Toward haplotype studies in polyploid plants to assist breeding

Polyploids are typically classified as either autopolyploids or allopolyploids (Figure 1). Autopolyploids result from whole-genome duplication within the same species, while allopolyploids derive from the hybridization of different species followed by chromosome doubling. Taxonomically, plant allopolyploids are thought to be the most common polyploids, although autopolyploid plants and allopolyploid plants might be at parity in numbers (Barker et al., 2016). During speciation, polyploidization allows plants to adapt to different environments (Soltis et al., 2009). Mutation and hybridization increase the heterozygosity of the genome, while genome rearrangements during polyploidization lead to the formation of new chromosomes and new chromosome rearrangements, which complicate polyploid genomes and the following studies.