IonBreeders : bioinformatics plugins toward genomics-assisted breeding

Détails bibliographiques
Publié dans:	Breeding science. - 1998. - 70(2020), 3 vom: 01. Juni, Seite 396-401
Auteur principal:	Ogiso-Tanaka, Eri (Auteur)
Autres auteurs:	Yabe, Shiori, Tanaka, Tsuyoshi
Format:	Article en ligne
Langue:	English
Publié:	2020
Accès à la collection:	Breeding science
Sujets:	Journal Article genomic prediction genotyping next-generation sequencing plugin

Description
Résumé:	Copyright © 2020 by JAPANESE SOCIETY OF BREEDING. 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
Description:	Date Revised 28.09.2020 published: Print-Electronic Citation Status PubMed-not-MEDLINE
ISSN:	1344-7610
DOI:	10.1270/jsbbs.19141