1
|
El Hanafi S, Jiang Y, Kehel Z, Schulthess AW, Zhao Y, Mascher M, Haupt M, Himmelbach A, Stein N, Amri A, Reif JC. Genomic predictions to leverage phenotypic data across genebanks. FRONTIERS IN PLANT SCIENCE 2023; 14:1227656. [PMID: 37701801 PMCID: PMC10493331 DOI: 10.3389/fpls.2023.1227656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023]
Abstract
Genome-wide prediction is a powerful tool in breeding. Initial results suggest that genome-wide approaches are also promising for enhancing the use of the genebank material: predicting the performance of plant genetic resources can unlock their hidden potential and fill the information gap in genebanks across the world and, hence, underpin prebreeding programs. As a proof of concept, we evaluated the power of across-genebank prediction for extensive germplasm collections relying on historical data on flowering/heading date, plant height, and thousand kernel weight of 9,344 barley (Hordeum vulgare L.) plant genetic resources from the German Federal Ex situ Genebank for Agricultural and Horticultural Crops (IPK) and of 1,089 accessions from the International Center for Agriculture Research in the Dry Areas (ICARDA) genebank. Based on prediction abilities for each trait, three scenarios for predictive characterization were compared: 1) a benchmark scenario, where test and training sets only contain ICARDA accessions, 2) across-genebank predictions using IPK as training and ICARDA as test set, and 3) integrated genebank predictions that include IPK with 30% of ICARDA accessions as a training set to predict the rest of ICARDA accessions. Within the population of ICARDA accessions, prediction abilities were low to moderate, which was presumably caused by a limited number of accessions used to train the model. Interestingly, ICARDA prediction abilities were boosted up to ninefold by using training sets composed of IPK plus 30% of ICARDA accessions. Pervasive genotype × environment interactions (GEIs) can become a potential obstacle to train robust genome-wide prediction models across genebanks. This suggests that the potential adverse effect of GEI on prediction ability was counterbalanced by the augmented training set with certain connectivity to the test set. Therefore, across-genebank predictions hold the promise to improve the curation of the world's genebank collections and contribute significantly to the long-term development of traditional genebanks toward biodigital resource centers.
Collapse
Affiliation(s)
- Samira El Hanafi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Zakaria Kehel
- International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Max Haupt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Ahmed Amri
- International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| |
Collapse
|
2
|
He T, Angessa TT, Li C. Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0015. [PMID: 37040291 PMCID: PMC10076058 DOI: 10.34133/plantphenomics.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/27/2022] [Indexed: 06/19/2023]
Abstract
Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley (Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.
Collapse
Affiliation(s)
- Tianhua He
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| |
Collapse
|
3
|
Khanna A, Anumalla M, Catolos M, Bartholomé J, Fritsche-Neto R, Platten JD, Pisano DJ, Gulles A, Sta Cruz MT, Ramos J, Faustino G, Bhosale S, Hussain W. Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines. RICE (NEW YORK, N.Y.) 2022; 15:14. [PMID: 35247120 PMCID: PMC8898209 DOI: 10.1186/s12284-022-00559-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Estimating genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI's rice drought breeding program was used to estimate the genetic trends and assess the breeding program's success. We also identified top-performing lines based on grain yield breeding values as an elite panel for implementing future population improvement-based breeding schemes. A two-stage approach of pedigree-based mixed model analysis was used to analyze the data and extract the breeding values and estimate the genetic trends for grain yield under non-stress, drought, and in combined data of non-stress and drought. Lower grain yield values were observed in all the drought trials. Heritability for grain yield estimates ranged between 0.20 and 0.94 under the drought trials and 0.43-0.83 under non-stress trials. Under non-stress conditions, the genetic gain of 0.21% (10.22 kg/ha/year) for genotypes and 0.17% (7.90 kg/ha/year) for checks was observed. The genetic trend under drought conditions exhibited a positive trend with the genetic gain of 0.13% (2.29 kg/ha/year) for genotypes and 0.55% (9.52 kg/ha/year) for checks. For combined analysis showed a genetic gain of 0.27% (8.32 kg/ha/year) for genotypes and 0.60% (13.69 kg/ha/year) for checks was observed. For elite panel selection, 200 promising lines were selected based on higher breeding values for grain yield and prediction accuracy of > 0.40. The breeding values of the 200 genotypes formulating the core panel ranged between 2366.17 and 4622.59 (kg/ha). A positive genetic rate was observed under all the three conditions; however, the rate of increase was lower than the required rate of 1.5% genetic gain. We propose a recurrent selection breeding strategy within the elite population with the integration of modern tools and technologies to boost the genetic gains in IRRI's drought breeding program. The elite breeding panel identified in this study forms an easily available and highly enriched genetic resource for future recurrent selection programs to boost the genetic gains.
Collapse
Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Jérôme Bartholomé
- AGAP Institute, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Roberto Fritsche-Neto
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - John Damien Platten
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Daniel Joseph Pisano
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Alaine Gulles
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Joie Ramos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Gem Faustino
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
| |
Collapse
|
4
|
Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
Collapse
Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
| |
Collapse
|
5
|
Babić V, Andjelkovic V, Jovovic Z, Babic M, Vasic V, Kravic N. Diversity Assessment of the Montenegrin Maize Landrace Gene Pool Maintained in Two Gene Banks. PLANTS 2021; 10:plants10081503. [PMID: 34451548 PMCID: PMC8399334 DOI: 10.3390/plants10081503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 12/04/2022]
Abstract
Due to the loss of agro-biodiversity, there is a strong effort to find apparent and efficient mechanisms for the conservation and sustainable use of genetic diversity. A joint monitoring of the diversity and collections structure of the Montenegrin maize landraces conserved in the Serbian (MRIZPGB) and Montenegrin (MGB) gene banks has been conducted in order to improve the composition of the collections and to identify and eliminate possible redundancy. Based on a separate analysis of white- and yellow-orange maize landraces, it can be concluded that the diversity and evolution of distinct maize landraces grown and collected in Montenegro have been simultaneously shaped by both environmental (i.e., natural selection) and socially driven factors (farmers’ selection, migration and colonization processes of the human population). Although it has been determined that the authenticity and variability of the Montenegrin maize landraces gene pool have largely been preserved in the MRIZPGB collection, a significant amount of redundancy was observed. The obtained results will contribute to the cost-efficient conservation of the maize gene pool in the Montenegrin and Serbian gene banks. The recognized and well-preserved original variability of the MRIZPGB and MGB Montenegrin gene pool represents a valuable source for pre-breeding activities on broadening the white and flint maize breeding programmes under temperate conditions.
