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.
System Variables
- HPC_QTL-SEQ_DIR - installation directory
- HPC_QTL-SEQ_BIN - executable directory
Citation
If you publish research that uses QTL-seq you have to cite it as follows:
Hiroki Takagi, Akira Abe, Kentaro Yoshida, Shunichi Kosugi, Satoshi Natsume, Chikako Mitsuoka, Aiko Uemura, Hiroe Utsushi, Muluneh Tamiru, Shohei Takuno, Hideki Innan, Liliana M. Cano, Sophien Kamoun, Ryohei Terauchi (2013). QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant journal 74:174-183. [URL]
Yu Sugihara, Lester Young, Hiroki Yaegashi, Satoshi Natsume, Daniel J. Shea, Hiroki Takagi, Helen Booker, Hideki Innan, Ryohei Terauchi, Akira Abe (2020). High performance pipeline for MutMap and QTL-seq.[URL]