Table1_GAHP: An integrated software package on genetic analysis with bi-parental immortalized heterozygous populations.docx

GAHP is a freely available software package for genetic analysis with bi-parental immortalized heterozygous and pure-line populations. The package is project-based and integrated with multiple functions. All operations and running results are properly saved in a project, which can be recovered when the project is re-open by the package. Four functionalities have been implemented in the current version of GAHP, i.e., 1) MHP: visualization of genetic linkage maps; 2) VHP: analysis of variance (ANOVA) and estimation of heritability on phenotypic data; 3) QHP: quantitative trait locus (QTL) mapping on both genotypic and phenotypic data; 4) SHP: simulation of bi-parental immortalized heterozygous and pure-line populations, and power analysis of QTL mapping. VHP and QHP can be conducted in individual populations, as well as in multiple populations by the combined analysis. Input files are arranged either in the plain text format with an extension name same as the functionality or in the MS Excel formats. Output files have the same prefix name as the input file, but with different extensions to indicate their contents. Three characters before the extension names stand for the types of populations used in analysis. In the interface of the software package, input files are grouped by functionality, and output files are grouped by individual or combined mapping populations. In addition to the text-format outputs, the constructed linkage map can be visualized per chromosome or for a number of selected chromosomes; line plots and bi-plots can be drawn from QTL mapping results and phenotypic data. Functionalities and analysis methods available in GAHP help the investigation of genetic architectures of complex traits and the mechanism of heterosis in plants.

GAHP是一款免费可用的遗传分析软件包，可用于双亲永久杂合群体（bi-parental immortalized heterozygous populations）与纯系群体（pure-line populations）的遗传分析。该软件包采用项目化架构，集成了多项功能；所有操作与运行结果都会妥善存储至项目中，重新打开该软件即可恢复项目数据。当前版本的GAHP共包含四项核心功能：1）MHP：遗传连锁图谱可视化；2）VHP：针对表型数据的方差分析（analysis of variance, ANOVA）与遗传力估算；3）QHP：基于基因型与表型数据的数量性状位点（quantitative trait locus, QTL）定位；4）SHP：双亲永久杂合与纯系群体模拟，以及QTL定位效力分析。VHP与QHP既支持单群体分析，也可通过联合分析实现多群体分析。输入文件可采用两种格式：一是与功能名称匹配扩展名的纯文本格式，二是微软Excel（MS Excel）格式。输出文件与输入文件前缀名一致，但扩展名不同以标识其内容类型；扩展名前的三位字符代表本次分析所用的群体类型。在该软件的界面中，输入文件按功能分组，输出文件则按单群体或联合定位群体分组。除文本格式输出外，构建的遗传连锁图谱可按单条染色体或选定的多条染色体进行可视化；QTL定位结果与表型数据可用于绘制折线图与双标图（bi-plots）。GAHP内置的各项功能与分析方法，可为植物复杂性状遗传架构及杂种优势（heterosis）机制研究提供有力支撑。