Transcriptome analysis and genetic diversity of <i>Allium victorialis</i> germplasms from the Changbai Mountains

The Changbai Mountains comprise one of the main distribution areas of <i>A. victorialis</i> in China, and this species is endangered owing to habitat changes and overexploitation. However, <i>A. victorialis</i> 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 <i>A. victorialis</i> germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six <i>A. victorialis</i> samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing <i>de novo</i> 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 <i>A. victorialis</i> was genetically distant from some related species, e.g. <i>Allium sativum</i>, <i>Allium fistulosum</i>, and <i>Allium cepa</i>, but genetically close to <i>Allium tuberosum</i>. The two <i>A. victorialis</i> var. <i>listera</i> samples were phylogenetically separated from the other four samples, and these two samples should be regarded as <i>Allium listera</i>. In addition, two KASP markers for discriminating the Dongfeng samples from the other four <i>A</i>. <i>victorialis</i> samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of <i>Allium</i> species, as well as for the conservation of <i>A. victorialis</i> germplasms from the Changbai Mountains and other populations of this species.