Bulk Segregant Analysis (BSA)

Introduction to BSA

BSA, bulk segregant analysis, is a QTL mapping technique for identifying genomic loci affecting a trait of interest. The technique involves forming two groups crossing by individual in the extremely opposite phenotypes or a mutant of interest is crossed to wild-type, then two bulks are created by selecting individuals from the tails of the phenotypic distribution followed by pool sequencing, then the allele frequencies are estimated for the two bulks, differences would be exhibited between the two bulks if the regions of genome containing causal loci.

Overview of BSA

Analysis pipeline

Key Advantages and Features

  • Short experimental period
  • Accurate mapping results
  • Cost-effective

Common methods

  • QTL-seq: mapping of natural mutation gene
  • Mutmap: mapping of artificial mutation gene

BSA workflow:

Bulk Segregant Analysis (BSA) workflow

Service Specifications

Sample requirements and preparation

• Samples types: Two extreme phenotype parents or wild-type phenotype parents, extreme phenotype offspring mixed pool with at least 20 individuals
• DNA sample: ~1.5 μg (concentration ≥ 30 ng/μl; OD260/280=1.8~2.0)


• Illumina HiSeq platforms
• Parental pool 20X, offspring pool 30X
• Analysis of sequencing quality metrics

Bioinformatics Analysis

We provide customized bioinformatics analysis including:

• Raw data QC
• Reference alignment
• SNP, Indel, SV detection and annotation
• Allele frequency analysis
• Position mapping of trait of interest
• Functional annotation of candidate genes


• Raw data(FASTQ)
• Data analysis report