GAHP: An integrated software package on genetic analysis with bi-parental immortalized heterozygous populations
文献类型： 外文期刊
作者： Zhang, Luyan 1 ; Wang, Xinhui 3 ; Wang, Kaiyi 3 ; Wang, Jiankang 1 ;
作者机构： 1.Chinese Acad Agr Sci CAAS, Natl Key Facil Crop Gene Resources & Genet Improve, Beijing, Peoples R China
2.Chinese Acad Agr Sci CAAS, Inst Crop Sci, Beijing, Peoples R China
3.Beijing Acad Agr & Forestry Sci, Informat Technol Res Ctr, Beijing, Peoples R China
4.Chinese Acad Agr Sci CAAS, Natl Nanfan Res Inst Sanya, Hainan, Peoples R China
关键词： bi-parental population; immortalized heterozygous population; analysis of variance; QTL mapping; genetic simulation
期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.772； 五年影响因子：4.933 ）
ISSN：
年卷期： 2022 年 13 卷
页码：
收录情况： SCI
摘要： 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.
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