Comparative analysis of genetic diversity of lotus (Nelumbo) using SSR and SRAP markers

The lotus genus, Nelumbo Adans., comprises two species, N. nucifera Gaertn. and N. lutea (Willd.) Pers. N. nucifera is distributed in Asia and northern Australia, and is cultivated as a commercial crop for the showy flowers, seeds and rhizomes. N. lutea is distributed in the Americas and has been used to create interspecific hybrids. The present study was conducted to assess the genetic diversity and relatedness for accessions of N. nucifera, N. lutea and interspecific hybrids using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers for comparative analysis. Forty-three Nelumbo accessions were genotyped using 38 SSR and 16 SRAP primer pairs. The SSR markers yielded 161 polymorphic loci with an average polymorphism information content (PIC) of 0.575, whereas the 16 SRAP primer pairs generated 119 polymorphic alleles with an average PIC of 0.741. Dendrograms constructed with the UPGMA method from the SSR and SRAP data showed similar clusters with some exceptions. Two major groups were identified: group I included N. nucifera and four hybrids, and revealed complex genetic relationships among flower, seed and rhizome lotus; group II included N. lutea and nine hybrids, and confirmed the interspecific genetic distinction between N. nucifera and N. lutea. The results of UPGMA clustering were consistent with those of the PCA and population structure analysis. Mantel's test indicated there was good concordance between the SSR and SRAP data (r = 0.732), and highly significant correlations between combined SSR–SRAP and separate SSR (r = 0.935) and SRAP (r = 0.926) data. Overall, both types of molecular marker were shown to be valuable tools for the analysis of genetic relationships, but combination of the SSR and SRAP data was more informative for assessment of genetic diversity of Nelumbo. These findings provide a basis for future use of these molecular markers in the genetic analysis of Nelumbo.

► We compared the relatedness of SSR and SRAP markers for genetic diversity of Nelumbo.
► Both markers yielded similar results and were effective for assessment of the diversity of lotus.
► Combination of the two markers improved their effectiveness for the evaluation of genetic diversity.
► We confirmed relationships between N. nucifera and N. lutea, and flower, seed, and rhizome lotuses.