QTL-BSA: A Bulked Segregant Analysis and Visualization Pipeline for QTL-seq

Area of Science:

• Plant genomics
• Quantitative genetics
• Bioinformatics

Background:

• Whole Genome Sequencing (WGS) generates extensive data for identifying trait-associated genomic loci in plants.
• Genome-assisted Quantitative Trait Loci sequencing (QTL-seq) combined with bulked segregant analysis (BSA) is increasingly popular for trait discovery.
• A lack of user-friendly software hinders the widespread adoption of QTL-seq analysis and visualization.

Purpose of the Study:

• To develop a publicly available, user-friendly software tool for the rapid identification and visualization of candidate Quantitative Trait Loci (QTLs) from QTL-seq data.
• To provide a comprehensive solution for programming and visualization tasks in QTL-seq analysis.
• To demonstrate the utility of the developed tool through a proof-of-concept study in rice.

Main Methods:

• Development of the QTL-BSA (QTL-bulked segregant analysis and visualization pipeline) software.
• Application of QTL-BSA to analyze QTL-seq data from rice with partial blast resistance.
• Utilized Whole Genome Sequencing (WGS) and bulked segregant analysis (BSA) on segregating progeny.

Main Results:

• The QTL-BSA tool successfully facilitated rapid discovery and identification of genes related to partial blast resistance in rice.
• A major QTL was identified on chromosome 6, located between 1.52 and 4.32 Mb, consistent with previous studies.
• Functional annotation of genes and QTLs within the identified genomic region was performed.

Conclusions:

• QTL-BSA provides a comprehensive and user-friendly solution for QTL-seq analysis, enabling efficient identification and visualization of candidate QTLs.
• The tool is expected to be widely adopted by the research community for plant trait discovery.
• This pipeline accelerates the process of gene discovery for important agricultural traits like disease resistance.