Genetic diversity and population structure of <i>Miscanthus lutarioriparius</i>, an endemic plant of China

Miscanthus lutarioriparius is a native perennial Miscanthus species of China, which is currently used as raw material of papermaking and bioenergy crop. It also has been considered as a promising eco-bioindustrial plant, which can offer raw material and gene for the biomass industry. However, lack of germplasm resources and genetic diversity information of M. lutarioriparius have become the bottleneck that prevents the stable and further development of the biomass industry. In the present study, genetic diversity of 153 M. lutarioriparius individuals nine populations was studied using 27 Start Codon Targeted (SCoT) markers. High polymorphic bands (97.67%), polymorphic information content (0.26) and allele number (1.88) showed SCoT as a reliable marker system for genetic analysis in M. lutarioriparius. At the species, the percentage of polymorphic loci [PPL] was 97.2%, Nei’s gene diversity [H] was 0.36, Shannon index [I] was 0.54 and Expected Heterozygosity [He] was 0.56. Genetic variation within populations (84.91%) was higher than among populations (15.09%) based on analysis of molecular variance (AMOVA). Moderate level of genetic differentiation was found in M. lutarioriparius populations (Fst = 0.15), which is further confirmed by STRUCTURE, principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) analysis that could reveal a clear separation between groups of the north and south of Yangtze River. The gene flow of the populations within the respective south and north of Yangtze River area was higher, but lower between the areas. There was no obvious correlation between genetic distance and geographic distance. The breeding systems, geographical isolation and fragmented habitat of M. lutarioriparius may be due to the high level of genetic diversity, moderate genetic differentiation, and the population, structure. The study further suggests some measure for conservation of genetic resources and provides the genetic basis for improving the efficiency of breeding based on the results of diversity analysis.