Reconstruction of Genome Ancestry Blocks in Complex Plant Populations

Complex plant populations such as multiparental populations and polyploid families require novel statistical approaches to enable QTL analysis. Here we present two hidden Markov model frameworks, coined RABBIT and TetraOrigin, that allow the reconstruction of genome ancestry blocks in diploid multiparental populations [1] and in tetraploid full-sib families, respectively. The model underlying RABBIT accounts for the joint pattern of recombination breakpoints between two homologous chromosomes and accounts for missing data and allelic genotyping errors in the genotype data of both sampled individuals and founders. Compared to diploids, in tetraploids additional complexity needs to be addressed including the phasing of eight (2*4) parental homologous, double reduction and preferential pairing of chromosomes. We evaluated our methods, and compared them to other methods, by simulation studies and using real data from an Arabidopsis MAGIC population and a potato full sib family. We showed that RABBIT is more robust and accurate in reconstructing the genome ancestry blocks, and that TetraOrigin yields parental linkage phasing that is robust to complex chromosome pairing behaviors during meiosis and to erroneous genetic maps, and that the subsequent probabilistic ancestral inference is accurate.

[1] Zheng C, Boer MP, van Eeuwijk FA: Reconstruction of genome ancestry blocks in multiparental populations. Genetics 2015, 200(4):1073-1087.