AlloMap6: an R package for genetic linkage analysis in allohexaploids

作     者：Xuli Zhu Huan Li Meixia Ye Libo Jiang Mengmeng Sang Rongling Wu 

作者机构：Master''s student in computational genetics in the Center for Computational Biology at Beijing Forestry University Doctoral student in plant genomics in the Center for Computational Biology Beijing Forestry University Lecturer in computational biology and bioinformatics at the Center for Computational Biology at Beijing Forestry University China PhD candidate in computational genetics in the Center for Computational Biology at Beijing Forestry University China Doctoral student in computational genetics in the Center for Computational Biology at Beijing Forestry University China Distinguished Professor of statistics at The Pennsylvania State University USA Director of the Center for Statistical Genetics at The Pennsylvania State University USA 

出 版 物：《Briefings in bioinformatics》 (生物信息学简报)

年 卷 期：2017年第18卷第6期

页      面：919-927页

学科分类：0710[理学-生物学] 07[理学] 09[农学] 

主　　题：EM algorithm allohexaploid persimmon preferential pairing factor recombination fraction 

摘      要：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.