Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data

Jens Keilwagen; Heike Lehnert; Ekaterina D Badaeva; Hakan Özkan; Shivali Sharma; Peter Civáň; Benjamin Kilian

doi:10.3389/fpls.2023.1166854

Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data

Front Plant Sci. 2023 Jun 6:14:1166854. doi: 10.3389/fpls.2023.1166854. eCollection 2023.

Authors

Jens Keilwagen¹, Heike Lehnert¹, Ekaterina D Badaeva^{2

3}, Hakan Özkan⁴, Shivali Sharma⁵, Peter Civáň⁶, Benjamin Kilian⁵

Affiliations

¹ Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany.
² N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
³ The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.
⁴ Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Türkiye.
⁵ Global Crop Diversity Trust, Bonn, Germany.
⁶ Université Clermont Auvergne, INRAE, Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France.

Abstract

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.

Keywords: Triticum; coverage; crop wild relatives; duplicates; genetic diversity; heterogeneity; interspecific introgression; plant genetic resources.

Grants and funding

This work was undertaken as part of the initiative “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives” and as part of the initiative “Biodiversity for Opportunities, Livelihoods and Development (BOLD),” both supported by the Government of Norway. Grant numbers from the Norwegian Government: *QZA-14/0005* and *QZA-20/0154*. This work was also supported by the Russian Science Foundation (grant no. 21-76-30003).