DNA Markers for Identification and Evaluation of Genetic Resources in Forest Trees: Case Studies in Abies, Picea and Populus

Ziegenhagen, Birgit; Fladung, Matthias

doi:10.1007/3-540-26538-4_25

Cited by 5 publications

(4 citation statements)

References 35 publications

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“…Putative tetraploid poplar fusion lines are first studied with respect to the destiny of the nuclei; thus, clone-specific nuclear microsatellite (SSR) markers (Bruegmann and Fladung 2013), are employed that are often used for clone identification, the evaluation of genetic resources, or parentage analysis (Ziegenhagen and Fladung 2004;Liesebach et al 2010;Schröder and Fladung 2010). To unravel the destiny of the chloroplasts, species-specific SNP markers have been developed for chloroplasts of different poplar species (Schröder et al 2011;2012).…”

Section: Introductionmentioning

confidence: 99%

Development of mitochondrial SNP markers in different Populus species

Kersten¹,

Voss²,

Fladung³

2014

Trees

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Key message We aim to develop, for the first time, poplar species-specific mitochondrial SNP markers which can be employed as diagnostic tool, e.g., to identify mitochondria belonging to different poplar species used in protoplast fusion experiments and for population genetics approaches. Abstract In most higher plant species, the inheritance of chloroplasts and mitochondria is maternal. In contrast to chloroplast DNA, however, the mitochondrial genome, especially for woody plants including poplar, has seldom been the object of molecular biological research. Published studies on mitochondrial DNA variation in poplar have dealt with genetic relationships using RFLP analyses for population genetic purposes, but so far not for species identification. In this study, we for the first time aim to develop poplar species-specific mitochondrial SNP markers which can be employed as a diagnostic tool, e.g., to identify mitochondria belonging to different poplar species used in protoplast fusion experiments. In total, seven mitochondrial regions were PCR amplified, sequenced and screened for SNPs differentiating clones belonging to six different poplar species from three sections. Two regions (Sc438, contig42) revealed to be monomorphic in the six Populus species. For the five other regions, SNPs could be identified that are suitable for distinguishing between Populus species, either by a SNP-related CAPS (cleaved amplified polymorphic site) marker to be employed in robust PCR-RFLPs, or simply on the basis of the sequence to be screened by PCR and subsequent Sanger sequencing. As a proof of concept, the developed mitochondrial SNP markers confirmed results obtained with chloroplast SNP markers in interspecific poplar hybrids, either with respect to the direction of the cross or the reclassification of putative pure lines as hybrid lines.

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Section: Introductionmentioning

confidence: 99%

Development of mitochondrial SNP markers in different Populus species

Kersten¹,

Voss²,

Fladung³

2014

Trees

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“…Specifically, in the local varieties the samara stalk length was greater (nearly three times) than in F. ornus, while the apical leaf length/width ratio and the number of samaras/raceme of manna ash samples were approximately two and a half and eight times lower, respectively, separating the two groups compared. Variety identification based on morphological data can be verified using molecular analysis, because the environmental effects, epistatic interactions and pleiotropic effects can interfere with morphological traits evaluation, as in many forest trees [63].…”

Section: Discussionmentioning

confidence: 99%

Genetic Distinctiveness Highlights the Conservation Value of a Sicilian Manna Ash Germplasm Collection Assigned to Fraxinus angustifolia (Oleaceae)

Abbate

Mercati

Noto

et al. 2020

Plants

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The cosmopolitan genus Fraxinus comprises about 40 species occupying several habitats in the Northern Hemisphere. With some species hybridizing and sharing genetic variants, questions remain on the species assignment of germplasm within the genus Fraxinus despite numerous species-specific assessments. A multidisciplinary approach was employed to provide a definitive insight into the genetics of an endangered Fraxinus “manna ash” collection, located in a rich plant biodiversity hotspot of the Madonie Mountains (Sicily). Although the collection size was small, genetic diversity, assessed by chloroplast (cpSSR) and nuclear (nSSR) microsatellites (SSR—Simple Sequence Repeats), allowed identifying three different chloroplast haplotypes, with one (H5) dominant, and several polymorphic loci, able to discriminate most of the local accessions studied. Molecular data were linked to cytofluorimetric and phenotypic evaluations and, contrary to popular belief that manna ash is Fraxinus ornus L., the germplasm currently used for manna production belongs to Fraxinus angustifolia Vahl. Interestingly, joint analysis of our genetic panel with a large European dataset of Fraxinus spp. suggested the presence of a possible glacial refuge in Sicily, confirming its importance as biodiversity source. Our results will be helpful for the design of long-term conservation programs for genetic resources, such as in situ and ex situ conservation, seed collection and tree reintroduction.

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“…Since morphologically and anatomically different plant clones may look similar, it is essential to reliably identify those including discrimination from each other and from conspecific individuals or representatives of other closely related species. In forestry, the problem of individual identification is especially crucial since the external look of trees is highly dependable on environmental parameters [ 4 ]. At particular stages of natural ontogenesis of forest trees, for example, seedlings and saplings, and especially as calluses or explants in vitro cell culture, individuals may be indiscernible not only individually but also as far as species diagnoses are concerned.…”

Section: Introductionmentioning

confidence: 99%

Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae)

Политов

Belokon

et al. 2015

International Journal of Plant Genomics

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Testing systems for molecular identification of micropropagated elite aspen (Populus tremula L.) genotypes were developed on the base on microsatellite (SSR) loci. Out of 33 tested microsatellite loci, 14 were selected due to sustainable PCR amplification and substantial variability in elite clones of aspen aimed for establishment of fast-rotated forest plantations. All eight tested clones had different multilocus genotypes. Among 114 trees from three reference native stands located near the established plantations, 80 haplotypes were identified while some repeated genotypes were attributed to natural clones which appeared as a result of sprouting. The selected set of SSR markers showed reliable individual identification with low probability of appearance of identical aspen genotypes (a minimum of 4.8 · 10−10 and 1 × 10−4 for unrelated and related individuals, resp.). Case studies demonstrating practical applications of the test system are described including analysis of clonal structure and levels of genetic diversity in three natural aspen stands growing in the regions where plantations made of elite clones were established.

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DNA Markers for Identification and Evaluation of Genetic Resources in Forest Trees: Case Studies in Abies, Picea and Populus

Cited by 5 publications

References 35 publications

Development of mitochondrial SNP markers in different Populus species

Development of mitochondrial SNP markers in different Populus species

Genetic Distinctiveness Highlights the Conservation Value of a Sicilian Manna Ash Germplasm Collection Assigned to Fraxinus angustifolia (Oleaceae)

Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae)

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