A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae) (original) (raw)
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Applications of Redwood Genotyping by Using Microsatellite Markers 1
2011
A panel of polymorphic microsatellite markers have been developed in coast redwood (Sequoia sempervirens). Two loci in particular (Seq18D7-3 and Seq21E5) demonstrate the potential of microsatellite genotyping in the assessment of genetic diversity and inheritance in redwoods. The highly polymorphic Seq18D7-3 marker provided evidence for the planting of non-local redwood seedlings in a restored area of a state park and was used to genotype progeny from a controlled cross. A putative chloroplast microsatellite locus (Seq21E5) was shown to be paternally inherited in two controlled crosses and can therefore be used as a marker for alleles carried in pollen. Significant differences in allelic diversity were observed at the Seq21E5 locus in redwood populations with different ecological and management histories. Advantages of microsatellite analysis and its limitations (including the problem of null alleles) are discussed as well as its potential as a tool for forest management and conserv...
Applications of redwood genotyping by using microsatellite markers
2007
A panel of polymorphic microsatellite markers have been developed in coast redwood (Sequoia sempervirens). Two loci in particular (Seq18D7-3 and Seq21E5) demonstrate the potential of microsatellite genotyping in the assessment of genetic diversity and inheritance in redwoods. The highly polymorphic Seq18D7-3 marker provided evidence for the planting of non-local redwood seedlings in a restored area of a state park and was used to genotype progeny from a controlled cross. A putative chloroplast microsatellite locus (Seq21E5) was shown to be paternally inherited in two controlled crosses and can therefore be used as a marker for alleles carried in pollen. Significant differences in allelic diversity were observed at the Seq21E5 locus in redwood populations with different ecological and management histories. Advantages of microsatellite analysis and its limitations (including the problem of null alleles) are discussed as well as its potential as a tool for forest management and conservation.
Plant Genetic Resources: Characterization and Utilization, 2018
The range-wide genetic structure of the highly productive and valuable timber species Sequoia sempervirens (D. Don) Endl. is still insufficiently studied, although published data based on different genetic markers (nuclear and chloroplast microsatellites, AFLP, RFLP and isozymes) demonstrated relatively low population structure. However, more genetic markers are needed to increase the efficiency of population genetic studies in coast redwood. Therefore, we developed seven nuclear and five chloroplast microsatellite or simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) and the complete chloroplast genome sequence, respectively. All selected markers were tested in a range-wide sample representing trees from 16 locations. They are highly polymorphic microsatellite loci with the number of alleles ranging from 3 to 17, and the number of effective alleles from 1.1 to 2.48. Coast redwood is a hexaploid species, and its chloroplasts are paternally inherited. Theref...
PLOS ONE, 2020
Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial...
The American Midland Naturalist, 2011
We developed a suite of tetranucleotide microsatellite loci and applied them to a study of genetic variation across the geographic range of coast redwood [Sequoia sempervirens (D. Don) Endl.]. The objectives of the study were to determine if the microsatellite loci could provide useful information on genetic diversity in this hexaploid species and to investigate earlier reports of divergent lineages within coast redwood. The microsatellite loci were highly variable, yielding a total of 142 alleles. Up to six alleles were detected in each individual consistent with the ploidy of coast redwood and suggesting that parental genomes must have been at least partially homologous. This does not rule out autoployploidy in the evolution of the redwood genome. We treated the microsatellite alleles as presence-absence data and we also estimated full genotypes assuming peak intensities varied with allele dosage. Both types of analyses revealed similar trends. Variation within the 17 watersheds sampled, explained most of the genetic diversity, with less than 4% of the variation attributable to watersheds. Our data showed a weak divergence between more or less continuous populations north of 36.8uN (the Sonoma-Mendocino county border) and disjunct populations south of this latitude. This is further north than indicated from earlier studies of marker systems that would be under selection and may reflect a demographic break. In view of the importance of clonal growth, we suggest that redwood may have difficulty adapting to new climatic conditions or of migrating into displaced habitats with anticipated climate change. Furthermore, the southern lineage of populations is likely to be at greatest risk and is therefore of conservation priority.
