of three-way hybrids is challenging. Three-way crosses are relevant for hybrid breeding in barley ( L.) and maize ( L.) adapted to East Africa. The main goal of our study was to implement and evaluate genome-wide prediction approaches of the performance of three-way hybrids using data of single-cross hybrids for a scenario in which parental lines of the three-way hybrids originate from three genetically distinct subpopulations. We extended the ridge regression best linear unbiased prediction (RRBLUP) and devised a genomic selection model allowing for subpopulation-specific marker effects (GSA-RRBLUP: general and subpopulation-specific additive RRBLUP). Using an empirical barley data set, we showed that applying GSA-RRBLUP tripled the prediction ability of three-way hybrids from 0.095 to 0.308 compared with RRBLUP, modeling one additive effect for all three subpopulations. The experimental findings were further substantiated with computer simulations. Our results emphasize the potential of GSA-RRBLUP to improve genome-wide hybrid prediction of three-way hybrids for scenarios of genetically diverse parental populations. Because of the advantages of the GSA-RRBLUP model in dealing with hybrids from different parental populations, it may also be a promising approach to boost the prediction ability for hybrid breeding programs based on genetically diverse heterotic groups.
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Abstract
Hybrid breeding in barley ( L.) offers great opportunities to accelerate the rate of genetic improvement and to boost yield stability. A crucial requirement consists of the efficient selection of superior hybrid combinations. We used comprehensive phenotypic and genomic data from a commercial breeding program with the goal of examining the potential to predict the hybrid performances. The phenotypic data were comprised of replicated grain yield trials for 385 two-way and 408 three-way hybrids evaluated in up to 47 environments. The parental lines were genotyped using a 3k single nucleotide polymorphism (SNP) array based on an Illumina Infinium assay. We implemented ridge regression best linear unbiased prediction modeling for additive and dominance effects and evaluated the prediction ability using five-fold cross validations. The prediction ability of hybrid performances based on general combining ability (GCA) effects was moderate, amounting to 0.56 and 0.48 for two- and three-way hybrids, respectively. The potential of GCA-based hybrid prediction requires that both parental components have been evaluated in a hybrid background. This is not necessary for genomic prediction for which we also observed moderate cross-validated prediction abilities of 0.51 and 0.58 for two- and three-way hybrids, respectively. This exemplifies the potential of genomic prediction in hybrid barley. Interestingly, prediction ability using the two-way hybrids as training population and the three-way hybrids as test population or vice versa was low, presumably, because of the different genetic makeup of the parental source populations. Consequently, further research is needed to optimize genomic prediction approaches combining different source populations in barley.
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Affiliation(s)
| | - L. Balázs
- a Universität Bremen , Bremen, Germany
| | | | - A. Soran
- b Universitatea Babes-Bolyai , Cluj, Romania
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Tang-Quan K, Kolk M, Deuse T, Philipp N, Kay M, Robbins R, Reichenspurner H, Schrepfer S. 128: Immunogenicity of Fetal Mesenchymal Stem Cells from the Umbilical Cord Line for Regenerative Therapies. J Heart Lung Transplant 2010. [DOI: 10.1016/j.healun.2009.11.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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