Cargando…
MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species
BACKGROUND: With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F(1) population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional sta...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701343/ https://www.ncbi.nlm.nih.gov/pubmed/29169342 http://dx.doi.org/10.1186/s12859-017-1908-1 |
_version_ | 1783281316511350784 |
---|---|
author | Liu, Fenxiang Tong, Chunfa Tao, Shentong Wu, Jiyan Chen, Yuhua Yao, Dan Li, Huogen Shi, Jisen |
author_facet | Liu, Fenxiang Tong, Chunfa Tao, Shentong Wu, Jiyan Chen, Yuhua Yao, Dan Li, Huogen Shi, Jisen |
author_sort | Liu, Fenxiang |
collection | PubMed |
description | BACKGROUND: With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F(1) population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines. RESULTS: We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi’s information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F(1) population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations. CONCLUSIONS: We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F(1) population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1908-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5701343 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57013432017-12-01 MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species Liu, Fenxiang Tong, Chunfa Tao, Shentong Wu, Jiyan Chen, Yuhua Yao, Dan Li, Huogen Shi, Jisen BMC Bioinformatics Software BACKGROUND: With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F(1) population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines. RESULTS: We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi’s information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F(1) population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations. CONCLUSIONS: We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F(1) population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1908-1) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-23 /pmc/articles/PMC5701343/ /pubmed/29169342 http://dx.doi.org/10.1186/s12859-017-1908-1 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Liu, Fenxiang Tong, Chunfa Tao, Shentong Wu, Jiyan Chen, Yuhua Yao, Dan Li, Huogen Shi, Jisen MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species |
title | MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species |
title_full | MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species |
title_fullStr | MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species |
title_full_unstemmed | MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species |
title_short | MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F(1) population of outbred species |
title_sort | mvqtlcim: composite interval mapping of multivariate traits in a hybrid f(1) population of outbred species |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701343/ https://www.ncbi.nlm.nih.gov/pubmed/29169342 http://dx.doi.org/10.1186/s12859-017-1908-1 |
work_keys_str_mv | AT liufenxiang mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT tongchunfa mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT taoshentong mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT wujiyan mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT chenyuhua mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT yaodan mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT lihuogen mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies AT shijisen mvqtlcimcompositeintervalmappingofmultivariatetraitsinahybridf1populationofoutbredspecies |