Abstract
BackgroundSweetpotato (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.ResultsIn 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 RAD-tags 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 6× than with I. trifida 4X and I. trifida 2×. Besides, 5042 SSRs were detected in I. trifida 6×, 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.ConclusionThese results provided new evidence that cultivated sweetpotato originated from I. trifida 6×, and that I. trifida 6× evolved from I. trifida 4X and I. trifida 2×. Therefore, using I. trifida 6× as the model plant of sweetpotato research should be more practical than using I. trifida 2× in the future. Meanwhile, sequence information and markers from the present study will be helpful for sweetpotato and I. trifida studies in the future.
Highlights
Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important crops from the family of Convolvulaceae
Genomes of sweetpotato and I. trifida 6× were larger in size than I. trifida 2× and I. trifida 4X, the total number of raw reads had no significant difference
The results indicated a total of 5042 Simple sequence repeat (SSR) were identified from 55,167,516 bp of 180,286 reads in I. trifida 6X, with an average of one SSR per 3.6 kb. 2951 SSR contained sequences (Table 3)
Summary
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. The relationship, between them, and among them and sweetpotato, is remaining unclear. Sweetpotato (Ipomoea batatas (L.) Lam.) is the only species that is widely cultivated as a major staple crop in over 100 countries [2]. It plays an important role in food security in numerous African countries [1, 3]. It is widely accepted that I. trifida is the closest wild species of sweetpotato [7, 8]. Feng et al BMC Plant Biology (2018) 18:181 the genetic relationships between sweetpotato and its wild species have not been fu1ly elucidated
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