Abstract The hexaploid sweetpotato is one of the most important root crops worldwide. However, its genetic origins are controversial. In this study, we identified two progenitors of sweetpotato by horizontal gene transferred Ib T-DNA and haplotype-based phylogenetic analysis. The diploid progenitor is the diploid form of I. aequatoriensis , contributed the B 1 subgenome, Ib T-DNA2 and lineage 2 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato is I. batatas 4x, donating the B 2 subgenome, Ib T-DNA1 and lineage 1 type of chloroplast genome. Sweetpotato derived from the reciprocal cross between the diploid and tetraploid progenitors and a subsequent whole genome duplication. We also detected biased gene exchanges between subgenomes. The B 1 to B 2 subgenome conversions were almost 3-fold higher than the B 2 to B 1 subgenome conversions. This study sheds lights on the evolution of sweetpotato and paves a way for the improvement of sweetpotato.

Horizontal transferred T-DNA and haplotype-based phylogenetic analysis uncovers the origin of sweetpotato