Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

Abstract

The Changbai Mountains comprise one of the main distribution areas of A. victorialis in China, and this species is endangered owing to habitat changes and overexploitation. However, A. victorialis germplasms have not been systematically collected and studied. The aims of this study were to obtain some detailed genetic information, analyze the genetic diversity, and further promote the protection of A. victorialis germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six A. victorialis samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing de novo assembly of the RNA-seq data, and at least 92% of these genes were found to have only one mRNA isoform. These sequences and their functional annotations provided a large-scale genetic resource of this species. Phylogenetic analysis showed that A. victorialis was genetically distant from some related species, e.g. Allium sativum , Allium fistulosum , and Allium cepa , but genetically close to Allium tuberosum . The two A. victorialis var. listera samples were phylogenetically separated from the other four samples, and these two samples should be regarded as Allium listera . In addition, two KASP markers for discriminating the Dongfeng samples from the other four A . victorialis samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of Allium species, as well as for the conservation of A. victorialis germplasms from the Changbai Mountains and other populations of this species.