High-performance pipeline for MutMap and QTL-seq

Yu Sugihara; Lester Young; Hiroki Yaegashi; Satoshi Natsume; Daniel J Shea; Hiroki Takagi; Helen Booker; Hideki Innan; Ryohei Terauchi; Akira Abe

doi:10.7717/peerj.13170

High-performance pipeline for MutMap and QTL-seq

PeerJ. 2022 Mar 18:10:e13170. doi: 10.7717/peerj.13170. eCollection 2022.

Authors

Yu Sugihara^{1

2}, Lester Young³, Hiroki Yaegashi¹, Satoshi Natsume¹, Daniel J Shea¹, Hiroki Takagi⁴, Helen Booker^{3

5}, Hideki Innan⁶, Ryohei Terauchi^{1

2}, Akira Abe¹

Affiliations

¹ Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan.
² Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
³ Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
⁴ Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan.
⁵ Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada.
⁶ Graduate University for Advanced Studies, Hayama, Japan.

Abstract

Summary: Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies.

Availability: The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).

Keywords: Agricultural science; Bioinformatics; Bulked-segregant analysis; Mutation mapping; QTL analysis.

Publication types

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

MeSH terms

Chromosome Mapping / methods
Phenotype
Quantitative Trait Loci* / genetics
Software*

Grants and funding

This work was supported by JSPS KAKENHI Grant Number 20H02962 to Akira Abe. Support for Lester Young and Helen Booker was through Saskatchewan Agriculture Ministry’s Agriculture Development Fund Grants 20160222 and 20170199 and Agriculture and AgriFoods Canada’s Diverse Field Crops Cluster ASC-05. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.