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Summary  Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker‐assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser ( iBrowser ), a bioinformatics tool aimed at visualizing introgressions at nucleotide or  SNP  (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous  SNP s from Variant Call Format ( VCF ) information and filters out heterozygous  SNP s, multi‐nucleotide polymorphisms ( MNP s) and insertion–deletions (InDels). For data analysis  iBrowser  makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format ( GFF ) information. In an example of tomato ( Solanum lycopersicum ) accessions we visualize  SNP  patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien  DNA  in a panel of the closely related  S. pimpinellifolium  by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the  iBrowser  in a panel of 597  Arabidopsis  accessions, detecting the boundaries of a  SNP ‐free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of  iBrowser  makes the software appropriate for a broad set of analyses including  SNP  mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes  iBrowser  a valuable breeding tool.

Introgression browser: high‐throughput whole‐genome SNP visualization