A Novel Method for Molecular Identification of Plants in Larix Mill. Using Single Nucleotide Polymorphic Characters from Complete Chloroplast Genomes—Analysis on Eight Species/Varieties as an Example

The low experimental cost of high-throughput sequencing technology for yielding sequence data of complete chloroplast genomes has made it possible to challenge the accurate identification of Larix plants. In this study, five hundred and twenty-seven single nucleotide polymorphic characters from the complete chloroplast genomes were used for the first time as molecular traits to identify Larix plants and compile a molecular classification key. There are differences in aspects of single nucleotide polymorphic characters between species and varieties. Among the eight species/varieties, L. himalaica W. C. Cheng & L. K. Fu, L. sibirica Ledeb . and L. deciduas Mill . has larger number of diverged single nucleotide characters. Genetic variation levels among the four genotypes as named L. gmelinii (Rupr.) Kuzen. var. gmelinii , L. gmelinii var. olgensis (A. Henry) Ostenf. & Syrach, L. gmelinii var. japonica (Maxim. ex Regel) Pilg. and L. cajanderi Mayr are comparatively low. Our results indicated that single nucleotide polymorphic characters from the chloroplast genomes could be used for discrimination of different genotypes in Larix . This study is valuable for identification, conservation and utilization of plant germplasm resources of Larix .