Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data
Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, we provide information about predicted introgressions at 1-Mb...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1166854/full |
| _version_ | 1797810490205798400 |
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| author | Jens Keilwagen Heike Lehnert Ekaterina D. Badaeva Ekaterina D. Badaeva Hakan Özkan Shivali Sharma Peter Civáň Benjamin Kilian |
| author_facet | Jens Keilwagen Heike Lehnert Ekaterina D. Badaeva Ekaterina D. Badaeva Hakan Özkan Shivali Sharma Peter Civáň Benjamin Kilian |
| author_sort | Jens Keilwagen |
| collection | DOAJ |
| description | Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, we provide information about predicted introgressions at 1-Mb resolution for 9,172 wheat samples as a resource for breeders and scientists. We recommend that all plant genetic resources, including genebank collections, be characterized using a combination of variant calling and introgression prediction. This is necessary to identify potential duplicates in collections efficiently and reliably, and to select promising germplasms with potentially beneficial introgressions for further characterization and prospective breeding application. |
| first_indexed | 2024-03-13T07:08:41Z |
| format | Article |
| id | doaj.art-6b16e7a18e964bd3b2e5841276e6f555 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-13T07:08:41Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-6b16e7a18e964bd3b2e5841276e6f5552023-06-06T04:57:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-06-011410.3389/fpls.2023.11668541166854Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing dataJens Keilwagen0Heike Lehnert1Ekaterina D. Badaeva2Ekaterina D. Badaeva3Hakan Özkan4Shivali Sharma5Peter Civáň6Benjamin Kilian7Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, GermanyInstitute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, GermanyN.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, RussiaThe Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, RussiaDepartment of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, TürkiyeGlobal Crop Diversity Trust, Bonn, GermanyUniversité Clermont Auvergne, INRAE, Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, FranceGlobal Crop Diversity Trust, Bonn, GermanyRecently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, we provide information about predicted introgressions at 1-Mb resolution for 9,172 wheat samples as a resource for breeders and scientists. We recommend that all plant genetic resources, including genebank collections, be characterized using a combination of variant calling and introgression prediction. This is necessary to identify potential duplicates in collections efficiently and reliably, and to select promising germplasms with potentially beneficial introgressions for further characterization and prospective breeding application.https://www.frontiersin.org/articles/10.3389/fpls.2023.1166854/fullplant genetic resourcescrop wild relativesgenetic diversityinterspecific introgressioncoverageduplicates |
| spellingShingle | Jens Keilwagen Heike Lehnert Ekaterina D. Badaeva Ekaterina D. Badaeva Hakan Özkan Shivali Sharma Peter Civáň Benjamin Kilian Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data Frontiers in Plant Science plant genetic resources crop wild relatives genetic diversity interspecific introgression coverage duplicates |
| title | Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data |
| title_full | Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data |
| title_fullStr | Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data |
| title_full_unstemmed | Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data |
| title_short | Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data |
| title_sort | finding needles in a haystack identification of inter specific introgressions in wheat genebank collections using low coverage sequencing data |
| topic | plant genetic resources crop wild relatives genetic diversity interspecific introgression coverage duplicates |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1166854/full |
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