Ogiso-Tanaka Eri, Yabe Shiori, Tanaka Tsuyoshi
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
Breed Sci. 2020 Jun;70(3):396-401. doi: 10.1270/jsbbs.19141. Epub 2020 Jun 5.
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.
新一代测序（NGS）技术所产生的多态性信息已使全基因组标记辅助育种得以应用。然而，处理如此大规模的数据对实验研究人员和育种者来说仍是一项挑战，这就迫切需要开发一种灵活且简便的NGS数据分析工具。我们开发了“IonBreeders”作为生物信息学插件，它实现了从基因分型到基因组预测的一般分析步骤。IonBreeders包含三个插件，即“ABH”“IMPUTATION”和“GENOMIC PREDICTION”，分别用于基因分型数据的格式转换、基因分型数据的预处理和插补以及基因组预测。“ABH”将源自NGS的基因分型数据转换为ABH格式，这是我们后续插件以及其他育种软件工具（R/qtl、MapMaker和AntMap）所认可的格式。“IMPUTATION”会滤除无信息的标记并插补缺失的标记基因型。在“GENOMIC PREDICTION”中，用户可根据其目标性状、数量性状基因座效应和标记数量使用四种统计方法，并构建用于基因组选择的预测模型。IonBreeders在Torrent Suite中运行，但也可通过使用免费软件或我们提供的脚本进行格式转换来处理标准格式的基因型数据，例如变异调用格式（VCF）。
