Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato.

The hexaploid sweetpotato (Ipomoea batatas) is one of the most important root crops worldwide. However, its genetic origin remains controversial, and its domestication history remains unknown. In this study, we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato. The diploid progenitor was likely closely related to Ipomoea aequatoriensis and contributed the B 1 subgenome, Ib T-DNA2, and the lineage 1 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato was most likely I. batatas 4x, which donated the B 2 subgenome, Ib T-DNA1, and the lineage 2 type of chloroplast genome. Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors, followed by a subsequent whole-genome duplication. In addition, we detected biased gene exchanges between the subgenomes; the rate of B 1 to B 2 subgenome conversions was nearly three times higher than that of B 2 to B 1 subgenome conversions. Our analyses revealed that genes involved in storage root formation, maintenance of genome stability, biotic resistance, sugar transport, and potassium uptake were selected during the speciation and domestication of sweetpotato. This study sheds light on the evolution of sweetpotato and paves the way for improvement of this crop. Elucidation of the origin and domestication history in crops is vital for breeding and genetic engineering efforts.Genetic and phylogenetic evidence was used to identify the two probable progenitors of sweetpotato: a diploid closely related to Ipomoea aequatoriensis and the tetraploid I. batatas 4x. Genes under selection during speciation and domestication were identified, and biased gene exchanges between the subgenomes were documented. This study sheds light on the evolution of sweetpotato and paves the way for its improvement. [ABSTRACT FROM AUTHOR]