Plastome and RAD-seq of Polygonatum odoratum

Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely
cultivated medicinal herb in China. However, this useful herb is
understudied despite being known as a medicinal resource with top grade
medical and edible properties since long. In this study, P. odoratum and
four cultivars were investigated. The variations in morphological
characteristics and vegetative phases of each cultivars were observed. For
genetic aspect, the plastid genome of P. odoratum varies in length from
154,569 bp to 155,491 bp, containing a large single-copy region of
83,486—84,459 bp, a small single-copy region of 18,292—18,471 bp, and two
inverted repeats of 26,302—26,370 bp. A total of 131 genes were predicted,
including 85 protein-coding, 38 tRNA, and eight rRNA genes. Genome
comparisons revealed a slight variation in the sequence across the five
accessions, but two highly variable regions (trnC-petN and rpl32-trnL)
were detected when comparing the four different cultivars. For the RAD-seq
markers, a total of 33.64 Gb of clean data, with an average value of 1.08
Gb per sample, were analyzed for presence of single nucleotide
polymorphisms (SNPs). Well-resolved phylogenies of the P. odoratum
cultivars are constructed; the non-monophyletic relationship in the
plastome-based phylogenetic trees, yet monophyletic form in the RAD-based
linkage map suggested possibility of hybrid cultivar for P. odoratum
“Dazhu” (GDDZ), which was further supported by morphological observations.
Quality assessment based on the standards of the Chinese Pharmacopoeia on
Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study
recorded that PORs from P. odoratum ‘Zhongzhu’ (GDZZ) met the minimum
criteria for the acceptance as raw material for medicinal drug production.
This study has provided insights on the morphological variations, genetic
background, and medicinal qualities of P. odoratum cultivars that could be
explored for future genetic improvement as well as breeding programs of P.
odoratum for POR production.