In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

VIEWpoly Citation

If you use VIEWpoly in your research, please cite:

Taniguti, C. H., de Siqueira Gesteira, G., Lau, J., da Silva Pereira, G., Zeng, Z.-B., Byrne, D., Riera-Lizarazu, O., & Mollinari, M. (2022). VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. Journal of Open Source Software, 7(74), 4242. https://doi.org/10.21105/joss.04242

Linkage Mapping Software Citations

MAPpoly

Mollinari, M., & Garcia, A. A. F. (2019). Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3: Genes|Genomes|Genetics, 9(10), 3297–3314. https://doi.org/10.1534/g3.119.400378

polymapR

Bourke, P. M., van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M., & Maliepaard, C. (2018). PolymapR - Linkage analysis and genetic map construction from F 1 populations of outcrossing polyploids. Bioinformatics, 34(20), 3496–3502. https://doi.org/10.1093/bioinformatics/bty371

OneMap

Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Lau, J., Gesteira, G. de S., Oliveira, T. de P., Ferreira, G. C., Pereira, G. da S., Byrne, D., Mollinari, M., Riera-Lizarazu, O., & Garcia, A. A. F. (2022). Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12. https://doi.org/10.1093/gigascience/giad092

QTL Analysis Software Citations

QTLpoly

da Silva Pereira, G., Gemenet, D. C., Mollinari, M., Olukolu, B. A., Wood, J. C., Diaz, F., Mosquera, V., Gruneberg, W. J., Khan, A., Buell, C. R., Yencho, G. C., & Zeng, Z.-B. (2020). Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population. Genetics, 215(3), 579–595. https://doi.org/10.1534/genetics.120.303080

diaQTL

Amadeu, R. R., Muñoz, P. R., Zheng, C., & Endelman, J. B. (2021). QTL mapping in outbred tetraploid (and diploid) diallel populations. Genetics, 219(3). https://doi.org/10.1093/genetics/iyab124

polyqtlR

Bourke, P. M., Voorrips, R. E., Hackett, C. A., van Geest, G., Willemsen, J. H., Arens, P., Smulders, M. J. M., Visser, R. G. F., & Maliepaard, C. (2021). Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR. Bioinformatics, 37(21), 3822–3829. https://doi.org/10.1093/bioinformatics/btab574

GWASpoly

Rosyara, U. R., de Jong, W. S., Douches, D. S., & Endelman, J. B. (2016). Software for Genome‐Wide Association Studies in Autopolyploids and Its Application to Potato. The Plant Genome, 9(2). https://doi.org/10.3835/plantgenome2015.08.0073

Visualization Tools Citations

HIDECAN

Angelin-Bonnet, O., Vignes, M., Biggs, P. J., Baldwin, S., & Thomson, S. (2024). Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package. Genes, 15(10). https://doi.org/10.3390/genes15101244

JBrowseR

Hershberg, E. A., Stevens, G., Diesh, C., Xie, P., de Jesus Martinez, T., Buels, R., Stein, L., & Holmes, I. (2021). JBrowseR: an R interface to the JBrowse 2 genome browser. Bioinformatics, 37(21), 3914–3915. https://doi.org/10.1093/bioinformatics/btab459

Acknowledgments

VIEWpoly was developed during the Tools for Polyploid Project by researchers at Texas A&M University and North Carolina State University. It is now updated and maintained by Breeding Insight.

Funding support from the USDA Agricultural Research Service through the University of Florida Institute of Food and Agricultural Sciences is gratefully acknowledged.