Comparative transcriptome analysis provides a useful tool for the exploration of plant-pathogen interaction by allowing in-depth comparison of gene expression between unaffected, inoculated and ...wounded organisms. Here we present the results of comparative transcriptome analysis in genetically identical one-year-old Scots pine ramets after wounding and inoculation with
. We identified 230 genes that were more than 2-fold upregulated in inoculated samples (compared to controls) and 116 downregulated genes. Comparison of inoculated samp les with wounded samples identified 32 differentially expressed genes (30 were upregulated after inoculation). Several of the genes upregulated after inoculation are involved in protection from oxidative stress, while genes involved in photosynthesis, water transport and drought stress tolerance were downregulated. An NRT3 family protein was the most upregulated transcript in response to both inoculation and wounding, while a U-box domain-containing protein gene was the most upregulated gene comparing inoculation to wounding. The observed transcriptome dynamics suggest involvement of auxin, ethylene, jasmonate, gibberellin and reactive oxygen species pathways and cell wall modification regulation in response to
infection. The results are compared to methyl jasmonate induced transcriptome dynamics.
Silver birch (
Betula pendula
Roth.) is an ecologically and economically important deciduous tree species in Northern Europe. In vitro culture initiation and shoot rejuvenation from birches in their ...reproductive phase is difficult and often unsuccessful. Currently, markers to evaluate the degree of juvenility of birch in vitro shoots, which could be used to track the rejuvenation process and to determine factors affecting it, have not been developed. The aims of this study were to assess expression of juvenility related microRNAs and target genes during micropropagation of silver birch, and to investigate factors affecting juvenility of birch genotypes with different in vitro morphogenic ability. Potential precursor sequences and target genes of the microRNAs miR156 and miR172 were determined by alignment to the birch unigene set. Ten potential miR156 and miR172 precursor sequences were identified, and were tested for the ability to form the required stem-loop structure. Based on precursor sequences, primers were designed for real time PCR analysis of precursor miRNA expression. Expression patterns of two miR156 family precursors (miR156_511 and miR156_789) and one miR172 precursor (miR172_1931) and two target genes (
BpSPL1
and
BpAP2
) had the best correlation with juvenility/maturity in the analysed in vitro propagated silver birch samples. Expression patterns of these miRNA precursors and target genes were also investigated in samples cultured under different in vitro conditions. This study provides an initial survey of molecular markers for assessment of phase change in birch in vitro micropropagation.
Key message
This study investigated expression of juvenility related micro RNAs and target genes in
Betula pendula
micropropagated material with differing juvenility and in vitro culture conditions.
is an economically detrimental weed found in cereal growing areas worldwide. Knowledge about the variation of dormancy and germination characteristics, as well as of the genetic diversity and ...structure can provide additional information about different populations within a region. Identification and development of potential indicators or markers of seed germination behavior, would be useful for modelling emergence and seed bank dynamics. This study aimed to describe the initial germination, dormancy, and morphological characteristics of seeds from different Latvian populations of
and to investigate the genetic structure of local populations. Seed samples from 26 to 41 locations in different regions of Latvia were collected over three years. Seed morphology, initial germination, and the effect of dormancy-breaking treatments were determined. Seeds from 18 Latvian populations with contrasting seed dormancy characteristics were genotyped. Although morphological differences between seeds from different regions were revealed, genetic analysis of the selected populations indicated that the population structure was not related to geographical location, which probably reflects the impact of anthropogenic dispersal of
seeds. The effect of dormancy-breaking treatments varied between years, between climatic zones and between populations, indicating environmental influences as well as inherited dormancy.
