Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I-trifida using RAD-seq

Background: Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important crops from the family of Convolvulaceae. It is widely reported that cultivated sweetpotato was originated from Ipomoea trifida. However, diploid, tetraploid and hexaploid I. trifida were found in nature. The relationship, between them, and among them and sweetpotato, is remaining unclear. Results: In the present study, we detected the genome diversity and relationship of sweetpotato and different polyploidy types I. trifida using Restriction-site Associated DNA Sequencing (RAD-seq). A total of 38,605 RADtags containing 832,204 SNPs had been identified. These tags were annotated using five public databases, about 11,519 tags were aligned to functional genes in various pathways. Based on SNP genotype, phylogenetic relation analysis results confirmed that cultivated sweetpotato has a closer relationship with I. trifida 6x than with I. trifida 4X and I. trifida 2x. Besides, 5042 SSRs were detected in I. trifida 6x, and 3202 pairs of high-quality SSR primers were developed. A total of 68 primers were randomly selected and synthesized, of which 61 were successfully amplified. Conclusion: These results provided new evidence that cultivated sweetpotato originated from I. trifida 6x, and that I. trifida 6x evolved from I. trifida 4X and I. trifida 2x. Therefore, using I. trifida 6x as the model plant of sweetpotato research should be more practical than using I. trifida 2x in the future. Meanwhile, sequence information and markers from the present study will be helpful for sweetpotato and I. trifida studies in the future.