Geographical genetic structure of Lespedeza cuneata var. cuneata in Japan: necessity of genetic considerations in slope revegetation

The use of non-local seeds for revegetation may cause genetic disturbances in the local populations. This study focused on Lespedeza cuneata var. cuneata, one of the most frequently used native plants for slope revegetation in Japan. The aims of this study were to: (1) clarify the geographical genetic structure of L. cuneata var. cuneata in Japan, and (2) to assess the genetic differences between individuals in natural habitats and those growing on revegetation slopes or those cultivated from revegetation seeds. Single nucleotide polymorphisms (SNPs) of 773 loci across 370 individuals, and 16 haplotypes across 354 individuals, were obtained using a genome-wide SNP genotyping or by sequencing two chloroplast DNA regions. The geographical genetic structure of L. cuneata var. cuneata in natural habitats was primarily characterized by a nationwide southwest to northeast genetic cline, and secondarily by genetic differentiation into four regions: Hokkaido, East Japan, West Japan, and Kyushu. The revegetation seeds imported from China were frequently contaminated with other Lespedeza species and L. cuneata var. cuneata germinated from Chinese seeds were genetically distant from individuals in natural habitats in Japan. On the revegetation slopes, the geographic distribution of genetic variation was different from that in natural habitats, thus posing a risk of genetic disturbance. For the four main islands of Japan, to implement the revegetation considering the geographical genetic structure of L. cuneata var. cuneata, it is recommended to distinguish the four regions (Hokkaido, East Japan, West Japan, and Kyushu) to supply seeds of local provenance.