Microsatellite DNA as shared genetic markers among conifer species (original) (raw)
Related papers
Survey of microsatellite DNA in pine
Genome, 1997
A large insert genomic library from eastern white pine (Pinus strobus) was probed for the microsatellite motifs (AC), and (AG),, all 10 trinucleotide motifs, and 22 of the 33 possible tetranucleotide motifs. For comparison with a species from a different subgenus, a loblolly pine (Pinus taeda) genomic library was also probed with the same set of di-and tri-nucleotide repeats and 11 of the tetranucleotide repeats. The four most abundant microsatellite motifs in both species were (AC),, (AG),, (AAT),, and (ATC),, which as a group accounted for over half the microsatellite sites investigated. The two dinucleotide repeats % were the most abundant microsatellite motifs tested in both species, each at 2 4 . 5 sitedmegabase pair (Mbp), but the two trinucleotide motifs were nearly as abundant and are considered good candidates for pine microsatellite marker development efforts. Eastern white pine had more than twice as many (AC), as (AG), loci, in contrast with loblolly pine and most other plant a species in which (AG), is more abundant. In both pine species the minimum estimated genome density for all microsatellites, excluding (AT), repeats, was 16 sitesmbp.
Transpecific microsatellites for hard pines
TAG Theoretical and Applied Genetics, 2002
Microsatellites are difficult to recover from large plant genomes so cross-specific utilisation is an important source of markers. Fifty microsatellites were tested for cross-specific amplification and polymorphism to two New World hard pine species, slash pine (Pinus elliottii var. elliottii) and Caribbean pine (P. caribaea var. hondurensis). Twenty-nine (58%) markers amplified in both hard pine species, and 23 of these 29 were polymorphic. Soft pine (subgenus Strobus) microsatellite markers did amplify, but none were polymorphic. Pinus elliottii var. elliottii and P. caribaea var. hondurensis showed mutational changes in the flanking regions and the repeat motif that were informative for Pinus spp. phylogenetic relationships. Most allele length variation could be attributed to variability in repeat unit number. There was no evidence for ascertainment bias.
PLOS ONE, 2018
Pinus albicaulis (whitebark pine) is a widely-distributed but rapidly declining high elevation western North American tree and a candidate for listing under the U.S. Endangered Species Act. Our objectives were to develop reliable nuclear microsatellite markers that can be used to assess within-population genetic diversity as well as seed and pollen migration dynamics, and to validate markers using two geographically proximal P. albicaulis populations. We identified 1,667 microsatellite-containing sequences from shotgun DNA libraries of P. albicaulis. Primer pairs were designed for 308 unique microsatellite-containing loci, and these were evaluated for PCR amplification success and segregation in a panel of diploid needle tissue. DNA was extracted with an SDS protocol, and primers were screened through gel electrophoresis. Microsatellites were genotyped through fluorescent primer fragment analysis. Ten novel and 13 transferred loci were found to be reproducible in analyses based on 20 foliage samples from each of two locations: Henderson Mountain, Custer Gallatin National Forest, Montana, and Mt. Washburn, Yellowstone National Park, Wyoming (USA). Transferred loci had higher numbers of alleles and expected heterozygosities than novel loci, but also revealed evidence for a higher frequency of null alleles. Eight of the 13 transferred loci deviated significantly from Hardy-Weinberg Equilibrium, and showed large positive F IS values that were likely inflated by null alleles. Mantel's tests of transferred and novel markers showed no correlation between genetic and geographic distances within or among the two sampled populations. AMOVA suggests that 91% of genetic variability occurs within populations and 9% between the two populations. Studies assessing genetic diversity using these microsatellite loci can help guide future management and restoration activities for P. albicaulis.
Theoretical and Applied Genetics, 1994
A high-density genetic map based on restriction fragment length polymorphisms (RFLPs) is being constructed for loblolly pine (Pinus taeda L.). Consequently, a large number of DNA probes from loblolly pine are potentially available for use in other species. We have used some of these DNA probes to detect RFLPs in 12 conifers and an angiosperm. Thirty complementary DNA and two genomic DNA probes from loblolly pine were hybridized to Southern Nots containing DNA from five species of Pinus (P. elliottii, P. lambertiana, P. radiata, P. sylvestris, and P. taeda), one species from each of four other genera of Pinaceae (Abies concolor, Larix laricina, Picea abies, and Pseudotsuga menziesii), one species from each of three other families of Coniferales [Sequoia sempervirens (Taxodiaceae), Torreya californica (Taxaceae) and Calocedrus decurrens (Cupressaceae)], and to one angiosperm species (Populus nigra). Results showed that mapped DNA probes from lobolly pine will cross-hybridize to genomic DNA of other species of Pinus and some other genera of the Pinaceae. Only a small proportion of the probes hybridized to genomic DNA from three other families of the Coniferales and the one angiosperm examined. This study demonstrates that mapped DNA probes from loblolly pine can be used to construct RFLP maps for related species, thus enabling the opportunity for comparative genome mapping in conifers.
Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra
Biologia, 2013
Pinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.
Randomly amplified polymorphic DNA linkage relationships in different Norway spruce populations
Canadian Journal of Forest Research, 2001
We tested the constancy of linkage relationships of randomly amplified polymorphic DNA (RAPD) marker loci used to construct a population-based consensus map in material from an Italian stand of Picea abies (L.) Karst. in 29 individuals from three Norwegian populations. Thirteen marker loci linked in the Italian stand did show a consistent locus ordering in the Norwegian population. The remaining 16 unlinked marker loci were spread over different linkage groups and (or) too far apart both in the population map and in this study. The limited validity of RAPD markers as genomic "hallmarks" resilient across populations is discussed. We also investigated the reliability of RAPD markers; only 58% of the RAPD markers previously used to construct the consensus map in the Italian population were repeatable in the same material. Of the repeatable ones 76.3% were amplified and found polymorphic in 29 megagametophyte sibships from three Norwegian populations.
Linkage relationships of allozyme loci in Pinus sylvestris
Hereditas, 2008
Linkage relationships among 27 allozyme loci in Pinus sylvestris (Scots pine) were analyzed. A total of 266 of the 351 possible two-locus combinations were tested. Four linkage groups could be established. The first group (A) contained the following loci: Got-2, Lap-2, Adh-2, Adh-I, Pgi-2. The loci Got-/ and Dia-4 probably also belong to this linkage group. The second linkage group (B) included two loci: Lap-I and F-Est. Three loci (G6Pd-I, Aco, and G6Pd-2) were assigned to the third linkage group (C). The fourth group (D) included two loci: Got-3 and Sdh-2. It was not possible to determine the location of the other two-locus combinations for which evidence of significant linkage was obtained. These results are compared to earlier linkage maps of Pinus sylvestris and other conifers.
Dendrobiology, 2018
Frequent discordant phylogenies inferred from different loci, as well as the presence of sufficiently diverged gene variants within a single species isolate are indicative of potentially frequent non-monophyly in the genus Pinus. Interspecies hybridisation and incomplete lineage sorting have been suggested as possible explanations for the observed phylogenetic discrepancies. However, there is no direct evidence to support any of the proposed scenarios for the Eurasian five-needle pines. We used natural hybrids between Pinus sibirica and P. pumila, as well as their parental species, as a model to reproduce the scenario of non-monophyly in the subgenus Strobus. Three non-linked nuclear DNA loci (LEA, AGP6 and 4CL) were applied to detect introgressive alleles and to genetically discriminate the studied species. Comparative sequence analyses revealed two clusters of species-specific alleles for each of the markers, characteristic for either P. sibirica or P. pumila. No hybrid-specific alleles were found. We also found no hybrids with a genotype characteristic of only one of the parental species for all three loci. On average, the hybrids were characterised by an equal ratio of alleles from the P. sibirica and P. pumila clusters. We reveal that some trees of pure species originating from allopatric locations have non-specific loci that can be a result of genetic exchange between these species in the distant past or incomplete lineage sorting.
Properties of AFLP markers in inheritance and genetic diversity studies of Pinus sylvestris L
Heredity, 1999
We analysed the properties of AFLP markers in Pinus sylvestris. Using primers with three selective nucleotides, the AFLP protocol produced large numbers of ampli®ed bands and could only be used with a restricted number of primer combinations. Replacement of the EcoRI +3 primer by an EcoRI +4 primer halved the number of bands, facilitating analysis. The inheritance of all but about 8.4% of the ampli®ed bands has been con®rmed to be Mendelian. We compared band patterns among selected P. sylvestris trees from northern Sweden, two Asian species of Pinus and one species from the genus Picea. The dendrogram obtained was generally concordant with the taxonomic data, although the genetic similarity values between trees from dierent genera did not entirely follow accepted inter-and intraspeci®c relationships. This deviation was less pronounced using primer combinations that generated fewer bands. More than 69.1% of the bands that were polymorphic in two P. sylvestris trees or 29 of their F 1 progeny were in a pseudo-testcross con®guration and thus were useful for the development of a linkage map for each parent. These markers have been analysed in four other crosses, and 83% of the bands could be mapped in at least one cross. Depending on the level of heterozygosity of the parents, the eciency of such mapping will vary, but the AFLP technique appears to be a powerful way to generate, very quickly, large numbers of markers that are useful for constructing and comparing linkage maps.