Adam Vivian-Smith
Research Scientist
Authors
Anders Ræbild Kesara Anamthawat-Jónsson Ulrika Egertsdotter Juha Immanen Anna Monrad Jensen Athina Koutouleas Helle Jakobe Martens Kaisa Nieminen Jill Katharina Olofsson Anna-Catharina Röper Jarkko Salojärvi Martina Strömvik Mohammad Vatanparast Adam Vivian-SmithAbstract
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Authors
Simo Maduna Adam Vivian-Smith Ólöf Dóra Bartels Jónsdóttir Albert Imsland Cornelya Klutsch Tommi Nyman Hans Geir Eiken Snorre HagenAbstract
We determined the mitogenome of Cyclopterus lumpus using a hybrid sequencing approach, and another four closely related species in the Liparidae based on available next-generation sequence data. We found that the mitogenome of C. lumpus was 17,266 bp in length, where the length and organisation were comparable to those reported for cottoids. However, we found a GC-homopolymer region in the intergenic space between tRNALeu2 and ND1 in liparids and cyclopterids. Phylogenetic reconstruction confirmed the monophyly of infraorders and firmly supported a sister-group relationship between Cyclopteridae and Liparidae. Purifying selection was the predominant force in the evolution of cottoid mitogenomes. There was significant evidence of relaxed selective pressures along the lineage of deep-sea fish, while selection was intensified in the freshwater lineage. Overall, our analysis provides a necessary expansion in the availability of mitogenomic sequences and sheds light on mitogenomic adaptation in Cottoidei fish inhabiting different aquatic environments.
Abstract
Methyl jasmonate (MeJA) treatment elicits induced resistance (IR) against pests and diseases in Norway spruce (Picea abies). We recently demonstrated using mRNA-seq that this MeJA-IR is associated with both a prolonged upregulation of inducible defenses and defense priming. Gene expression can be regulated at both a transcrip-tional and post-transcriptional level by small RNAs, including microRNAs (miRNAs). Here we explore the effects of MeJA treatment and subsequent challenge by wounding on the Norway spruce miRNA transcriptome. We found clusters of prolonged down- or upregulated miRNAs as well as miRNAs whose expression was primed after MeJA treatment and subsequent wounding challenge. Differentially expressed miRNAs included miR160, miR167, miR172, miR319, and the miR482/2118 superfamily. The most prominent mRNA targets predicted to be differentially expressed by miRNA activity belonged to the nucleotide-binding site leucine-rich repeat (NBS- LRR) family. Among other predicted miRNA targets were genes regulating jasmonic acid biosynthesis. Our re-sults indicate that miRNAs have an important role in the regulation of MeJA-IR in Norway spruce.
Authors
Simo Maduna Adam Vivian-Smith Ólöf Dóra Bartels Jónsdóttir Albert Imsland Cornelya Klutsch Tommi Nyman Hans Geir Eiken Snorre HagenAbstract
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.
Authors
Baiba Krivmane Ilze Šņepste Vilnis Šķipars Igor A. Yakovlev Carl Gunnar Fossdal Adam Vivian-Smith Dainis RuņģisAbstract
MicroRNAs (miRNAs) are non-protein coding RNAs of ~20–24 nucleotides in length that play an important role in many biological and metabolic processes, including the regulation of gene expression, plant growth and developmental processes, as well as responses to stress and pathogens. The aim of this study was to identify and characterize novel and conserved microRNAs expressed in methyl jasmonate-treated Scots pine needles. In addition, potential precursor sequences and target genes of the identified miRNAs were determined by alignment to the Pinus unigene set. Potential precursor sequences were identified using the miRAtool, conserved miRNA precursors were also tested for the ability to form the required stem-loop structure, and the minimal folding free energy indexes were calculated. By comparison with miRBase, 4975 annotated sequences were identified and assigned to 173 miRNA groups, belonging to a total of 60 conserved miRNA families. A total of 1029 potential novel miRNAs, grouped into 34 families were found, and 46 predicted precursor sequences were identified. A total of 136 potential target genes targeted by 28 families were identified. The majority of previously reported highly conserved plant miRNAs were identified in this study, as well as some conserved miRNAs previously reported to be monocot specific. No conserved dicot-specific miRNAs were identified. A number of potential gymnosperm or conifer specific miRNAs were found, shared among a range of conifer species.
