Transcriptome versus Genomic Microsatellite Markers: Highly Informative Multiplexes for Genotyping Abies alba Mill. and Congeneric Species (original) (raw)
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Journal of Forest Research, 2019
The momi fir (Abies firma) has been targeted as a species for genetic resource conservation because of the recent decline in its natural populations. Additional molecular marker resources are needed to examine gene flow to understand the genetic dynamics of each population. We developed 15 genomic microsatellite (SSR) markers for A. firma and applied them to separate biparentage assignments of dispersed seeds in a natural population by assaying embryos and megagametophytes. The 15 markers were polymorphic, with the expected heterozygosity averaging greater than 0.74. Separate biparentage analysis, using the seven selected effective markers, was successful to assign paternal and maternal trees separately and thus estimate the paternal and maternal immigrant gene flow from nearby populations. The newly developed genomic SSR markers in the present study, by constructing a marker set together with previously developed markers, will provide higher discriminatory power for parentage analysis and should be useful for estimating gene flow for ongoing conservation genetics studies of A. firma.
Molecular Ecology Notes, 2005
The spruce ( Picea ) species are ecologically and economically important in Canada. Highly informative markers with high multiplex ratios are needed to assist spruce genomics, genetics, and breeding programs. Selectively amplified microsatellite polymorphic loci (SAMPL) markers are highly suitable for these programs. We have developed, optimized, and characterized a set of 10 new SAMPL primers in combination with 16 Mse I primers and resolved a large number of polymorphic SAMPL markers in spruce. The SAMPL primers were designed from the compound microsatellite repeats found in Norway spruce ( Picea abies ) and white spruce ( Picea glauca ). A total of 6313 polymorphic SAMPL makers were produced by 160 SAMPL-Mse I primers combinations in eight progeny of a spruce mapping population.
Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs
Theoretical and Applied Genetics, 2004
Microsatellites, or simple sequence repeats (SSRs), are usually regarded as the "markers of choice" in population genetics research because they exhibit high variability. The development cost of these markers is usually high. In addition, microsatellite primers developed for one species often do not cross-amplify in related species, requiring separate development for each species. However, microsatellites found in expressed sequence tags (ESTs) might better cross-amplify as they reside in or near conserved coding DNA. In this study, we identified 14 Pinus taeda (loblolly pine) EST-SSRs from public EST databases and tested for their cross-species transferability to P. contorta ssp. latifolia, P. ponderosa, and P. sylvestris. As part of our development of a P. contorta microsatellite set, we also compared their transferability to that of 99 traditional microsatellite markers developed in P. taeda and tested on P. contorta ssp. latifolia. Compared to traditional microsatellites, EST-SSRs had higher transfer rates across pine species; however, the level of polymorphism of microsatellites derived from ESTs was lower. Sequence analyses revealed that the frequencies of insertions/deletions and base substitutions were lower in EST-SSRs than in other types of microsatellites, confirming that EST-SSRs are more conserved than traditional SSRs. Our results also provide a battery of 23 polymorphic, robust microsatellite primer pairs for lodgepole pine.
PloS one, 2014
Microsatellites or simple sequence repeats (SSRs) are highly informative molecular markers for various biological studies in plants. In spruce (Picea) and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana) and red spruce (Picea rubens) using a simple but efficient method based on a combination of AFLP and microsatellite technologies. A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce...
BMC Research Notes
Background: Sugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple. Findings: A set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species. Conclusions: Genic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.
Theoretical and Applied Genetics, 2002
The development of microsatellite markers can be a time-consuming process, especially in species such as conifers where many microsatellites have been shown to be associated with the repetitive fraction of the genome and to produce complex banding patterns following electrophoresis. Therefore, procedures to eliminate this fraction from further processing are sought. In this paper, we report on the development of 53 dinucleotide SSR markers in Norway spruce, 35 of which (66%) produce simple, polymorphic patterns. This high efficiency is obtained by introducing a dot-blot selection against high copy number sequences, performed on the microsatellite-containing clones. The resulting markers turned out to be polymorphic and useful for population genetic studies and for linkage mapping. Seven additional markers that were not subject to the dot-blot selection are also presented.
Conservation Genetics Resources, 2014
The silver fox (Vulpes vulpes), a coat color variant of the red fox, is one of the most important fur-bearing animals. To date, development of microsatellite loci for the silver fox has been limited and mainly based on cross-amplification by using canine SSR primers. In this study, 28 polymorphic microsatellite markers were isolated and identified for silver fox through the construction and screening of an (AC) n-enriched library. The number of alleles per locus ranged from 2 to 8 based on 48 individuals tested. The expected and observed hetero-Microsatellite markers for the silver fox ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 5890-5895 (2015) zygosity and polymorphism information content per locus ranged from 0.2544 to 0.859, 0.2083 to 0.7917, and 0.2181 to 0.821, respectively. The polymorphic markers presented in this study may be useful for future analysis of the genetic diversity and population structure of farmed silver fox and wild red fox.