A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea

Abstract

Milk thistle (Silybum marianum) belongs to the Asteraceae family and is a medicinal plant native to the Mediterranean Basin. Silymarin in achene is a widely used herbal product for chronic liver disease. There is growing interest in natural medicine using milk thistle in Korea, but the raw material completely relies on imports. Despite its economic importance, phenotypic evaluations of native resources of milk thistle in Korea have not been carried out. In addition, genomic research and molecular marker development are very limited in milk thistle. In this study, we evaluated 220 milk thistle resources consisting of 172 accessions collected from the domestic market, and 48 accessions isolated from 6 accessions distributed by the National Agrobiodiversity Center in Korea. Six plant characteristics (height, seed weight, number of flowers, seed weight per flower, spine length, and color at harvest) were measured, and six samples (M01–M06) were selected to represent the genetic diversity of the population for genomic research. To develop PCR-based and co-dominant insertion/deletion (InDel) markers, we performed genome-wide InDel detection by comparing the whole-genome resequencing data of the six selected accessions with the reference genome sequence (GCA_001541825). As a result, 177 InDel markers with high distinguishability and reproducibility were selected from the 30,845 InDel variants. Unknowingly imported alien plant resources could easily be genetically mixed, and jeopardized seed purity can cause continuous difficulties in the development of high value-added agricultural platforms utilizing natural products. The selected plant materials and 177 validated InDel markers developed via whole-genome resequencing analysis could be valuable resources for breeding, conservation, and ecological studies of natives to Korea, along with acceleration of Silybum marianum industrialization.

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

“…2). Two plant species were the only genomes with more than 1000 operon variants: Thlaspi arvense with 1,017 variants (genome assembly id GCA_018983045 (Geng et al, 2021)) and Silybum marianum with 2,097 variants (genome assembly id GCA_001541825.1 (Shim et al, 2023))(Table 1 and Supplementary table 1). In contrast, fungal genome assemblies generally had fewer variants; the highest number was 81, found in the ascomycete Leptosphaeria maculans (genome assembly id GCA_022343315 (Tian et al, 2024)).…”

Trends and Prospects of Genetic and Molecular Research in Plants

“…This Special Issue presents five articles related to genomic analysis and markers. Shim et al [ 11 ] investigated the characteristics of 6 types of plants from 220 types of milk thistle ( Silybum marianum L. Gaertn.)…”