Authors
Melissa Magerøy Samuel W. Wilkinson Torstein Tengs Hugh Cross Marit Almvik Pierre Petriacq Adam Vivian-Smith Tao Zhao Carl Gunnar Fossdal Paal KrokeneAbstract
In response to various stimuli, plants acquire resistance against pests and/or pathogens. Such acquired or induced resistance allows plants to rapidly adapt to their environment. Spraying the bark of mature Norway spruce (Picea abies) trees with the phytohormone methyl jasmonate (MeJA) enhances resistance to tree‐killing bark beetles and their associated phytopathogenic fungi. Analysis of spruce chemical defenses and beetle colonization success suggests that MeJA treatment both directly induces immune responses and primes inducible defenses for a faster and stronger response to subsequent beetle attack. We used metabolite and transcriptome profiling to explore the mechanisms underlying MeJA‐induced resistance in Norway spruce. We demonstrated that MeJA treatment caused substantial changes in the bark transcriptional response to a triggering stress (mechanical wounding). Profiling of mRNA expression showed a suite of spruce inducible defenses are primed following MeJA treatment. Although monoterpenes and diterpene resin acids increased more rapidly after wounding in MeJA‐treated than control bark, expression of their biosynthesis genes did not. We suggest that priming of inducible defenses is part of a complex mixture of defense responses that underpins the increased resistance against bark beetle colonization observed in Norway spruce. This study provides the most detailed insights yet into the mechanisms underlying induced resistance in a long‐lived gymnosperm.
Authors
Mehdi Daemi-Saeidabad Abdolali Shojaeiyan Adam Vivian-Smith Hans K. Stenøien Mohsen Falahati-AnbaranAbstract
Many studies on Heracleum have shown poor correspondence between observed molecular clusters and established taxonomic classification amongst closely related species. This might reflect both unresolved taxonomy but perhaps also a lack of good genetic markers. This lack of appropriate and cost effective species-specific genetic markers hinders a resolved relationship for the species complex, and this in turn causes profound management challenges for a genus that contains both endemic species, with important ecological roles, and species with an invasive potential. Microsatellites are traditionally considered markers of choice for comprehensive, yet inexpensive, analyses of genetic variation, including examination of population structure, species identity, linkage map construction and cryptic speciation. In this study, we have used double digest restriction site associated DNA sequencing (ddRADseq) to develop microsatellite markers in Heracleum rechingeri. Genomic DNA from three individuals were digested with Sbf1 and Nde1 and size selected for library construction. The size-selected fragments were sequenced on an Ion Torrent sequencer and a total of 54 microsatellite sequences were bioinformatically confirmed. Twenty five loci were then tested for amplification, resulting in 19 of these being successfully amplified across eight species, comprising both the so-called thick-stemmed species (H. persicum, H. rechingeri, H. gorganicum and H. lasiopetalum), and thin-stemmed species (H. anisactis, H. pastinasifolium and H. transcaucasicum). Both Bayesian and distance-based clustering, and principal coordinate analyses clearly separated these into two groups. Surprisingly, three H. pastinacifolium populations were not separated from populations of the morphologically similar endemic species, H. anisactis, suggesting lack of genetic differentiation. Likewise, high genetic similarity was found between H. persicum and H. rechingeri populations, questioning taxonomic separation at the species level between these taxa. Further analyses are needed to re-evaluate the taxonomic significance of observed morphological variability currently applied to distinguish these sister taxa. Nevertheless, our results represent progress in the effort to develop cost-efficient molecular tools for species discrimination in this genus.
Abstract
The genus Scapania comprises a group of leafy liverworts distributed throughout many bryophytic assemblages. While many Scapania species grow widely, some are assessed as endangered and appear to be specialists with distinct niche environments. Several are found only in alpine forest communities, inhabiting decaying logs in streams, typical of an environment that is threatened by both logging activity and changes to watercourses. Another species, S. nimbosa, has an unusual Oceanic-Montane distribution across Ireland, Scotland, Norway, China and Nepal. Since gemmae and sexual reproduction are absent the species is hypothesized to be primarily dispersed by fragmentation. In Norway S. nimbosa occupies an area of only 13 x 20 km, at altitudes between 300-980 m, and is frequently found with another more abundant asexual species, S. ornithopodioides. This makes S. nimbosa susceptible to local extinction through climate change or perhaps interspecific competition. Genomics is being increasingly used to infer demography and the evolutionary history of a species. Ascertaining levels of genetic variation can also contribute towards an effective conservation management plan. Besides, very little is known about the genomic organization and sexual determination in leafy liverworts. To generate new knowledge about the genus Scapania we sequenced the genomes of the sexual species S. nemorea (both male and female isolates), S. undulata (a single isolate), and several asexual S. ornithopodiodes and S. nimbosa isolates. Illumina paired-end (2x 300 bp) and Oxford Nanopore long reads were used to create genomic references. Initially organellar genomes were assembled, annotated and genetic variation was discovered. This revealed that variation is indeed present even for S. nimbosa and S. ornithopodioides at Norwegian sites. Next we focussed on creating a high quality nuclear reference genome for S. nemorea using the SPAdes assembler (v3.13). Qualities of each assembly and isolate were assessed with QUAST and BUSCO. While one assembly spans 202.6 Mb (10930 scaffolds; N50 of 66 Kb), other isolates of S. nemorea show larger assembled genome sizes and different Kmer distributions, consistent with the expected alternative sexual chromosome complement. We further analyse genomic synteny and diversity, but emphasize that difficulties in extracting DNA from herbarium specimens really hamper analysis.
Authors
Ari Hietala Isabella Børja Hugh B. Cross Nina Elisabeth Nagy Jørn Henrik Sønstebø Volkmar Timmermann Adam Vivian-Smith Halvor SolheimAbstract
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Authors
Ari Hietala Isabella Børja Hugh Cross Nina Elisabeth Nagy Halvor Solheim Volkmar Timmermann Adam Vivian-SmithAbstract
European ash (Fraxinus excelsior), a keystone species with wide distribution and habitat range in Europe, is threatened at a continental scale by an invasive alien ascomycete, Hymenoscyphus fraxineus. In its native range of Asia, this fungus is a leaf endophyte with weak parasitic capacity and robust saprobic competence in local ash species that are closely related to European ash. In European ash, H. fraxineus has a similar functional role as in Asia, but the fungus also aggressively kills shoots, resulting in crown dieback and tree death. H. fraxineus is a typical invasive species, as its spread relies on high propagule pressure. While crown dieback of European ash is the most obvious symptom of ash dieback, the annual colonization of ash leaves is a crucial key dependency for the invasiveness of H. fraxineus, since its fruiting bodies are formed on overwintered leaf vein tissues in soil debris. Leaves of European ash host a wide range of indigenous epiphytes, endophytes, facultative parasites and biotrophic fungi, including Hymenoscyphus albidus, a relative of H. fraxineus that competes for the same sporulation niche as the invader. At face value, leaves of European ash are colonized by a large and diverse indigenous mycobiome. In order to understand why this invader became successful in Europe, we discuss and summarize the current knowledge of diversity, seasonal dynamics and traits of H. fraxineus and indigenous fungi associated with leaves of European ash.
Authors
Melissa Magerøy Hugh B. Cross Torstein Tengs Carl Gunnar Fossdal Pierre Petriacq Adam Vivian-Smith Tao Zhao Paal KrokeneAbstract
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Authors
Mark McMullan Maryam Rafiqi Gemy Kaithakottil Bernardo J. Clavijo Lorelei Bilham Elizabeth Orton Lawrence Percival-Alwyn Ben J. Ward Anne Edwards Diane G.O. Saunders Gonzalo Garcia Accinelli Jonathan Wright Walter Verweij Georgios Koutsovoulos Kentaro Yoshida Tsuyoshi Hosoya Louisa Williamson Philip Jennings Renaud Ioos Claude Husson Ari Hietala Adam Vivian-Smith Halvor Solheim Dan MaClean Christine Fosker Neil Hall James K.M. Brown David Swarbreck Mark Blaxter J. Allan Downie Matthew D. ClarkAbstract
Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H.fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H.fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H.fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