Forest ecosystems in Europe are expected to experience changes in temperature and water regimes associated with increased risks of extreme environmental events and disasters. Genetic diversity and ...relatedness has been linked to resilience of forest stands and landscapes. Genetic diversity indicators were compared between a Norway spruce population naturally regenerated after extensive windthrow and Norway spruce progeny populations derived from two seed orchards. In addition, genetic diversity in an undisturbed stand in a long established national park and a spruce genetic resource stand were analyzed. Populations were genotyped at 11 simple sequence repeat (SSR) loci. Average genetic diversity indicators were similar across populations. However, the total number of alleles, average number of alleles over all loci, effective number of alleles, average gene diversity, and average allelic richness were highest in the naturally regenerated population and lowest in one of the seed orchard progeny populations. The genetic diversity in progeny from seed orchards used for stand renewal is comparable to the genetic diversity in naturally regenerated stands. However, fluctuations in seed production between years can have a large impact on genetic diversity in seed orchard progeny. The use of improved Norway spruce germplasm deployed via clonal seed orchards for forest renewal can maintain similar levels of genetic diversity compared to naturally regenerated stands, while also increasing production and timber quality.
Transposition of mobile elements has been implicated in genome instability, rearrangements and therefore also adaptation to changing environmental conditions. Transposons could influence gene ...activity directly by transposition inside or close to coding regions by their disruption or by addition of regulative sequences. Further, class I transposable elements, which are the most abundant in plant genomes, utilize a RNA intermediate in their life cycle, therefore retrotransposons could act by producing non-coding RNAs that could affect other transcripts by RNA interference. Transposition activity is suppressed by chromatin modifications, and both classes of transposons have been shown to be activated in plants under various stress conditions and developmental stages. Using a nonspecific amplification approach, we demonstrate the differential transcriptional activation of sequences with homology to transposable elements and other associated sequences in the complex genome of Scots pine (Pinus sylvestris L.) after exposure to heat stress, infestation with pine woolly aphids, and salicylic acid and abscisic acid treatment. Sequences with homology to several retrotransposon classes and families were identified, as well as several chimeric transcript types. Some of them represent chloroplast sequence insertions into the pine nuclear genome and these sequences are highly represented in EST databases of a wide range of species. In this study, we identified several retrotransposon classes and families with differing levels of similarity with known transposable elements from other plant species, and which are differentially expressed under various stress conditions in Scots pine.
Retrotransposable elements (REs) and related sequences form a large proportion of conifer genomes. During genome evolution, some RE sequences are degraded or eliminated, but some are evolutionarily ...stable, and can be identified even in distantly related species. Use of genome sequence information from loblolly pine (
Pinus taeda
) enables investigation of divergent non-coding RE sequences in other pine and conifer species, including Scots pine (
Pinus sylvestris
). Non-specific inter-retrotransposon amplified polymorphism technique (IRAP) as well as the amplification polymorphism of 12 RE families were investigated in 80 gymnosperm species. The obtained results were compared with phylogenetic relationships among gymnosperms. Investigation of distantly related gymnosperm species reveals persistent RE sequences, such as
IFG
and
Pineywoods
, distributed among a wide range of plant lineages
.
RE sequence divergence was observed, reflecting periods of inactivity and degradation during speciation of pine lineages, as demonstrated by the delineation of the main pine subgenera. Intraspecific variation of 10 RE copy numbers (CN) between Scots pine individuals ranged from 8.9 to 26.6% of the overall mean estimates. CN analyses were performed in 16 additional gymnosperm species. The analysed pine species contained a similar complement of RE families; however, CN and genome occupation proportions differ. A decrease in RE CN estimates can reflect sequence divergence, associated with independent transposition events. Transposition of some REs can be induced by stress conditions; therefore, even distantly related species inhabiting extreme environments could have similar patterns or distribution of these elements.
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary ...diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
•Effective chloroplast SSR marker set was selected for Ribes plants.•Chloroplast SSR markers are very good at distinguishing between different Ribes species.•Ribes germplasm show great diversity, but ...all breeding programs work in the same direction and reduce it.
