Genetic diversity and the population structure at two ploidy levels of Lycoris radiata as revealed by SCoT analysis

• Lycoris radiata is a species with high genetic diversity at species level.
• The diploid stains of L. radiata had a relatively higher genetic diversity compared to the triploid strains.
• The polulations of L. radiata at two ploidy levels are divided into three genetic groups.
• Yangtze River can affect population diffusion, which played an important role in the genetic differentiation of L. radiata.
• The triploid sterile species of L. radiata might possess two origins.

Ploidy differences can occur between and within species. To decipher the genetic structure of a species with different ploidy levels, we investigated an area of China where diploid and triploid individuals of Lycoris radiata co-occur. Twenty-six populations of L. radiata were sampled across its natural range, and SCoT markers were used to assess the genetic diversity and population structure. Chromosome counts revealed that 10 populations were diploid and 16 were triploid, each population showed a single cytotype. SCoT analysis revealed high genetic diversity at the species level (PPB = 93.1%; H = 0.258; I = 0.396). However, compared to the triploid strains of Lycoris, the diploid strains had a relatively higher genetic diversity. One possible interpretation for these results is that the triploid strains only propagated using bulb division, while the diploid strains reproduced using sexual propagation and bulb division. Our investigation of the genetic structure, based on UPGMA and PCoA cluster analyses, revealed that populations of L. radiata are divided into three genetic groups. In addition, our results indicate that Yangtze River can affect population diffusion, which played an important role in the genetic differentiation of L. radiata. Lastly, our results suggest that the triploid sterile species of L. radiata might possess two origins.