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Authors
Isabella Børja Volkmar Timmermann Ari Hietala Mari Mette Tollefsrud Nina Elisabeth Nagy Adam Vivian-Smith Hugh Cross Jørn Henrik Sønstebø Tor Myking Halvor SolheimAbstract
In Norway the common ash (Fraxinus excelsior L.) has its northernmost distribution in Europe. It grows along the coastal range as small fragmented populations. The first occurrence of ash dieback caused by Hymenoscyphus fraxineus in Norway was reported in 2008. At that time, the disease had already spread through large areas of southern and south-eastern parts of Norway. Since then the disease continued spreading with a speed of about 50- 60 km per year along the western coastal range. To monitor the disease development over time, we established eight permanent monitoring plots in south-eastern and western Norway in 2009 and 2012, respectively. In all plots tree mortality was high, especially among the youngest trees in south-eastern Norway. The extent of crown damage has continually increased in all diameter classes for both regions. In 2009, 76.8 % of all trees on the five monitoring plots in south-eastern Norway were considered to be healthy or slightly damaged, and only 8.9 % to be severely damaged. In 2015, 51.7 % were dead, 13.5 % severely damaged and only 25.7 % remained healthy or slightly damaged. To assess the infection pressure and spore dispersal patterns of the pathogen, we used a Burkard volumetric spore sampler placed in an infested ash stand in southern Norway. We examined the airborne ascospores of H. fraxineus and H. albidus captured on the sampling tape microscopically and with real-time PCR assays specific to these fungi. We detected very few ascospores of H. albidus, whereas ascospores of H. fraxineus dominated throughout entire sampling periods of 2009, 2010 and 2011. Spore discharge occurred mainly between the hours of 5 and 8 a.m., though the distinctive sporulation had yearly variation between 5-7 a.m. We observed the same diurnal pattern throughout the entire sampling period, with a seasonal peak in spore liberation between mid-July and midAugust, after which the number of ascospores decreased substantially. Similar diurnal patterns were observed throughout the sampling period except that after mid-August the number of trapped ascospores substantially decreased. To compare the genetic pattern of common ash in the northern and central ranges of Europe we analyzed the Norwegian samples together with available samples from central Europe by using chloroplast and nuclear microsatellite markers. We found that the northern range of common ash was colonized via a single migration route that originated in eastern or south-eastern Europe with little influence originating from other southern or western European refugia. In the northern range margins, genetic diversity decreased and population differentiation increased, coherent with a post-glacial colonization history characterized by founder events and population fluctuations. Based on our findings we discuss the future management and conservational implications.
Abstract
The plant hormone auxin is a vital component for plant reproduction as it regulates the development of both male and female reproductive organs, including ovules and gynoecia. Furthermore, auxin plays important roles in the development and growth of seeds and fruits. Auxin responses can be detected in ovules shortly after fertilization, and it has been suggested that this accumulation is a prerequisite for the developmental reprogramming of the ovules to seeds, and of the gynoecium to a fruit. However, the roles of auxin at the final stages of ovule development, and the sources of auxin leading to the observed responses in ovules after fertilization have remained elusive. Here we have characterized the auxin readout in Arabidopsis ovules, at the pre-anthesis, anthesis and in the immediate post-fertilization stages, using the R2D2 auxin sensor. In addition we have mapped the expression of auxin biosynthesis and conjugation genes, as well as that of auxin transporting proteins, during the same developmental stages. These analyses reveal specific spatiotemporal patterns of the different auxin homeostasis regulators. Auxin biosynthesis genes and auxin transport proteins define a prepatterning of vascular cell identity in the pre-anthesis funiculus. Furthermore, our data suggests that auxin efflux from the ovule is restricted in an anther-dependent manner, presumably to synchronize reproductive organ development and thereby optimizing the chances of successful fertilization. Finally, de novo auxin biosynthesis together with reduced auxin conjugation and transport result in an enhanced auxin readout throughout the sporophytic tissues of the ovules soon after fertilization. Together, our results suggest a sophisticated set of regulatory cascades that allow successful fertilization and the subsequent transition of the female reproductive structures into seeds and fruits.
