Haplotype-based phylogenetic analysis uncovers the tetraploid progenitor of sweet potato

Abstract The hexaploid sweet potato is one of the most important root crops worldwide. However, its genetic origins, especially that of its tetraploid progenitor, are unclear. In this study, we conceived a pipeline consisting of a genome-wide variation-based phylogeny and a novel haplotype-based phylogenetic analysis (HPA) to determine that the tetraploid accession CIP695141 of Ipomoea batatas 4x from Peru is the tetraploid progenitor of sweet potato. We detected biased gene exchanges between subgenomes. The B1 to B2 subgenome conversions were almost 3-fold higher than the B2 to B1 subgenome conversions. Our analyses revealed that the genes involved in storage root formation, sugar transport, stress resistance, and maintenance of genome stability have been selected during the speciation and domestication of sweet potato. This study sheds lights on the evolution of sweet potato and paves a way for the improvement of sweet potato.