Genetic structure analysis and DNA fingerprint construction of 293 lotus (Nelumbo spp.) accessions based on SSR markers

• The genetic structure was mainly affected by the geographic origin. • The identifying ability of the 93 SSR markers was high. • The fingerprint profile of the 293 lotus accessions were constructed using 18 SSRs. Lotus ( Nelumbo spp.) is a widely cultivated perennial aquatic plant with important edible, medicinal, and ornamental value. The long history of natural evolution and artificial selection has resulted in a complex genetic background of lotus germplasm and making it difficult to accurately identify the varieties based on their morphological traits alone. In this study, we analyzed the genetic structure using 93 SSR markers and constructed DNA fingerprints of 293 lotus accessions. Genetic similarity coefficients (GS) of the lotus accessions ranged from 0.146 to 1, with an average value of 0.626. In the phylogenetic analysis, the 293 lotus accessions were clustered into three major groups, and the Group I was further classified into six subgroups (A–F). The clustering results revealed that the genetic structure was mainly affected by the geographic origin. This was confirmed by the subsequent PCoA analysis. In addition, the r 2 (squares allele-frequency correlations) values of the 93 SSR markers generated from linkage disequilibrium (LD) analysis ranged from 0.02 to 1 with an average value of 0.08 at P < 0.01 level, and 84.36 % of which were <0.1. The weak LD degree indicated that the SSR markers used in our study tended to segregate independently. The cumulative probability of identity of the 93 SSR markers was extremely low with a value of 9.128 × 10 –50 for PI and 9.702 × 10 –24 for PIsibs , respectively. The 93 SSR markers were applied to distinguish the lotus accessions successively according to their PIC values, and DNA fingerprints profile of the 293 lotus accessions were finally constructed using 18 SSR markers. The results of this study provided an important scientific basis for the identification, utilization and protection of lotus germplasm resources.