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IonBreeders: bioinformatics plugins toward genomics-assisted breeding.

Authors
  • Ogiso-Tanaka, Eri1
  • Yabe, Shiori1
  • Tanaka, Tsuyoshi1
  • 1 Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan. , (Japan)
Type
Published Article
Journal
Breeding science
Publication Date
Jun 01, 2020
Volume
70
Issue
3
Pages
396–401
Identifiers
DOI: 10.1270/jsbbs.19141
PMID: 32714063
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Polymorphism information generated by next-generation sequencing (NGS) technologies has enabled applications of genome-wide markers assisted breeding. However, handling such large-scale data remains a challenge for experimental researchers and breeders, calling for the urgent development of a flexible and straightforward analysis tool for NGS data. We developed "IonBreeders" as bioinformatics plugins that implement general analysis steps from genotyping to genomic prediction. IonBreeders comprises three plugins, "ABH", "IMPUTATION", and "GENOMIC PREDICTION", for format conversion of genotyping data, preprocessing and imputation of genotyping data, and genomic prediction, respectively. "ABH" converts genotyping data derived from NGS into the ABH format, which is acceptable for our further plugins and with other breeding software tools, R/qtl, MapMaker, and AntMap. "IMPUTATION" filters out non-informative markers and imputes missing marker genotypes. In "GENOMIC PREDICTION", users can use four statistical methods based on their target trait, quantitative trait locus effect, and number of markers, and construct a prediction model for genomic selection. IonBreeders is operated in Torrent Suite, but can also handle genotype data in standard formats, e.g., Variant Call Format (VCF), by format conversion using free software or our provided scripts. Copyright © 2020 by JAPANESE SOCIETY OF BREEDING.

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