Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

By Sanzhen Liu, Cheng-Ting Yeh, Haibao Tang, Dan Nettleton, Patrick S. Schnable. PLoS ONE, 2012

350 citations recorded by the source corpus.

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.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/4633d360a5f759cb0ba124d0e5ed487583bcf4d8

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. M. Gowda
2. Dipnarayan Saha
3. A. Singh
4. B. Singh
5. K. Bansal
6. L. Arya
7. M. Verma

In Plant Science

1. A. Singh
2. B. Singh

Citations in the corpus

• Marker-Assisted Plant Breeding: Principles and Practices (2015, methodology): “Bulked segregant RNA-Seq (BSR-Seq) is a modification of BSA that uses RNA sequence data from the two phenotypic extreme bulks to identify markers tightly linked to the gene responsible for the target trait (Liu et al. 2012).”
• MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq (2013, methodology): “The utility of RNA-seq analysis for mapping has been demonstrated recently in self-pollinated individuals derived from inbred mapping strains in maize (Liu et al. 2012), but this has not been tested in more noisy data sets from outbred animal populations.”
• Genetic and Genomic Resources of Small Millets (2016, background): “The recent upsurge in the availability of genomic resources in numerous crops has enhanced the process of efficient characterization of germplasm and their use in crop improvement (Louwaars et al., 2006).”