statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations

Wenhao Li; Martin P Boer; Bart-Jan van Rossum; Chaozhi Zheng; Ronny V L Joosen; Fred A van Eeuwijk

doi:10.1093/bioinformatics/btac662

statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations

Bioinformatics. 2022 Nov 15;38(22):5134-5136. doi: 10.1093/bioinformatics/btac662.

Authors

Wenhao Li¹, Martin P Boer¹, Bart-Jan van Rossum¹, Chaozhi Zheng¹, Ronny V L Joosen², Fred A van Eeuwijk¹

Affiliations

¹ Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands.
² Rijk Zwaan Breeding B.V., De Lier 2678 ZG, The Netherlands.

Abstract

Motivation: Multi-parent populations (MPPs) are popular for QTL mapping because they combine wide genetic diversity in parents with easy control of population structure, but a limited number of software tools for QTL mapping are specifically developed for general MPP designs.

Results: We developed an R package called statgenMPP, adopting a unified identity-by-descent (IBD)-based mixed model approach for QTL analysis in MPPs. The package offers easy-to-use functionalities of IBD calculations, mixed model solutions and visualizations for QTL mapping in a wide range of MPP designs, including diallele, nested-association mapping populations, multi-parent advanced genetic inter-cross populations and other complicated MPPs with known crossing schemes.

Availability and implementation: The R package statgenMPP is open-source and freely available on CRAN at https://CRAN.R-project.org/package=statgenMPP.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Mapping
Software*

Grants and funding

Rijk Zwaan Breeding B.V.