Table_2_Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing.xlsx

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.

与农艺性状相关的标记是分子育种的基础。基因分型测序（GBS）数据能够检测包括单核苷酸多态性（SNPs）和短插入或缺失（InDels）在内的小型多态性，这些多态性可用于例如标记辅助选择、种群遗传学和全基因组关联研究（GWAS）。在此，我们旨在基于GBS数据检测大麦和小麦中的大染色体变异。这些变异可能包括重复、删除、替换以及包括杂交在内的DNA甲基化改变。我们展示了GBS覆盖度分析能够检测到Hordeum vulgare/Hordeum bulbosum杂交系。此外，我们还在大麦和小麦集合中识别出大染色体变异。因此，包括杂交和拷贝数变异（CNV）在内的大染色体变异能够轻易被检测到，并可作为研究育种中的标记使用，而无需额外的湿实验室实验。