Introduction

Genetic linkage maps are indispensable tools in genetic, genomic and breeding studies. As one of genotyping-by-sequencing methods, RAD-Seq (restriction-site associated DNA sequencing) has gained particular popularity for construction of high-density linkage maps. Current RAD analytical tools are being predominantly used for typing codominant markers. However, no genotyping algorithm has been developed for dominant markers (resulting from recognition site disruption). Given their abundance in eukaryotic genomes, utilization of dominant markers would greatly diminish the extensive sequencing effort required for large-scale marker development. In this study, we established, for the first time, a novel statistical framework for de novo dominant genotyping in mapping populations. An integrated package called RADtyping was developed by incorporating both de novo codominant and dominant genotyping algorithms. We demonstrated the superb performance of RADtyping in achieving remarkably high genotyping accuracy based on simulated and real mapping datasets. The RADtyping package is freely available at http://www2.ouc.edu.cn/mollusk/ detailen.asp?id=727.

Publications

  1. RADtyping: an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations.
    Cite this
    Fu X, Dou J, Mao J, Su H, Jiao W, Zhang L, Hu X, Huang X, Wang S, Bao Z, 2013-01-01 - PloS one

Credits

  1. Xiaoteng Fu
    Developer

    Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, China

  2. Jinzhuang Dou
    Developer

  3. Junxia Mao
    Developer

  4. Hailin Su
    Developer

  5. Wenqian Jiao
    Developer

  6. Lingling Zhang
    Developer

  7. Xiaoli Hu
    Developer

  8. Xiaoting Huang
    Developer

  9. Shi Wang
    Developer

  10. Zhenmin Bao
    Investigator

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Summary
AccessionBT001305
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByZhenmin Bao