Citation


WheatGmap

Zhang, L., Dong, C., Chen, Z., Gui, L., Chen, C., Li, D., Xie, Z., Zhang, Q., Zhang, X., Xia, C., Liu, X., Kong, X., & Wang, J. (2020). WheatGmap: A Comprehensive Platform for Wheat Gene Mapping and Genomic Studies. Molecular Plant. https://doi.org/https://doi.org/10.1016/j.molp.2020.11.018


Genome and Gene annotation

Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., Pozniak, C. J., Choulet, F., Distelfeld, A., Poland, J., Ronen, G., Barad, O., Baruch, K., Keeble-Gagnère, G., Mascher, M., Ben-Zvi, G., Josselin, A. A., Himmelbach, A., Balfourier, F., … Wang, L. (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361(6403). https://doi.org/10.1126/science.aar7191

Ramírez-González, R. H., Borrill, P., Lang, D., Harrington, S. A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., Van Ex, F., Pasha, A., Khedikar, Y., Robinson, S. J., Cory, A. T., Florio, T., Concia, L., Juery, C., Schoonbeek, H., Steuernagel, B., Xiang, D., … Uauy, C. (2018). The transcriptional landscape of polyploid wheat. Science, 361(6403). https://doi.org/10.1126/science.aar6089


BSA mapping

SNP-index:

Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., Yoshida, K., Mitsuoka, C., Tamiru, M., Innan, H., Cano, L., Kamoun, S., & Terauchi, R. (2012). Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology, 30(2). https://doi.org/10.1038/nbt.2095

Mansfeld, B. N., & Grumet, R. (2018). QTLseqr: An R Package for Bulk Segregant Analysis with Next-Generation Sequencing. The Plant Genome, 11(2), 0. https://doi.org/10.3835/plantgenome2018.01.0006

varBScore:

Dong, C., Zhang, L., Chen, Z., Xia, C., & Gu, Y. (2020). Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat. 11(August), 1–12. https://doi.org/10.3389/fpls.2020.01249

ED:

Gorsi, B., Yost, H. J., Demarest, B. L., Bisgrove, B. W., Hill, J. T., & Su, Y.-C. (2013). MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq. Genome Research, 23(4), 687–697. https://doi.org/10.1101/gr.146936.112

G prime:

Gorsi, B., Yost, H. J., Demarest, B. L., Bisgrove, B. W., Hill, J. T., & Su, Y.-C. (2013). MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq. Genome Research, 23(4), 687–697. https://doi.org/10.1101/gr.146936.112

QTLseqr:

Mansfeld, B. N., & Grumet, R. (2018). QTLseqr: An R Package for Bulk Segregant Analysis with Next-Generation Sequencing. The Plant Genome, 11(2), 0. https://doi.org/10.3835/plantgenome2018.01.0006


BSA Demo

Harrington, S. A., Cobo, N., Karafiátová, M., Doležel, J., Borrill, P., & Uauy, C. (2019). Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.00963

Gardiner, L.-J., Bansept-Basler, P., El-Soda, M., Hall, A., & O’Sullivan, D. M. (2019). A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene. BioRxiv, 793604. https://doi.org/10.1101/793604

Dong, C., Zhang, L., Chen, Z., Xia, C., & Gu, Y. (2020). Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat. 11(August), 1–12. https://doi.org/10.3389/fpls.2020.01249