Introgression browser: high‐throughput whole‐genome SNP visualization

Abstract

SUMMARYBreeding 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 SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi-nucleotide polymorphisms (MNPs) 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.

Tracing ancestor rice of Suriname Maroons back to its African origin

“…4b; Supplementary Fig. 3) was calculated using a modified 26 approach with Introgression Browser (vdef67dd) and FastTree2 40 (v2.1.7). As 99.9% of the polymorphic positions in the genome are excluded by the regular method of deleting positions in which any accession presents either no sequencing coverage, MNPs, InDels or heterozygous SNPs, we decided to keep heterozygous SNPs and regions of no coverage.…”

“…1), the Surinamese sample clusters near a group largely consisting of Western Guinean forest countries. Genetic distance was calculated using concatenated SNPs following a modified 26 methodology, where distances to the Surinamese sample showed that the Western Guinean forest countries were closer than Eastern countries ( Fig. 3b and Supplementary Fig.…”

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

“…Given that the genomes of most donor species are poorly characterized, marker data at best allow only the position of an introgressed segment to be defined on the basis of the loss of wheat markers; they cannot determine either the size of the introduced segment or analyse its genetic content. The recently developed ‘Introgression Browser’ (Aflitos et al ., ) combines genotypic data with phylogenetic inferences to identify the origin of an introgressed segment, but to do so, a high‐quality reference sequence of the host genome is needed, along with a large set of donor sequence data. The first of these requirements is being addressed by a concerted effort to acquire a reference sequence for bread wheat (http://www.wheatgenome.org).…”

Gramene database: Navigating plant comparative genomics resources

“…(A) Genetic variations available in tomato, e.g. , missense variation in vcZWL8FA [11]. (B) Genomic variations (SNP data for ZWL8FA ) mapped to the Genome Browser.…”