Evaluation of genetic diversity in wild populations of Peganum harmala L., a medicinal plant

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

One of the well-known medicinal plants in the Falcaria genus is Sickleweed. Falcaria species exhibit a high degree of genetic variability, posing challenges in the examination of genetic diversity due to the significant potential for hybridization and introgression among them. Utilizing morphological traits and molecular markers may prove to be a valuable approach in evaluating and harnessing germplasm, considering the current obstacles faced in breeding this medicinal herb. In 2021, fifteen Sickleweed populations were cultivated in pots under field conditions, employing a randomized complete block design with three replications. This aimed to assess genetic diversity and conduct marker-trait association analyses utilizing morpho-physiological characteristics and SSR markers. The Sickleweed populations displayed considerable genetic diversity across all traits. Through cluster analysis of traits and the utilization of the UPGMA method based on the Gower distance matrix, the population was classified into three distinct clusters. Upon examining all genotypes, 52 polymorphic bands were detected, with an average of 8.68 bands per primer. The average expected heterozygosity across all loci was 0.864, while the average PIC was 0.855. Molecular data analysis employing the Jaccard similarity index and UPGMA method revealed the division of Sickleweed populations into two major groups. Furthermore, the results of molecular variance analysis indicated that variation within the population exceeded that between populations. Thirty-two SSR fragments were found to be significantly associated with genomic regions controlling the studied traits, determined through the application of stepwise regression. Selection based on molecular markers offers a rapid method for breeding programs, with the genetic information obtained from these markers playing a crucial role. Therefore, alongside traits, selecting superior genotypes and populations of high value in breeding programs becomes feasible. The findings highlight that certain markers are linked to multiple traits, emphasizing the critical importance of this characteristic in plant breeding for the simultaneous improvement of numerous traits. The study's insights regarding markers hold potential for application in Sickleweed breeding programs.

Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses

Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.

Deciphering allelic variability and population structure in buckwheat: An analogy between the efficiency of ISSR and SSR markers

Food and nutritional security continue to be the issues of concern in developing countries like ours. Exploring the reservoir of high potential unexplored genetic resources could address the world's food and nutritional insecurity. The availability of diverse data and the population structure of any crop germplasm is a valuable genetic resource for discovering genes that can help achieve food and nutritional stability. We used seven ISSR and seven SSR markers to investigate diversity among 63 buckwheat genotypes, including landraces from India's northwestern Himalayas. Various parameters such as percent polymorphism, PIC, resolving power, and marker index was used to evaluate the inequitable efficacy of these markers. We foundthat both marker systems are effective in detecting polymorphism in buckwheat germplasm. Seven ISSRs produced 55 polymorphic bands, while seven SSRs produced 32bands. When compared to ISSRs, SSRs had a greater average PIC value (0.43) than that of (0.36). ISSRs, on the other hand, had a resolving power of (4.38) compared to (1.42) for SSRs. The hierarchical cluster analysis dendrogram divided genotypes into three major clusters. We found that both marker systems were equally accurate in grouping buckwheat genotypes according to their geographical origins. Using 7 ISSR and 7 SSR markers, the model-based STRUCTURE analysis established a population with two sub-populations that correspond to species-based groupings. Within the population, there was a high level of genetic diversity. These results have consequences for both buckwheat breeding and conservation efforts.

De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

BACKGROUND

Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers.

RESULTS

In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances.

