ArticlePloS one2012
Gene mapping via bulked segregant RNA-Seq (BSR-Seq).
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 199 papers.
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199 citing papers in PubMed, 392 citations in OpenAlex.
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- Understanding Callus Types in Maize by Genetic Mapping and Transcriptional Profiling.Plants (Basel, Switzerland) · 2025Article
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- Integrating Genetic Mapping and BSR-Seq Analysis to Identify Candidate Genes Controlling Fruitfulness inPlants (Basel, Switzerland) · 2025Article
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- Molecular mapping of candidate genes in determining red color of perilla leaf.Advanced biotechnology · 2025Article
- Mapping and characterization of a novel powdery mildew resistance locus (PM2) inFrontiers in plant science · 2025Article
- An epiallele of a gene encoding a PfkB-type carbohydrate kinase affects plant architecture in maize.The Plant cell · 2024Article
- Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves.G3 (Bethesda, Md.) · 2024Article
- Tyrp1 is the mendelian determinant of the Axolotl (Ambystoma mexicanum) copper mutant.Scientific reports · 2024Article
- Conjunctive BSA-Seq and BSR-Seq to Map the Genes of Yellow Leaf Mutations in Hot Peppers (Genes · 2024Article
- Identification of Dwarfing Candidate Genes inPlants (Basel, Switzerland) · 2024Article
139 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples by analyzing the same RNA-Seq data using an empirical Bayesian approach. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone 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, we 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.
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