QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations
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DOI：
10.1016/j.cj.2015.01.001
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发表时间：
2015-06-01
期刊：
影响因子：
6.6
通讯作者：
Wang, Jiankang
中科院分区：
文献类型：
--
作者：
Meng, Lei;Li, Huihui;Wang, Jiankang
QTL IciMapping是一个免费的公共软件，能够在双亲本群体中建立高密度的连锁图谱和定量性状位点（QTL）的定位。该软件包集成了八个功能：(1)BIN：冗余标记的分箱；(2) MAP：双亲本群体连锁图谱的构建；(3) CMP：由多个共享共同标记的链接图构建共识图；(4) SDL：分离畸变位点的映射；(5) BIP：加性、显性和遗传上位基因的定位；(6) MET: QTL-by-environment交互作用分析；(7) CSL：利用染色体片段替代系定位加性和遗传上位基因；(8) NAM: NAM群体的QTL定位。输入文件可以排列为纯文本、MS Excel 2003或MS Excel 2007格式。输出文件具有与输入相同的前缀名称，但扩展名不同。例如，BIN中有两个输出文件，一个用于总结每个BIN中已识别的BIN组和已删除的标记，另一个用于使用MAP功能。MAP生成了8个输出文件，包括已完成的连锁图的摘要、单个标记的孟德尔比率测试、重组频率的估计、LOD分数和遗传距离，以及使用BIP、SDL和MET功能的输入文件。BIP生成了30多个输出文件，包括所有扫描位置的结果、确定的QTL、排列测试和多达六种映射方法的检测能力。还开发了三个补充工具来显示完整的遗传连锁图，估计两个位点之间的重组频率，并对多环境试验进行方差分析。(C) 2015中国作物科学学会，中国农业科学院作物科学研究所。这是一篇基于CC by-nc-nd许可（http://creativecommons.org/licenses/by-nc-nd/4.0/）的开放获取文章。
QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials. (C) 2015 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).