Introducing Bulked Segregant RNA-Seq (BSR-Seq)

Bulked segregant analysis (BSA) is an efficient method to map genes responsible for mutant phenotypes. BSR-Seq makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified.

BSR-Seq provides not only the map position of a gene responsible for a mutant phenotype but also the effects of such a mutant on global patterns of gene expression. The expression patterns of genes within the mapping interval can be used to prioritize candidate genes based on the fact that the causal gene will often be down-regulated in the mutant pool as compared to the non-mutant pool. In addition, this strategy yields a collection of polymorphic SNPs that are tightly linked to the mutant. These SNPs could be used to fine map the mutant or clone the affected gene via chromosome walking. Hence, BSR-Seq is not only an efficient strategy for mapping genes, but also yields other data that facilitate gene cloning.

Researchers from Iowa State University demonstrated the utility of BSR-Seq by cloning the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. By subjecting the reference allele of gl3 to BSR-Seq, they were able to map the gl3 locus to an ~2 Mb interval. The single gene located in the ~2 Mb mapping interval whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independent transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.

  • Liu S, Yeh C-T, Tang HM, Nettleton D, Schnable PS (2012) Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq). PLoS ONE 7(5): e36406. [article]