CONCLUSION

Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

Estimation of genetic diversity and population structure in Tinospora cordifolia using SSR markers

Thirty polymorphic SSRs, derived from RNA sequencing of Tinospora cordifolia (willd.), were utilized for genetic diversity and population structure evaluation among 96 accessions collected from ten different geographical regions of India. A total of 7611 SSRs were identified from 268149 transcripts. Of all SSR loci, 69.07% of them were tri-nucleotide repeat motifs, followed by di-nucleotide repeat motifs (12.82%). A total of 230 alleles were generated by 30 SSRs with an average of 7.67 alleles per locus with comparatively higher polymorphic information content (average 0.68). The expected (He) and observed (Ho) heterozygosity means were 0.71 and 0.12, respectively. All the loci showed significant deviation from Hardy-Weinberg Equilibrium (HWE). The neighbor joining clustering based on jaccard's coefficient grouped all the 96 accessions into three major cluster which was also in congruence with model-based structure plot. The result of molecular variance (AMOVA) revealed higher genetic variance within populations than among populations. The result reflects an existence of high level of genetic diversity in the collected accessions of T. cordifolia. The accessions Tc131, Tc31, Tc129, Tc38, Tc16, Tc59, Tc60, Tc17, Tc106 and Tc130 was found to be potential and diverse in nature and the SSRs TCSSR-18, TCSSR-37, TCTSSR-59, TCTSSR-92, TCTSSR-123 and TCTSSR-126 as potential markers. These accessions and newly developed SSR markers provide valuable resource and could be strategically utilized for further genetic improvement of T. cordifolia.

Population genetic variability and distribution of the endangered Greek endemic Cicer graecum under climate change scenarios

The Mediterranean hot spot includes numerous endemic and socio-economically important plant species seriously threatened by climate change and habitat loss. In this study, the genetic diversity of five populations of Cicer graecum, an endangered endemic species from northern Peloponnisos, Greece and a wild relative of the cultivated Cicer arietinum, was investigated using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphism (AFLP) markers in order to determine levels and structure of genetic variability. Nei's gene diversity by ISSR and AFLP markers indicated medium to high genetic diversity at the population level. Moreover, AMOVA results suggest that most of the variation exists within (93 % for AFLPs and 65 % for ISSRs), rather than among populations. Furthermore, Principal Component Analysis based on ISSRs positively correlated the genetic differentiation among the populations to the geographic distances, suggesting that the gene flow among distant populations is limited. The ecological adaptation of C. graecum populations was also investigated by correlation of their genetic diversity with certain environmental variables. Aridity arose as the dominant factor positively affecting the genetic diversity of C. graecum populations. We modelled the realized climatic niche of C. graecum in an ensemble forecasting scheme under three different global circulation models and two climate change scenarios. In all cases, a severe range contraction for C. graecum is projected, highlighting the high extinction risk that is probably going to face during the coming decades. These results could be a valuable tool towards the implementation of an integrated in situ and ex situ conservation scheme approach for activating management programmes for this endemic and threatened species.

Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers

Background

Mallotus oblongifolius, an evergreen shrub endemic to Hainan Island, China, is important both medicinally and economically. Due to its special medicinal significance and the continuing rise of market demand, its populations in the wild have been subject to long-term illegal and unrestrained collection. Hence, an evaluation of genetic variability is essential for the conservation and genetic reserve development of this species.

Methods

Sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and genetic structure of 20 natural populations of M. oblongifolius growing in different eco-geographical regions of Hainan Island, China.

Results

We revealed a considerable genetic diversity (h = 0.336, I = 0.5057, SRAP markers; h = 0.3068, I = 0.4657, ISSR markers) and weak genetic differentiation (Gst = 0.2764 for SRAP, Gst = 0.2709 for ISSR) with the same gene flow (Nm = 1.3092 for SRAP, Nm = 1.346 for ISSR) among the M. oblongifolius populations. The Mantel Test showed that the distribution of genetic variation among populations could not be explained by the pronounced geographical distances (r = 0.01255, p = 0.5538). All results of the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), Neighbor-joining (NJ), Principal Coordinate Analysis (PCoA) and Bayesian analyses supported a habitat-specific genetic clustering model for M. oblongifolius, indicating a local adaptive divergence for the studied populations.

Discussion

We suggested that the habitat fragmentation and specificity for M. oblongifolius populations weakened the natural gene flow and promoted an adaptation to special habitats, which was the main reason for local adaptive divergence among M. oblongifolius.