Mapping mutations in plant genomes with the user-friendly web application CandiSNP

Area of Science:

• Plant genetics
• Molecular biology
• Bioinformatics

Background:

• Forward-genetic screens identify key plant signaling pathway components.
• Mutation mapping traditionally uses F2 recombinant populations and genome-wide polymorphisms.
• High-throughput sequencing (HTS) combined with bulk segregant analysis accelerates mutation identification.

Purpose of the Study:

• To develop a novel strategy for mapping causative mutations using SNP density plots.
• To create a user-friendly web application, CandiSNP, for analyzing HTS data.
• To validate the CandiSNP tool using data from Arabidopsis thaliana.

Main Methods:

• Utilized single nucleotide polymorphism (SNP) density plots for mutation mapping.
• Developed the CandiSNP web application to generate density plots from HTS data.
• Identified candidate causative mutations as SNPs causing non-synonymous changes.

Main Results:

• Demonstrated the effectiveness of SNP density plots for refining mutation positions.
• CandiSNP successfully highlights and lists candidate causative mutations.
• Proof-of-concept using Arabidopsis thaliana confirmed the tool's validity.

Conclusions:

• CandiSNP is a valuable, user-friendly tool for forward-genetic mutant screens.
• The application is particularly effective for analyzing HTS data from bulked back-crossed mutants.
• CandiSNP facilitates novel discoveries in plant genetics and is freely available online.