Campus Units

Agronomy, Statistics, Genetics and Genomics, Center for Plant Genomics

Document Type

Article

Publication Version

Published Version

Publication Date

5-2012

Journal or Book Title

PloS ONE

Volume

7

Issue

5

First Page

e36406

DOI

10.1371/journal.pone.0036406

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 mybtranscription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.

Comments

This article is published as 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. doi: 10.1371/journal.pone.0036406.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Copyright Owner

Liu et al.

Language

en

File Format

application/pdf

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