QTLseqr: An R Package for Bulk Segregant Analysis with Next-Generation Sequencing

Plant Genome. 2018 Jul;11(2). doi: 10.3835/plantgenome2018.01.0006.

Abstract

Next-Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G'. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G' values, and log (-values), enabling identification and plotting of QTL. The source code is available at .

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Gene Frequency
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / statistics & numerical data
  • Oryza / genetics
  • Plant Breeding / methods*
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci*