Glasnevin, Ireland
Glasnevin, Ireland

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Cubry P.,DBN Plant Molecular Laboratory | Cubry P.,French National Institute for Agricultural Research | Gallagher E.,DBN Plant Molecular Laboratory | O'Connor E.,University College Cork | And 2 more authors.
Tree Genetics and Genomes | Year: 2015

Black alder (Alnus glutinosa (L.) Gaertn.) is a widespread tree of European forests with a high potential for wood and biomass production. This study investigated the genetic origin and diversity in remnants of putative native alder forest stands in Ireland and compared it with other European populations to determine phylogeographic patterns. The efficiency of capture of the genetic diversity in a breeding population was also assessed. Data were obtained from chloroplast DNA (cpDNA) polymorphisms and from nuclear microsatellites. In silico PCR-RFLP was used to locate cpDNA sequence polymorphisms in order to develop flanking primers for high-resolution melting (HRM) analysis. The cpDNA polymorphism analysis detected two main haplotypes in Ireland. The same two are also found in Wales and England while only one is found in Scotland. The results suggest that Irish populations of alder have originated from at least two European glacial refugia. Black alder in Ireland exhibited no or very weak population differentiation using nuclear microsatellite markers, which is consistent for a wind-dispersed, outcrossing species. Based on the nuclear microsatellite data, a decline in population sizes is estimated to have occurred around a timeframe that coincides with a period of large-scale deforestation. The breeding population contained two haplotypes and showed a high level of genetic capture (86 % of microsatellite alleles) when compared with all samples combined. This study fills a gap in previous knowledge, provides an additional marker and an additional method for future studies. The characterisation of a breeding population provides valuable baseline data for a national alder tree improvement programme. © 2015, Springer-Verlag Berlin Heidelberg.


Fady B.,French National Institute for Agricultural Research | Aravanopoulos F.A.,Aristotle University of Thessaloniki | Alizoti P.,Aristotle University of Thessaloniki | Matyas C.,University of West Hungary | And 22 more authors.
Forest Ecology and Management | Year: 2016

The fate of peripheral forest tree populations is of particular interest in the context of climate change. These populations may concurrently be those where the most significant evolutionary changes will occur; those most facing increasing extinction risk; the source of migrants for the colonization of new areas at leading edges; or the source of genetic novelty for reinforcing standing genetic variation in various parts of the range. Deciding which strategy to implement for conserving and sustainably using the genetic resources of peripheral forest tree populations is a challenge.Here, we review the genetic and ecological processes acting on different types of peripheral populations and indicate why these processes may be of general interest for adapting forests and forest management to climate change. We particularly focus on peripheral populations at the rear edge of species distributions where environmental challenges are or will become most acute. We argue that peripheral forest tree populations are "natural laboratories" for resolving priority research questions such as how the complex interaction between demographic processes and natural selection shape local adaptation; and whether genetic adaptation will be sufficient to allow the long-term persistence of species within their current distribution.Peripheral populations are key assets for adaptive forestry which need specific measures for their preservation. The traditionally opposing views which may exist between conservation planning and sustainable forestry need to be reconciled and harmonized for managing peripheral populations. Based on existing knowledge, we suggest approaches and principles which may be used for the management and conservation of these distinctive and valuable populations, to maintain active genetic and ecological processes that have sustained them over time. © 2016 Elsevier B.V.


Kelleher C.T.,University of British Columbia | Kelleher C.T.,DBN Plant Molecular Laboratory | Wilkin J.,University of British Columbia | Zhuang J.,University of British Columbia | And 9 more authors.
Tree Genetics and Genomes | Year: 2012

The use of single-nucleotide polymorphisms (SNPs) as molecular markers in plant studies has become increasingly common. With the development of these markers, there is an interest in determining levels of variation in natural populations. Here, we identify and characterize levels of SNPs in wild populations of aspen (Populus tremuloides Michx.). Four populations were sampled from Alberta and British Columbia in Western Canada. A total of 35 gene regions were selected for analysis. The loci selected are mainly involved in wood formation and include regions from genes for lignin biosynthesis, cellulose biosynthesis, and other cell wall compounds and a number of transcription factors. Other genes included those coding for growth hormones, disease resistance, and light responses. Primers were developed from conserved regions in multi-species EST alignments. Regions were PCR amplified, and products (approximately 500 to 1,000 bp) were assessed for levels of SNPs using Ecotilling. From a total of approximately 25 kb 462 SNPs were identified, over 18 SNPs/kb. Thus, SNPs are an abundant and potentially useful molecular marker in aspen. Gene diversity (heterozygosity) varied in the gene regions, with an overall average of H T = 0. 18. Although gene diversity was considerable, genetic differentiation was low with the overall F ST value being 0. 004. A surrogate measure of linkage disequilibrium (LD) was calculated, and overall, the LD was shown to decay relatively rapidly with distance along the gene region. The results obtained from the wood formation genes in this study will enable further targeting of regions for association studies on lignin and cellulose variation in aspen and other Populus species. © 2012 Springer-Verlag.