Authors
Ari Hietala Hugh Cross Halvor Solheim Volkmar Timmermann Nina Elisabeth Nagy Isabella Børja Adam Vivian-Smith Jørn Henrik SønstebøAbstract
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Authors
Hugh Cross Jørn Henrik Sønstebø Nina Elisabeth Nagy Volkmar Timmermann Halvor Solheim Isabella Børja Håvard Kauserud Tor Carlsen Barbara Rzepka Katarzyna Wasak Adam Vivian-Smith Ari HietalaAbstract
High biodiversity is regarded as a barrier against biological invasions. We hypothesized that the invasion success of the pathogenic ascomycete Hymenoscyphus fraxineus threatening common ash in Europe relates to differences in dispersal and colonization success between the invader and the diverse native competitors. Ash leaf mycobiome was monitored by high-throughput sequencing of the fungal internal transcribed spacer region (ITS) and quantitative PCR profiling of H. fraxineus DNA. Initiation of ascospore production by H. fraxineus after overwintering was followed by pathogen accumulation in asymptomatic leaves. The induction of necrotic leaf lesions coincided with escalation of H. fraxineus DNA levels and changes in proportion of biotrophs, followed by an increase of ubiquitous endophytes with pathogenic potential. H. fraxineus uses high propagule pressure to establish in leaves as quiescent thalli that switch to pathogenic mode once these thalli reach a certain threshold – the massive feedback from the saprophytic phase enables this fungus to challenge host defenses and the resident competitors in mid-season when their density in host tissues is still low. Despite the general correspondence between the ITS-1 and ITS-2 datasets, marker biases were observed, which suggests that multiple barcodes provide better overall representation of mycobiomes.
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The necrotrophic fungus Drechslera teres causes net blotch disease in barley by secreting necrotrophic effectors (NEs) which, in the presence of corresponding host susceptibility factors (SF), act as virulence factors in order to enable host colonization. At present the resistance within most Norwegian cultivars is insufficient. This study aims at detecting QTL associated with resistance and susceptibility in the Nordic barley breeding material and at discovering new NE _ SF interactions. This knowledge together with an understanding of the genetic background of the Norwegian net blotch population will be utilized to speed up resistance breeding. Resistance of a segregating mapping population of a cross between the closely related Norwegian varieties Arve and Lavrans to three Norwegian D. teres isolates was assessed at seedling stage in the greenhouse and in adult plants in the field. QTL mapping revealed four major QTL on chromosomes 4H, 5H, 6H and 7H. The 5H and 6H QTL accounted for up to 47% and 14.1% of the genetic variance, respectively, and were found both in seedlings and adult plants with the latter QTL being an isolate-specific association. The high correlation of seedling and adult resistance (R2=0.49) suggests that components of adult plant resistance can be predicted already at the seedling stage. Selected isolates and their culture filtrates will be screened on selected barley lines to characterize novel NE - SF interactions and to map the corresponding sensitivity loci. Effector protein candidates will be purified and further analysed to verify their effect on disease development. Additionally, 365 Norwegian D. teres isolates and a selection of globally collected isolates are currently being ddRAD genotyped in order to obtain SNP markers to study the genetic diversity and population structure of the current Norwegian fungal population. This data will also allow us to perform Genome Wide Association Studies (GWAS) to identify potential novel NE genes.
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Authors
Adam Vivian-Smith Jørn Henrik Sønstebø Thomas Marcussen Eivind Uleberg Julie Graham Anita Sønsteby Inger MartinussenAbstract
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Authors
Ari Hietala Isabella Børja Hugh Cross Nina Elisabeth Nagy Halvor Solheim Jørn Henrik Sønstebø Volkmar Timmermann Adam Vivian-SmithAbstract
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Ari Hietala Hugh Cross Isabella Børja Nina Elisabeth Nagy Volkmar Timmermann Halvor Solheim Jørn Henrik Sønstebø Adam Vivian-SmithAbstract
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Adam Vivian-Smith Philippe Sakalis Eelke Roos Igor A. Yakovlev Kim Boutilier Hailing Jin Remko OffringaAbstract
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Fruit-set involves a series of physiological and morphological changes that are well described for tomato and Arabidopsis, but largely unknown for sweet pepper (Capsicum annuum). The aim of this paper is to investigate whether mechanisms of fruit-set observed in Arabidopsis and tomato are also applicable to C. annuum. To do this, we accurately timed the physiological and morphological changes in a post-pollinated and un-pollinated ovary. A vascular connection between ovule and replum was observed in fertilized ovaries that undergo fruit development, and this connection was absent in unfertilized ovaries that abort. This indicates that vascular connection between ovule and replum is an early indicator for successful fruit development after pollination and fertilization. Evaluation of histological changes in the carpel of a fertilized and unfertilized ovary indicated that increase in cell number and cell diameter both contribute to early fruit growth. Cell division contributes more during early fruit growth while cell expansion contributes more at later stages of fruit growth in C. annuum. The simultaneous occurrence of a peak in auxin concentration and a strong increase in cell diameter in the carpel of seeded fruits suggest that indole-3-acetic acid stimulates a major increase in cell diameter at later stages of fruit growth. The series of physiological and morphological events observed during fruit-set in C. annuum are similar to what has been reported for tomato and Arabidopsis. This indicates that tomato and Arabidopsis are suitable model plants to understand details of fruit-set mechanisms in C. annuum.
