Genetic diversity and population structure of wild lotus (Nelumbo nucifera Gaertn.) in China

Lotus (Nelumbo nucifera Gaertn.) is a special aquatic plant in China. However, habitat destruction by both natural factors and human activity have impacted many wild populations. Furthermore, the genetic diversity of these wild populations remains poorly understood. In this study, the genetic diversity and structure of wild lotus in China were evaluated based on 33 populations using 1 064 789 single nucleotide polymorphism (SNP) loci obtained by specific-locus amplified fragment sequencing (SLAF). Cluster, principal coordinate, and STRUCTURE analyses revealed that the northeast China populations were genetically separated from those of the Yangtze River Basin. Thus, wild lotus from these two regions represented two ecotypes of N. nucifera. Low genetic diversity within each population (average π = 1.04×10^-5) and a high degree of genetic differentiation among populations (average F_ST = 0.42) were found. For the Yangtze River Basin populations, π ranged from 0.KG-*35×10^-5 to 2.2×10^-5 among the various lakes. The Liangzi Lake area exhibited the highest diversity, with π ranging from 3.13×10^-6 to 2.3×10^-5 among the small lakes, indicating that lotus diversity was not evenly distributed. For populations in North China, π ranged from 3.05×10^-6 to 1.50×10^-5, with the Liangshan populations showing the highest diversity. Thus, higher genetic diversity was observed in the Yangtze River Basin populations than in the North China populations. The F_ST value from comparison was 0.34, indicating a high degree of genetic differentiation between the areas. Low genetic diversity within populations and high differentiation among populations could be attributed to clonal reproduction within populations and low genetic exchange among populations. Our results indicate that ex situ conservation should be supplemented with in situ preservation for wild lotus conservation.