Assessment of Genetic Diversity and Variety Identification Based on Developed Retrotransposon-Based Insertion Polymorphism (RBIP) Markers in Sweet Potato (Ipomoea Batatas (L.) Lam)

Sweet potato, a dicotyledonous and perennial plant, is the third most crucial tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. These LTR retrotransposons play a significant role in sweet potato genotypes. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. We report a structure-based analysis of the sweet potato genome for the main LTR-retrotransposon subfamilies, Ty3-gypsy and Ty1-copia , which revealed a total of 21555 LTR retrotransposons. By searching using hidden Markov models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were found. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. RBIP markers of the genetic diversity and population structure of 105 sweet potato germplasm resources revealed 56 amplicons with an average polymorphism of 91.07%. Sweet potato accessions were collected from 6 provinces of China, Japan and America. A UPGMA dendrogram, a model-based genetic structure and principal component analysis (PCA) divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato.