AlloMap6: An R package for genetic linkage analysis in allohexaploids

Xuli Zhu, Huan Li, Meixia Ye, Libo Jiang, Mengmeng Sang, Rongling Wu

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Allopolyploids are a group of polyploids with more than two sets of chromosomes derived from different species. Previous linkage analysis of allopolyploids is based on the assumption that different chromosomes pair randomly during meiosis. A more sophisticated model to relax this assumption has been developed for allotetraploids by incorporating the preferential pairing behavior of homologous over homoeologous chromosomes. Here, we show that the basic principle of this model can be extended to perform linkage analysis of higher-ploidy allohexaploids, where multiple preferential pairing factors are used to characterize chromosomal-pairing meiotic features between different constituent species.We implemented the extended model into an R package, called AlloMap6, allowing the recombination fractions and preferential pairing factors to be estimated simultaneously. Allomap6 has two major functionalities, computer simulation and real-data analysis. By analyzing a real data from a full-sib family of allohexaploid persimmon, we tested and validated the usefulness and utility of this package. AlloMap6 lays a foundation for allohexaploid genetic mapping and provides a new horizon to explore the chromosomal kinship of allohexaploids.

Original languageEnglish (US)
Pages (from-to)919-927
Number of pages9
JournalBriefings in bioinformatics
Issue number6
StatePublished - Nov 1 2017

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Molecular Biology


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