Collapse
Affiliation(s)
- Vojka Babić
- Maize Research Institute Zemun Polje, Slobodana Bajica 1, 11185 Belgrade, Serbia; (V.A.); (N.K.)
- Correspondence:
| | - Violeta Andjelkovic
- Maize Research Institute Zemun Polje, Slobodana Bajica 1, 11185 Belgrade, Serbia; (V.A.); (N.K.)
| | - Zoran Jovovic
- Faculty of Biotechnology, University of Montenegro, Mihaila Lalića 1, 81000 Podgorica, Montenegro;
| | - Milosav Babic
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Vladimir Vasic
- Department of Statistics and Mathematics, Faculty of Economics, University of Belgrade, Kamenička 6, 11000 Belgrade, Serbia;
| | - Natalija Kravic
- Maize Research Institute Zemun Polje, Slobodana Bajica 1, 11185 Belgrade, Serbia; (V.A.); (N.K.)
| |
Collapse
|
6
|
Gonzalez MY, Zhao Y, Jiang Y, Stein N, Habekuss A, Reif JC, Schulthess AW. Genomic prediction models trained with historical records enable populating the German ex situ genebank bio-digital resource center of barley (Hordeum sp.) with information on resistances to soilborne barley mosaic viruses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2181-2196. [PMID: 33768281 PMCID: PMC8263548 DOI: 10.1007/s00122-021-03815-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/10/2021] [Indexed: 05/04/2023]
Abstract
Genomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers. Phenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to ~ 5% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.
Collapse
Affiliation(s)
- Maria Y Gonzalez
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Antje Habekuss
- Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
| | - Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| |
Collapse
|
7
|
Nguyen GN, Norton SL. Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm. PLANTS (BASEL, SWITZERLAND) 2020; 9:E817. [PMID: 32610615 PMCID: PMC7411623 DOI: 10.3390/plants9070817] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023]
Abstract
Genetically diverse plant germplasm stored in ex-situ genebanks are excellent resources for breeding new high yielding and sustainable crop varieties to ensure future food security. Novel alleles have been discovered through routine genebank activities such as seed regeneration and characterization, with subsequent utilization providing significant genetic gains and improvements for the selection of favorable traits, including yield, biotic, and abiotic resistance. Although some genebanks have implemented cost-effective genotyping technologies through advances in DNA technology, the adoption of modern phenotyping is lagging. The introduction of advanced phenotyping technologies in recent decades has provided genebank scientists with time and cost-effective screening tools to obtain valuable phenotypic data for more traits on large germplasm collections during routine activities. The utilization of these phenotyping tools, coupled with high-throughput genotyping, will accelerate the use of genetic resources and fast-track the development of more resilient food crops for the future. In this review, we highlight current digital phenotyping methods that can capture traits during annual seed regeneration to enrich genebank phenotypic datasets. Next, we describe strategies for the collection and use of phenotypic data of specific traits for downstream research using high-throughput phenotyping technology. Finally, we examine the challenges and future perspectives of genebank phenomics.
Collapse
Affiliation(s)
- Giao N. Nguyen
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham 3400, Australia;
| | | |
Collapse
|
8
|
Jiang Y, Weise S, Graner A, Reif JC. Using Genome-Wide Predictions to Assess the Phenotypic Variation of a Barley ( Hordeum sp.) Gene Bank Collection for Important Agronomic Traits and Passport Information. FRONTIERS IN PLANT SCIENCE 2020; 11:604781. [PMID: 33505414 PMCID: PMC7829250 DOI: 10.3389/fpls.2020.604781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/14/2020] [Indexed: 05/10/2023]
Abstract
Genome-wide predictions are a powerful tool for predicting trait performance. Against this backdrop we aimed to evaluate the potential and limitations of genome-wide predictions to inform the barley collection of the Federal ex situ Genebank for Agricultural and Horticultural Crops with phenotypic data on complex traits including flowering time, plant height, thousand grain weight, as well as on growth habit and row type. We used previously published sequence data, providing information on 306,049 high-quality SNPs for 20,454 barley accessions. The prediction abilities of the two unordered categorical traits row type and growth type as well as the quantitative traits flowering time, plant height and thousand grain weight were investigated using different cross validation scenarios. Our results demonstrate that the unordered categorical traits can be predicted with high precision. In this way genome-wide prediction can be routinely deployed to extract information pertinent to the taxonomic status of gene bank accessions. In addition, the three quantitative traits were also predicted with high precision, thereby increasing the amount of information available for genotyped but not phenotyped accessions. Deeply phenotyped core collections, such as the barley 1,000 core set of the IPK Gatersleben, are a promising training population to calibrate genome-wide prediction models. Consequently, genome-wide predictions can substantially contribute to increase the attractiveness of gene bank collections and help evolve gene banks into bio-digital resource centers.
Collapse
|
9
|
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] [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.
Collapse
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
| |
Collapse
|