Currants and gooseberries (Ribes sp.) are important berry crops with high nutritional value, and the efficient development of new cultivars depends on the characterisation of Ribes genetic resources and successful inclusion into breeding materials. Ribes breeding programs are characterised by the extensive use of interspecific crosses to introduce required traits. In some cases, this makes it challenging to identify the genomic contribution of particular species to cultivars, thus limiting the understanding of the heredity of these traits. To clarify these issues, the present study aimed to evaluate the applicability of selected chloroplast SSR molecular markers to analyse germplasm consisting of genotypes developed through complicated multistage crosses among different Ribes species. This provides information on Ribes germplasm species composition and blackcurrant collection species structure, thus assessing the applicability and utility of the blackcurrant collection in breeding. Fifty cpSSR molecular markers previously developed for plants were assessed, and a set of 19 markers was selected for further analysis of a Ribes genetic resource collection. A set of 145 Ribes genotypes was analysed using the selected chloroplast markers: blackcurrants (R. nigrum L.), redcurrant (R. rubrum L.), European gooseberry (R. uva-crispa L.), mountain currant (R. alpinum L.), golden currant (R. aureum Pursh), R. americanum Mill., jostaberry (R. × nidigrolaria Rud.Bauer & A.Bauer), R. ussuriense Jancz., R. komarovii Pojark., R. sanguineum Pursh., R. latifolium Jancz., R. fasciculatum var. chinense Maxim., R. fragrans Pall., R. laxiflorum Pursh. and their interspecific hybrids. The cpSSR markers are suitable for differentiating Ribes species and thus are suitable for analysing germplasm collections, showing relationships regarding pedigree. The markers are good at showing the structure of a germplasm collection. However, in the case of complex interspecies crossings, identifying a specific percentage of a species within an accession cannot be guaranteed.
Potato onions (
Allium cepa
var
aggregatum
G. Don) are multiplying or aggregating onions, very similar to shallots and have been historically cultivated throughout Europe. Currently in Northern ...Europe they are maintained in home gardens and ex situ field collections. Potato onions are primarily vegetatively propagated, however in Estonia, near Lake Peipsi, this species has been propagated by seed since the seventeenth century. There is increasing interest in Northern Europe in utilizing this germplasm in organic and/or sustainable farming systems. The genetic diversity and relationship between and within European potato onion collections is unclear. From historical records it is known that cultivation, exchange and trade of potato onion has occurred throughout Europe for hundreds of years. This study utilised molecular markers to assess genetic diversity, duplication of genotypes and relationships among and between Nordic, Baltic, Czech and Croatian potato onion collections. Of 264 accessions, 80 catalogued as unique had identical genotypes with one or more other accessions, and are putative duplicates. The genetic diversity within two Estonian sexually propagated accessions was comparable to that found in all of the vegetatively propagated accessions. Accessions from the Nordic countries grouped together genetically, as did Latvian and Lithuanian accessions. Croatian accessions were genetically separated. These genetic relationships suggest historical movement of potato onion germplasm in North-Eastern Europe. The results, in conjunction with other passport and characterization data, can assist in the development of potato onion core collections, facilitating the conservation and utilization of valuable potato onion genetic resources.
Thaumatin-like proteins (TLPs) are pathogenesis-related proteins, which are involved in plant defense responses to pathogen infection. Expression of the
Pinus sylvestris
L.
TLP
gene is up-regulated ...by methyl jasmonate treatment and inoculation with
Heterobasidion annosum
. A full-length
Pinus taeda TLP
gene sequence was used to design PCR primers for amplification of the full-length
TLP
gene from
P. sylvestris
. A putative 705-bp open reading frame of
TLP
gene was cloned into
Escherichia coli
cells, and then subcloned into the overexpression vector pET100 using BL21 Star expression bacteria. Optimization of the expression of recombinant TLP was achieved by decreasing both expression temperature and IPTG concentration. The purified 24.6-kDa TLP shows antimicrobial activity against 12 fungal species.
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