WGG: a graphical tool for visualizing genome structures using SNPs detected by next-generation sequencing

Monitoring genome structure provides a great advantage for efficiently and accurately advancing breeding. However, genotyping using DNA markers distributed across the genome is time-consuming and labor-intensive for breeders. Here, we developed a graphical user interface application, "WGG: Whole Genome Genotyping", enabling rapid and easy visualization of genome structures based on single nucleotide polymorphisms (SNPs) detected by resequencing with next-generation sequencing short reads. The accuracy of WGG is enhanced by selecting SNPs from parental resequencing data and determining the majority genotype within each genomic region. As proof of principle, we efficiently developed near-isogenic lines in rice by monitoring genome backgrounds with WGG in intermediate generations. The identification of residual donor regions with WGG facilitated their elimination using DNA markers designed at these loci. Furthermore, we confirmed the applicability of WGG in rice recombinant inbred lines and heterozygous plants, Brassica rapa. In addition, WGG was confirmed to run smoothly on a standard desktop PC even with sufficient sequencing data, making it practical for breeders. WGG will be a powerful tool for visualizing genome structures in breeding intermediate generations, enabling whole-genome selection that will accelerate breeding in diverse crops.