Gallagher E.,Trinity College Dublin | Douglas C.G.,Teagasc | Kelly D.L.,Trinity College Dublin | Barth S.,Oak Park Research Center | And 2 more authors.
Biology and Environment | Year: 2013

To quantify levels of gene flow among and genetic variation within different age cohorts of pedunculate oak (Quercus robur L.) in a semi-natural oak woodland, diversity and parentage studies were undertaken on a stand in Ballytobin, Co. Kilkenny, Ireland. Trees were categorised into four size classes seedlings, saplings, mature trees and veterans, and genetic differentiation was estimated for three microsatellite markers using AMOVA. Parentage was assessed using a likelihood assignment approach. Between nine and fourteen alleles were detected per locus (mean gene diversity, h, 0.8312). All samples from Ballytobin were heterozygous. AMOVA between age cohorts (veterans, mature, saplings and seedlings) estimated that only 2% of the variation was partitioned among age cohort and the mean FST was low (0.015) but significant (P = 0.034). Parent-pair analysis revealed that out of 24 candidate trees, fifteen were assigned as parents to at least one offspring and, out of these, five were veteran. The average pollination distance was estimated at 47.8m with seven out of the twelve parent-pairs being within 50m of each other. The measured range of distances between trees indicated in the analysis as parents was between 22m and 150m. The highest values for number of parent/offspring assignments were between 40m and 49m. Overall, veteran oak at the site were found to be reproductively successful and a low level of differentiation was found between age cohorts indicating that population genetic diversity has been maintained over time. © ROYAL IRISH ACADEMY.


Perdereau A.C.,Teagasc | Perdereau A.C.,Trinity College Dublin | Kelleher C.T.,DBN Plant Molecular Laboratory | Douglas G.C.,Teagasc | Hodkinson T.R.,Trinity College Dublin
BMC Plant Biology | Year: 2014

Background: Salix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs).Results: A total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (HT = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean GST = 0.38). For the nuclear SSRs, GST was low at 0.07 and observed heterozygosity across populations was high (HO = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds.Conclusions: The data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material. © 2014 Perdereau et al.


Perdereau A.C.,Teagasc | Perdereau A.C.,Trinity College Dublin | Douglas G.C.,Teagasc | Hodkinson T.R.,Trinity College Dublin | Kelleher C.T.,DBN Plant Molecular Laboratory
Biotechnology for Biofuels | Year: 2013

Background: Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation. Results: Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix. Conclusions: The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes. © 2013 Perdereau et al.; licensee BioMed Central Ltd.


Beatty G.E.,Queen's University of Belfast | Barker L.,Queen's University of Belfast | Chen P.-P.,Queen's University of Belfast | Kelleher C.T.,DBN Plant Molecular Laboratory | Provan J.,Queen's University of Belfast
Annals of Botany | Year: 2015

Background and Aims Although hybridization can play a positive role in plant evolution, it has been shown that excessive unidirectional hybridization can result in replacement of a species' gene pool, and even the extinction of rare species via genetic assimilation. This study examines levels of introgression between the common Saxifraga spathularis and its rarer congener S. hirsuta, which have been observed to hybridize in the wild where they occur sympatrically. Methods Seven species-specific single nucleotide polymorphisms (SNPs) were analysed in 1025 plants representing both species and their hybrid, S. × polita, from 29 sites across their ranges in Ireland. In addition, species distribution modelling was carried out to determine whether the relative abundance of the two parental species is likely to change under future climate scenarios. Key Results Saxifraga spathularis individuals tended to be genetically pure, exhibiting little or no introgression from S. hirsuta, but significant levels of introgression of S. spathularis alleles into S. hirsuta were observed, indicating that populations exhibiting S. hirsuta morphology are more like a hybrid swarm, consisting of backcrosses and F2s. Populations of the hybrid, S. × polita, were generally comprised of F1s or F2s, with some evidence of backcrossing. Species distribution modelling under projected future climate scenarios indicated an increase in suitable habitats for both parental species. Conclusions Levels of introgression observed in this study in both S. spathularis and S. hirsuta would appear to be correlated with the relative abundance of the species. Significant introgression of S. spathularis alleles was detected in the majority of the S. hirsuta populations analysed and, consequently, ongoing introgression would appear to represent a threat to the genetic integrity of S. hirsuta, particularly in areas where the species exists sympatrically with its congener and where it is greatly outnumbered. © 2014 The Author.


Dang X.-D.,National University of Ireland, Maynooth | Kelleher C.T.,DBN Plant Molecular Laboratory | Howard-Williams E.,National University of Ireland, Maynooth | Howard-Williams E.,DBN Plant Molecular Laboratory | Meade C.V.,National University of Ireland, Maynooth
Molecular Ecology Resources | Year: 2012

We have evaluated High Resolution Melting (HRM) analysis as a method for one-step haplotype identification in phylogeographic analysis. Using two adjoined internal amplicons (c.360 and 390bp) at the chloroplast rps16 intron (c.750bp) we applied HRM to identify haplotypes in 21 populations of two European arctic-alpine herb species Arenaria ciliata and Arenaria norvegica (Caryophyllaceae). From 446 accessions studied, 20 composite rps16 haplotypes were identified by the melting-curve protocol, 18 of which could be identified uniquely. In a comparative sensitivity analysis with in silico PCR-RFLP, only seven of these 20 haplotypes could be identified uniquely. Observed in vitro experimental HRM profiles were corroborated by in silico HRM analysis generated on uMeltSM. In silico mutation analysis carried out on a 360bp wild-type rps16I amplicon determined that the expected rate of missed single-nucleotide polymorphisms (SNP) detection in vitro was similar to existing evaluations of HRM sensitivity, with transversion SNPs being more likely to go undetected compared to transition SNPs. In vitro HRM successfully discriminated between all amplicon templates differing by two or more base changes (352 cases) and between 11 pairs of amplicons where the only difference was a single transition or transversion SNP. Only one pairwise comparison yielded no discernable HRM curve difference between haplotypes, and these samples differed by one transversion (C/G) SNP. HRM analysis represents an untapped resource in phylogeographic analysis, and with appropriate primer design any polymorphic locus is potentially amenable to this single-reaction method for haplotype identification. © 2012 Blackwell Publishing Ltd.

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