Authors
Igor A. Yakovlev YeonKyeong Lee Adam Vivian-Smith Jorunn Elisabeth Olsen Carl Gunnar FossdalAbstract
In Norway spruce there is an enigmatic epigenetic memory of the temperature conditions during embryogenesis affecting vital phenological traits (Yakovlev et al. 2012). Adaptive phenological traits such as bud burst and bud set, observed as clinal variation in nature, are the ones affected.The epigenetic memory is establishment exclusively during embryogenesis in response to environmental impact. The epitype fixated by the time the embryo is fully developed without any change in the primary DNA sequence and is mitotically propogated. The epigenetic mechanism influence the phenotype through altered regulation of gene expression and is propagated throughout every growth cycle for the entire lifespan of this long lived species.The epigenetic memory may be realized through several molecular mechanisms including DNA methylation, and histone modifications affecting chromatin, as well as by small non-coding RNAs, and may also be related to the mechanisms silencing transposable or repetitive elements in the genome. MicroRNAs (miRNAs), endogenous small regulatory RNAs, are shown to be differentially expressed in genetically identically but epigenetically different progenies, in regards to the timing of bud burst and bud set (Yakovlev et al. 2010).We have started large scale studies using next regeneration sequencing approaches to identify and characterize the genes and regulatory elements involved in the initiation, maintenance, and heritability of the epigenetic memory. Epigenetic related changes in miRNA regulation during the establishment of the epigenetic memory are now studied in in vitro derived somatic embryos developing under cold (18C) and warm (30C) environmental conditions (that induce epitypes).We have constructed and sequenced 10 small RNA libraries during proliferation, maturation stage 1, 2 3 and the mature stage of embryo formation in the contrasted temperatures, in two control libraries during proliferation at 22C, as well as their mRNA transcriptomes using the Ion Torrent PGMTM (Life technologies) platform.We are expecting to determine at what stage(s) during embryogenesis the epigenetic memory marks are being laid down by identifying when the transcriptomic differences, of small RNA and mRNAs, between the epitypes are the most prominent during embryogenesis. The identification of novel miRNA candidates and the confirmation of conserved and novel miRNAs will be presented.
Authors
Aparna Tiwari Adam Vivian-Smith Roeland E. Voorrips Myckel E.J. Habets Lin B. Xue Remko Offringa Ep HeuvelinkAbstract
Background Parthenocarpy is a desirable trait in Capsicum annuum production because it improves fruit quality and results in a more regular fruit set. Previously, we identified several C. annuum genotypes that already show a certain level of parthenocarpy, and the seedless fruits obtained from these genotypes often contain carpel-like structures. In the Arabidopsis bel1 mutant ovule integuments are transformed into carpels, and we therefore carefully studied ovule development in C. annuum and correlated aberrant ovule development and carpelloid transformation with parthenocarpic fruit set. Results We identified several additional C. annuum genotypes with a certain level of parthenocarpy, and confirmed a positive correlation between parthenocarpic potential and the development of carpelloid structures. Investigations into the source of these carpel-like structures showed that while the majority of the ovules in C. annuum gynoecia are unitegmic and anatropous, several abnormal ovules were observed, abundant at the top and base of the placenta, with altered integument growth. Abnormal ovule primordia arose from the placenta and most likely transformed into carpelloid structures in analogy to the Arabidopsis bel1 mutant. When pollination was present fruit weight was positively correlated with seed number, but in the absence of seeds, fruit weight proportionally increased with the carpelloid mass and number. Capsicum genotypes with high parthenocarpic potential always showed stronger carpelloid development. The parthenocarpic potential appeared to be controlled by a single recessive gene, but no variation in coding sequence was observed in a candidate gene CaARF8. Conclusions Our results suggest that in the absence of fertilization most C. annuum genotypes, have parthenocarpic potential and carpelloid growth, which can substitute developing seeds in promoting fruit development.