Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean

Uncovering the role of DNA methyltransferases in grapevine - Plasmopara viticola interaction: From genome-wide characterization to global methylation patterns

Epigenetic regulation has recently gained prominence in the field of plant-pathogen interactions, providing a deeper understanding of the molecular mechanisms associated with plant infection. In grapevine interaction with pathogens, epigenetic regulation still remains a black box. In this work, we characterized grapevine DNA methyltransferase gene family and identified nine DNA methyltransferases genes across eight grapevine chromosomes coding for 17 proteins. We also assessed the modulation of global cytosine methylation and gene expression levels of these genes with the aim of establishing a connection between DNA methylation and grapevine resistance towards downy mildew. Our results revealed that, in the incompatible interaction, an early hypomethylation, coupled with downregulation of DNMT and CMT genes occurs very early after pathogen inoculation. Additionally, the compatible interaction is characterized by a hypermethylation at 6hpi. A temporal delay is evident between the shifts in DNA methyltransferases gene expression in both compatible and incompatible interactions which in turn may be reflected in the global methylation percentage. Overall, we present the first evidence of an epigenetic regulation role in grapevine defense against P. viticola.

Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense

Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.

Genetic divergence in Tunisian castor bean genotypes based on trap markers

In the present study, the representatives of the genus Ricinus communis collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 30 TRAP primers. The efficacy of the TRAP technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 30 primers for TRAP analysis produced 490 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (TRAP 04 x arb 1, TRAP 22 x arb 3 and TRAP 23 x arb 3) to 13 (TRAP 56 x arb 2), and the amplicon size ranged from 100 to 1600 bp. Of the 490 amplified bands, 377 were polymorphic, with an average of 5.71 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for TRAP 10 x arb 1 (0.555) and the highest PIC values were detected for TRAP 44 x arb 2 (0.961) with an average of 0.770. A dendrogram was constructed from a genetic distance matrix based on profiles of the 30 TRAP primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Moreover, functional TRAP markers would be efficiently useful in genetic studies for castor genetic improvement.

Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi-woody crop

Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication origin, genomic variation, and potential targets of selection underlying domestication traits remain unknown. Here, we performed a phylogenetic analysis, which suggests that the wild accessions were distinctively separated from the cultivated accessions. Genome sequencing of three accessions (one each wild, landrace, and cultivar) showed a large number of genetic variants between wild and cultivated castor bean (ZB306 or Hale), and relatively few variants between cultivar ZB306 and Hale. Comparative genome analysis revealed many candidate genes of selection and key pathways potentially involved in the transition from a perennial woody tree to annual crop. Interestingly, among 16 oil-related genes only three showed evidence of selection and the remainder showed low genetic variation at the population level, suggesting strong purifying selection in both the wild and domesticated gene pools. These results extend our understanding of the origin, genomic variation, and domestication, and provide a valuable resource for future gene-trait associations and castor bean breeding.

Genetic diversity in Tunisian castor genotypes (Ricinus communis L.) detected using RAPD markers

Castor (Ricinus communis L.) is a plant that is commercially very important to the world. It is produced in about 30 countries lying in the tropical belt of the world. It is an important plant for production of industrial oil. Assessment of genetic diversity of a crop species is a prerequisite to its improvement; hence it is important to identify the genetic diversity of castor genetic resources for development of improved cultivars. The present study is focused on estimation of genetic distance between 56 Tunisian castor genotypes, based on 18 RAPD markers. Seeds of castor were obtained from the University of Carthage, National Institute of Research in Rural Engineering, Waters and Forests (INRGREF), Regional Station of Gabí¨s, Tunisia. The ricin genotypes were obtained from 12 regions of Tunisia. The efficacy of the RAPD technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 18 primers for RAPD analysis produced 145 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (OPE-07) to 13 (SIGMA-D-01), and the amplicon size ranged from 100 to 1500 bp. Of the 145 amplified bands, 145 were polymorphic, with an average of 8.11 polymorphic bands per primer. The lowest values of polymorphic information content were recorded for RLZ 9 (0.618) and the the highest PIC values were detected for OPD-08 (0.846) with an average of 0.761. A dendrogram was constructed from a genetic distance matrix based on profiles of the 18 RAPD primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Genetically the closest were four genotypes from cluster 1 (BT-1 - S-5 and K-1 - N-3). Knowledge of the genetic diversity of castor can be used in future breeding programs for increased oil production to meet the ever increasing demand of castor oil for industrial uses as well as for biodiesel production.