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

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  • Ben N. Mansfeld
    Plant Breeding, Genetics and Biotechnology Program, Dep. of Horticulture, Michigan State Univ. East Lansing MI
  • Rebecca Grumet
    Plant Breeding, Genetics and Biotechnology Program, Dep. of Horticulture, Michigan State Univ. East Lansing MI

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<jats:sec><jats:label/><jats:p>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<jats:sub>10</jats:sub> (<jats:italic>p</jats:italic>‐values), enabling identification and plotting of QTL. The source code is available at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://github.com/bmansfeld/QTLseqr">https://github.com/bmansfeld/QTLseqr</jats:ext-link>.</jats:p></jats:sec>

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