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Deblieck M, Fatiukha A, Grundman N, Merchuk-Ovnat L, Saranga Y, Krugman T, Pillen K, Serfling A, Makalowski W, Ordon F, Perovic D. GenoTypeMapper: graphical genotyping on genetic and sequence-based maps. Plant Methods 2020; 16:123. [PMID: 32944061 PMCID: PMC7488165 DOI: 10.1186/s13007-020-00665-7] [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: 12/05/2019] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. RESULTS We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. CONCLUSIONS In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.
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Affiliation(s)
- Mathieu Deblieck
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andrii Fatiukha
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Norbert Grundman
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Lianne Merchuk-Ovnat
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Yehoshua Saranga
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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