QTL-seq¶
Description¶
Bulked segregant analysis, as implemented in QTL-seq (Takagi et al., 2013), is a powerful and efficient method to identify agronomically important loci in crop plants. QTL-seq was adapted from MutMap to identify quantitative trait loci. It utilizes sequences pooled from two segregating progeny populations with extreme opposite traits (e.g. resistant vs susceptible) and a single whole-genome resequencing of either of the parental cultivars. While the original QTL-seq algorithm did not assume a highly heterozygous genome, a “modified QTL-seq” has been developed to handle this situation using high resolution mapping (Itoh et al., 2019)
Environment Modules¶
Run module spider qtl-seq to find out what environment modules are available for this application.
Environment Variables¶
- HPC_QTLSEQ_DIR - installation directory
- HPC_QTLSEQ_BIN - executable directory
Citation¶
If you publish research that uses QTL-seq you have to cite it as follows:
Takagi, H., Abe, A., Yoshida, K., Kosugi, S., Natsume, S., Mitsuoka, C., Uemura, A., Utsushi, H., Tamiru, M., Takuno, S., Innan, H., Cano, L. M., Kamoun, S., & Terauchi, R. (2013). QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. The Plant Journal, 74(1), 174-183. https://doi.org/10.1111/tpj.12105
Sugihara, Y., Young, L., Yaegashi, H., Natsume, S., Shea, D. J., Takagi, H., Booker, H., Innan, H., Terauchi, R., & Abe, A. (2020). High-performance pipeline for MutMap and QTL-seq. PeerJ, 8, e10117. https://doi.org/10.7717/peerj.10117
Categories¶
biology, genomics