Molecular insights of genetic variation in milk thistle (Silybum marianum [L.] Gaertn.) populations collected from southwest Iran

Genetic diversity of a Silybum marianum (L.) Gaertn. germplasm collection revealed by DNA Diversity Array Technology (DArTseq)

Silybum marianum (L.) Gaertn. is a multipurpose crop native to the Mediterranean and middle east regions and mainly known for the hepatoprotective properties of fruit-derived silymarin. Despite growing interest in milk thistle as a versatile crop with medicinal value, its potential in agroindustry is hindered by incomplete domestication and limited genomic knowledge, impeding the development of competitive breeding programs. The present study aimed to evaluate genetic diversity in a panel of S. marianum accessions (n = 31), previously characterized for morphological and phytochemical traits, using 5,178 polymorphic DArTseq SNP markers. The genetic structure investigated using both parametric and non-parametric approaches (e.g. PCA, AWclust, Admixture), revealed three distinctive groups reflecting geographical origins. Indeed, Pop1 grouped accessions from Central Europe and UK, Pop3 consisted mainly of accessions of Italian origin, and Pop2 included accessions from different geographical areas. Interestingly, Italian genotypes showed a divergent phenotypic distribution, particularly in fruit oleic and linoleic acid content, compared to the other two groups. Genetic differentiation among the three groups, investigated by computing pairwise fixation index (FST), confirmed a greater differentiation of Pop3 compared to other subpopulations, also based on other diversity indices (e.g. private alleles, heterozygosity). Finally, 22 markers were declared as putatively under natural selection, of which seven significantly affected some important phenotypic traits such as oleic, arachidonic, behenic and linoleic acid content. These findings suggest that these markers, and overall, the seven SNP markers identified within Pop3, could be exploited in specific breeding programs, potentially aimed at diversifying the use of milk thistle. Indeed, incorporating genetic material from Pop3 haplotypes carrying the selected loci into milk thistle breeding populations might be the basis for developing milk thistle lines with higher levels of oleic, arachidonic, and behenic acids, and lower levels of linoleic acid, paving new avenues for enhancing the nutritional and agronomic characteristics of milk thistle.

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

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.

Genetic diversity among genotypes of Uncaria guianensis (Aubl.) J.F. Gmel. maintained in an in vitro germplasm bank

Phytotherapeutic preparations from Uncaria guianensis (Aubl.) J.F. Gmel. (Rubiaceae) are marketed worldwide and are mainly used for their anti-inflammatory activity. The species has not yet been domesticated and is threatened by deforestation and overexploitation. It is, therefore, important to preserve and manage this genetic resource in germplasm banks, so that the extractive provision of plant material can be replaced by cultivated production. The aim of this study was to evaluate the genetic diversity among 20 genotypes maintained under in vitro conditions using 9 primers start codon targeted (SCoT) polymorphism, and to determine the concentrations of the pentacyclic oxindole alkaloids (POAs); mitraphylline and isomitraphylline in methanolic extracts by high-performance liquid chromatography (HPLC). Plantlets were cultivated on woody plant medium supplemented with 20 g.L^-1 sucrose and 4.4 μM benzylaminopurine and incubated under a 16 h photoperiod for 45 days. SCoT analysis separated the genotypes into four divergent clusters and confirmed significant genetic diversity with up to 70% dissimilarity. Moreover, HPLC revealed considerable chemical variability and allowed the separation of the tested genotypes into high, medium and low producers of mitraphylline/isomitraphylline. Genotypes with the highest concentrations of POAs originated from the state of Acre and Amapá, while those with the lowest levels were from the state of Pará. The results demonstrate that the genetic diversity within the in vitro germplasm bank is sufficient to support breeding studies, selection of elite genotypes and the large-scale multiplication of plants that could serve as feedstock for the industrial-scale production of phytomedicines.

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The online version contains supplementary material available at 10.1007/s13205-021-03016-y.

Comparative assessment of ISSR, RAPD, and SCoT markers for genetic diversity in Clerodendrum species of North East India

Clerodendrum belonging to the family of Lamiaceae is used in indigenous systems of medicine to treat various life-threatening diseases. The genus has complex morphological variations which lead to limits in its precise taxonomic classifications. Genetic diversity study could enhance taxonomic authentication and evolutionary relationship among the species of Clerodendrum. In this study, nine species of Clerodendrum collected from different regions of North East India were screened using ISSR, RAPD, and SCoT molecular markers. The markers of ISSR, RAPD, and SCoT generated a total of 79, 126, and 145 amplicons with an average of 6.58, 7.86, and 8.53 amplicon per primer. The polymorphism information contents (PIC) for ISSR, RAPD, and SCoT ranged from 0.28 to 0.37, 0.39 to 0.69, and 0.30 to 0.62 with resolving power (Rp) varying from 5.26 to 11.11, 4.04 to 9.67, and 4.54 to 8.65, respectively. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based clustering methods grouped 94 genotypes into 6 clusters for ISSR and 3 clusters each for RAPD and SCoT markers. Similarly, population structure-based analysis divided 94 genotypes into 6 populations for ISSR and RAPD and 4 populations for SCoT markers. AMOVA analysis revealed that SCoT markers generated maximum genetic variations within and among genotypes, contrary to ISSR and RAPD markers. Results in this study, suggest that the competence of three markers was relatively the same in genotypes fingerprinting, but SCoT was more efficient in the detection of polymorphism for Clerodendrum species. Further, these results could be integrated in the exploration of diverse Clerodendrum species and germplasm utilization.

Exploring genetic variability in Prosopis cineraria using two gene targeted CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers

Two gene targeted molecular marker systems, CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism, were used to assess the genetic diversity and relatedness in Prosopis cineraria, a tree of abiotic stress tolerance, agroforestry and ethano-botanical importance. A total of ten wild populations consisting 49 individuals collected from different locations of Indian Thar Desert were examined for the genetic analysis of P. cineraria. Ten CBDP and seven SCoT primers, total 17 primers, generated 204 bands with an average of 12 bands per primer, of which 159 (76.8%) were polymorphic. The average PIC values for both CBDP and SCoT marker were 0.543 and 0.547, respectively. The cumulative data of these two markers were used to analyze different genetic diversity indices and compute pair-wise distances. The population genetic diversity analysis based on cumulative data of CBDP and SCoT markers revealed the high levels of genetic differentiation (GST = 0.341; GST > 0.15 as high), low value of gene flow (Nm = 0.966; Nm > 1 as high) and high fixation index (F_ST = 0. 415). The highest genetic diversity was observed among NGBAR populations followed by CHR populations, while SIK populations showed lowest genetic diversity. AMOVA revealed the percent molecular variation was higher within the populations (77%) compared to that of among populations (23%). The clustering pattern based on UPGMA and PCoA plot clearly demonstrated the genetic relationship among the genotypes collected from the different regions of Indian Thar Desert.