Microsatellite markers in coast redwood (Sequoia sempervirens)
Molecular Ecology Notes, 2004
Five polymorphic microsatellite markers are described for coast redwood, a hexaploid conifer. Dinucleotide (three), trinucleotide (one) and tetranucleotide (one) repeat loci were isolated from a genomic plasmid library and amplified in a test population of 25 secondgrowth redwoods. There were three to 11 alleles per locus and observed heterozygosities ranged from 0.00 to 0.80. The nonheterozygous locus (a CTTA repeat) is probably of chloroplast origin and may have potential as a marker for paternal inheritance.
American Journal of Botany, 2004
The ecology and evolutionary potential of coast redwood (Sequoia sempervirens) is significantly influenced by the important role clonal spread plays in its reproduction and site persistence. In nine second-growth stands, amplified fragment length polymorphisms (AFLPs) were used to identify redwood clonal architecture. Clones (multistem genets) dominated sites by representing an average of 70% of stems measured, ranging in size from two to 20 stems. As a result, a relatively small number of genets can monopolize a disproportionate amount of site resources, are more likely to persist over time, and have greater on-site genetic representation. Clones were not limited to fairy-ring structures, but consisted of a wide range of shapes including concentric rings, ring chains, disjunct. and linear structures. Between-ramet distances of up to 40 m were measured, indicating that clonal reproduction is not limited to basal sttlmp resprouting. Clonal structure in second-growth stands was similar to earlier reports from old growth, emphasizing the importance of site persistence and long-term, gradual site development. Smaller ramet numbers per genet in old growth is probably due to local within-genet self thinning. Management and conservation of redwoods will benefit from a better understanding of the dynamics and structure of clonal spread in these forests.
International Journal of Plant Genomics, 2015
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 struct...
Genetic constitution and diversity in four narrow endemic redwoods from the family Cupressaceae
Euphytica, 2009
The genetic constitution and diversity of four relictual redwoods are discussed in this review. These include monotypic genera of the family Cupressaceae: coast redwood (Sequoia sempervirens), giant sequoia (Sequoiadendron giganteum), dawn redwood (Metasequoia glyptostroboides), and alerce (Fitzroya cupressoides). All four species are narrow endemics, share a number of common phenotypic traits, including red wood, and are threatened species. Fossil history suggests that the ancestors of redwoods probably originated during the Cretaceous and Tertiary periods and Xourished thereafter for millions of years. Towards the end of the Tertiary period began their decline and struggle for existence that continued during the subsequent geologic upheavals and climate changes, until the survival of the presentday redwoods in the current restricted locations in the world (USA, China, and South America). Although two species, Sequoiadendron and Metasequoia, are diploids (2n = 22), and the other two are polyploids: Fitzroya a tetraploid (2n = 4x = 44), and Sequoia a hexaploid (2n = 6x = 66); they all share the same basic chromosome number x = 11. The genome size in the hexaploid Sequoia is one of the largest (31,500 MB) in the conifers, while the genome sizes of diploid Metasequoia and Sequoiadendron are about one-third (»10,000 MB) of Sequoia. Genetic diversity in the redwoods is lower than most other gymnosperms, except in Sequoia, which seems to rank near the upper quarter of the coniferous forest trees. Genomic research is sparse in the redwoods, and should be pursued for a better understanding of their genome structure, function, and adaptive genetic diversity.
Short Note: High Throughput Microsatellite Genotyping in Oak Species
Silvae Genetica, 2006
Microsatellites are widely used markers for multiple purposes in oaks. We describe a complete procedure for cheap DNA extraction and fast microsatellites genotyping by multiplex PCR. 10 loci were selected to form two multiplex kits including three loci that show a high differentiation between Quercus robur and Q. petraea. The loci were tested in three oak species and show a high mean genetic diversity of 0.84. The cumulative exclusion probability for parentage analysis was 0.999977 for single parent and 1.0 for paternity. Finally, the relatively high differentiation coefficient (Gst = 0.04) will facilitate species assignment based on genotypes in oaks.