A0967
Title: New methods to genotype allopolyploids
Authors: Karin Dorman - Iowa State University (United States) [presenting]
Abstract: Many economically important plants are allopolyploids, carrying multiple subgenomes or homoeologous copies of each chromosome, typically derived from two or more ancient diploid ancestors that combined to form the allopolyploid. Recent sequencing efforts have yielded reference subgenomes, thus inviting new strategies for genotyping allopolyploids from next-generation sequencing data. A genotyping method was recently introduced that models the hierarchical structure on the read alignments, showing that it could achieve better performance than algorithmic methods that split the reads by sequence similarity to the subgenomes. The method is extended to also handle the structural dependence among sites along the chromosomes. The result is nested layers of hidden information with inference by a modified EM algorithm. The method for synthetic allotetraploids is tested (real data, truth-known) and the new method is shown to improve over existing allopolyploid genotyping methods.
