WGG: a graphical tool for visualizing genome structures using SNPs detected by next-generation sequencing.
- 1Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
- 2Ishikawa Agriculture Research Center, 295-1 Saida Bo, Kanazawa, Ishikawa 920-3198, Japan.
Abstract
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.
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BibTeX
@article{takata2026graphical,
title = {{WGG: a graphical tool for visualizing genome structures using SNPs detected by next-generation sequencing.}},
author = {Marina Takata and Miki Sakemoto and Mutsuki Oishi and Makishi Hara and Masahide Yoshizumi and Tenta Segawa and Rintaro Harada and Hiroki Takagi},
journal = {Breeding science},
year = {2026},
month = jun,
doi = {10.1270/jsbbs.25080},
url = {https://europepmc.org/article/MED/42936854},
note = {CC BY},
}
RIS
TY - JOUR
TI - WGG: a graphical tool for visualizing genome structures using SNPs detected by next-generation sequencing.
AU - Marina Takata
AU - Miki Sakemoto
AU - Mutsuki Oishi
AU - Makishi Hara
AU - Masahide Yoshizumi
AU - Tenta Segawa
AU - Rintaro Harada
AU - Hiroki Takagi
PY - 2026
DA - 2026/06/11
JO - Breeding science
DO - 10.1270/jsbbs.25080
UR - https://europepmc.org/article/MED/42936854
AB - 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.
SN - 1344-7610
SN - 1347-3735
ER -