Abstract
Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.
Highlights
Due to the progress in DNA sequencing, collections of plant species can be compared at the genomelevel to analyze the diversity within the collection
We present a bioinformatics approach that is able to detect large chromosomal modifications using standard GBS coverage data and demonstrate its applicability for barley and wheat. We demonstrate that this method is able to detect large chromosomal modifications, e.g., introgression and copy number variations (CNV), if no pedigree or data from the parent plants is available
For introgression line 60 (ERR699850) that is supposed to have an introgression on chromosome 1HL and 7HL, the longest stretch of outliers was observed on chromosome 2HS that showed an increased GBS coverage
Summary
Due to the progress in DNA sequencing, collections of plant species can be compared at the genomelevel to analyze the diversity within the collection. Introgressions from crop wild relatives are substitutions or additions of large chromosomal regions and have been used to improve crop plants (Zamir, 2001; Dempewolf et al, 2017), e.g., as source of resistance or tolerance to biotic and abiotic stress in wheat (Rabinovich, 1998; Crespo-Herrera et al, 2017) Experimental methods, such as C-banding (Friebe et al, 1996), dot-blot genomic hybridization (Rey and Prieto, 2017), fluorescence in-situ hybridization (FISH) (Rayburn and Gill, 1986; Schneider et al, 2005), genomic in-situ hybridization (GISH) (Le et al, 1989; Schwarzacher et al, 1989) and acid or SDS-PAGE (Milovanović et al, 1998), are the state-of-the-art wet-lab techniques for detection and characterization of introgressions. If specific markers are available, PCR-based methods can be used to detect well-known introgressions (Ko et al, 2002)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
