Construction of Genetic Linkage Maps in Multiparental Populations

Chaozhi Zheng*, Martin P. Boer, Fred A. van Eeuwijk

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)


Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages.

Original languageEnglish
Pages (from-to)1031-1044
Number of pages14
Issue number4
Publication statusPublished - 1 Aug 2019


  • cross-pollinated (CP)
  • genetic map construction
  • hidden Markov model (HMM)
  • MPP
  • multiparent advanced generation intercross (MAGIC)
  • multiparental populations
  • nested association mapping (NAM)


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