Fingerprinting, structure, and genetic relationships among selected accessions of blue honeysuckle (Lonicera caerulea L.) from European collections.

Due to its value and economic importance, the genome of Lonicera caerulea L. has been widely studied in various fields of science. In this study the genetic structure and relationships between 24 accessions of L. caerulea of different origins were assessed. A total of 692, 814, and 258 loci were amplified using 43 RAPD (random amplified polymorphic DNA), 40 ISSR (intersimple sequence repeat), and 20 R-ISSR (RAPD+ISSR) primers, respectively. Among the amplified loci, 66-78% were polymorphic and 12-20% were private. Selected R-ISSR sequences were detected in Lonicera japonica transcripts. Cluster and STRUCTURE analyses performed for each of the techniques revealed the existing differences and unknown similarities between the genotypes. The r-factor values calculated in the Mantel test indicated highly significant positive correlations between the Nei distance matrices, similar to the F ST values (F ST_RAPD = 0.223, F ST_ISSR = 0.279, F ST_R-ISSR = 0.363) determined in the analysis of molecular variance. It was found that 78%, 72%, and 64% of the genetic variations were related to the differences observed within the populations, which suggest that the variations are mainly reflected in the differences among the genotypes. The principal coordinate analysis showed greater differences between the mean distances of the Lonicera genotype pair and the actual distances of the same pairs on the Nei matrix compared to multidimensional scaling. These differences were 45%, 56%, and 42% higher for RAPD, ISSR and R-ISSR, respectively.

Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye.

Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.

Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L. ) tolerance to nutrient deprivation stress identified using bulk segregant analysis

Background: An adaptive mechanism in plant roots is initiated in the event of nitrogen and potassium deficiency, and it facilitates the active uptake of these elements in order to ensure plant growth and survival in stress conditions. Signaling and transduction of signals in response to changing nitrogen and potassium concentrations is a complex process, affected by interactions between various gene expression products, and often subjected to modifications. Results: In order to identify genotypic differences between phenotypes of two populations of recombinant inbred rye lines (153/79-1 x Ot1-3 and Ot0-6 x Ot1-3) in response to nutrition stress caused by nitrogen and potassium deficiency at the seedling stage, bulk segregant analysis was utilized. Identification of genotypic differences between and within pooled DNA samples involved 424 RAPD, 120 ISSR primers and 50 combinations of R-ISSR. Identified markers were sequenced and converted to SCAR, attributing to them unique ESTs annotations, and chromosomal ones to selected localizations. Significant relationships with the examined trait were described for nine and eight RAPD markers, four and five ISSR, one and three R-ISSR markers for population 153/79-1 x Ot1-3 and Ot0-6 x Ot1-3, respectively. Sequences identified for the rye genome were characterized by a uniqueness and a similarity to the sequence of aquaporin PIP1, a gene encoding protein related to the function of the transcription factor in plant response to iron deficiency and the putative ethylene-responsive transcription factor, cytosolic acetyl-CoA carboxylase, HvHKT1 transporter, as well as HCBT proteins. Conclusion: Identified molecular markers differentiating rye genotypes of extreme response of root system on nitrogen and potassium deficiency play a significant role in systemic plant response to stress, including stress caused by nitrogen and potassium deficiency. They may constitute a system facilitating selection, and together with the material they are described in, they may be a starting point for research on mechanisms of sensing and transduction of signal across the plant.

Discrimination of population of recombinant inbred lines of rye (Secale cereale L. ) for different responses to nitrogen-potassium stress assessed at the seedling stage under in vitro conditions

Background: Plants differ in the methods used to acquire nutrients from environments with low nutrient availability, and may change the morphology of their ‘root architecture’ to be able to take up nutrients. Results: In the present study rye response to stress caused by high and low nitrogen-potassium treatments in mature embryos cultures was described within a population consisting of one hundred and thirty eight recombinant inbred lines of rye. Characterization of the response of recombinant inbred lines (RILs) to nutrient stress was presented as the results of analyses of morphological traits, and physiological and biochemical parameters of the seedlings grown in both treatments. A wide range of variability of individual RILs to induced stress was observed in the population of recombinant inbred lines, and was presented as the difference between the means of each of the analysed traits described at high- and low-nitrogen-potassium levels. Lines were grouped using Ward's agglomerative method on the basis of differences in coleoptyle length, with the longest root length and root number used as variables. Conclusions: Recombinant inbred lines at low nitrogen-potassium treatment developed: longer, shorter, or roots of similar length in comparison with the high nitrogen-potassium treatment. Discriminant function analysis showed that the discriminant variable able to clearly differentiate recombinant inbred lines in terms of their response to nutrient stress was the trait of the longest root length.

Antisense expression increases gene expression variability and locus interdependency.

Genome-wide transcription profiling has revealed extensive expression of non-coding RNAs antisense to genes, yet their functions, if any, remain to be understood. In this study, we perform a systematic analysis of sense-antisense expression in response to genetic and environmental changes in yeast. We find that antisense expression is associated with genes of larger expression variability. This is characterized by more 'switching off' at low levels of expression for genes with antisense compared to genes without, yet similar expression at maximal induction. By disrupting antisense transcription, we demonstrate that antisense expression confers an on-off switch on gene regulation for the SUR7 gene. Consistent with this, genes that must respond in a switch-like manner, such as stress-response and environment-specific genes, are enriched for antisense expression. In addition, our data provide evidence that antisense expression initiated from bidirectional promoters enables the spreading of regulatory signals from one locus to neighbouring genes. These results indicate a general regulatory effect of antisense expression on sense genes and emphasize the importance of antisense-initiating regions downstream of genes in models of gene regulation.