Project description:Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable. Here we have used genotyping by sequencing (GBS) to determine the genetic variation and population structure in red clover natural populations from Europe and Asia, and varieties or synthetic populations. Cluster analysis differentiated the collection into four large regional groups: Asia, Iberia, UK, and Central Europe. The five varieties clustered with the geographical area from which they were derived. Two methods (BayeScan and Samβada) were used to search for outlier loci indicating signatures of selection. A total of 60 loci were identified by both methods, but no specific genomic region was highlighted. The rate of decay in linkage disequilibrium was fast, and no significant evidence of any bottlenecks was found. Phenotypic analysis showed that a more prostrate and spreading growth habit was predominantly found among populations from Iberia and the UK. A genome wide association study identified a single nucleotide polymorphism (SNP) located in a homologue of the VEG2 gene from pea, associated with flowering time. The identification of genetic variation within the natural populations is likely to be useful for enhancing the breeding of red clover in the future.
Project description:Rhizobia are soil-borne bacteria forming symbiotic associations with legumes and fixing atmospheric dinitrogen. The nitrogen-fixation potential depends on the type of host plants and microsymbionts as well as environmental factors that affect the distribution of rhizobia. In this study, we compared genetic diversity of bacteria isolated from root nodules of Trifolium pratense grown in two geographical regions (Tromsø, Norway and Lublin, Poland) located in distinct climatic (subpolar and temperate) zones. To characterize these isolates genetically, three PCR-based techniques (ERIC, BOX, and RFLP of the 16S-23S rRNA intergenic spacer), 16S rRNA sequencing, and multi-locus sequence analysis of chromosomal house-keeping genes (atpD, recA, rpoB, gyrB, and glnII) were done. Our results indicate that a great majority of the isolates are T. pratense microsymbionts belonging to Rhizobium leguminosarum sv. trifolii. A high diversity among these strains was detected. However, a lower diversity within the population derived from the subpolar region in comparison to that of the temperate region was found. Multi-locus sequence analysis showed that a majority of the strains formed distinct clusters characteristic for the individual climatic regions. The subpolar strains belonged to two (A and B) and the temperate strains to three R. leguminosarum genospecies (B, E, and K), respectively.
Project description:Central European grasslands, such as calcareous grasslands and oat-grass meadows, are characterized by diverse environmental conditions and management regimes. Therefore, we aimed to determine potential differences in genetic and epigenetic variation patterns between the contrasting habitats and to identify the drivers of genetic and epigenetic variation. We investigated the genetic and epigenetic variation of the ecologically variable plant species Trifolium pratense L. applying amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses. We observed low levels of genetic and epigenetic differentiation among populations and between habitat types. Genetic and epigenetic variations were not interdependent. Thus, genetic variation was significantly isolated by habitat dissimilarity, whereas epigenetic variation was affected by environment. More specifically, we observed a significant correlation of epigenetic diversity with soil moisture and soil pH (the latter potentially resulting in phosphorus limitation). Genetic variation was, therefore, affected more strongly by habitat-specific environmental conditions induced by land use-related disturbance and gene flow patterns, while epigenetic variation was driven by challenging environmental conditions.