Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.
- 15 August 1995
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 92 (17), 7759-7763
- https://doi.org/10.1073/pnas.92.17.7759
Abstract
Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of several (dA)n.(dT)n mononucleotide stretches in chloroplast genomes. A chloroplast (cp) SSR was identified in three pine species (Pinus contorta, Pinus sylvestris, and Pinus thunbergii) 312 bp upstream of the psbA gene. DNA amplification of this repeated region from 11 pine species identified nine length variants. The polymorphic amplified fragments were isolated and the DNA sequence was determined, confirming that the length polymorphism was caused by variation in the length of the repeated region. In the pines, the chloroplast genome is transmitted through pollen and this PCR assay may be used to monitor gene flow in this genus. Analysis of 305 individuals from seven populations of Pinus leucodermis Ant. revealed the presence of four variants with intrapopulational diversities ranging from 0.000 to 0.629 and an average of 0.320. Restriction fragment length polymorphism analysis of cpDNA on the same populations previously failed to detect any variation. Population subdivision based on cpSSR was higher (Gst = 0.22, where Gst is coefficient of gene differentiation) than that revealed in a previous isozyme study (Gst = 0.05). We anticipate that SSR loci within the chloroplast genome should provide a highly informative assay for the analysis of the genetic structure of plant populations.Keywords
This publication has 17 references indexed in Scilit:
- Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plants.Proceedings of the National Academy of Sciences, 1994
- Survey of human and rat microsatellitesGenomics, 1992
- Evidence for replication slippage in the evolution of Oenothera chloroplast DNA.Molecular Biology and Evolution, 1991
- The chloroplast genome of the gymnosperm Pinus contorta: a physical map and a complete collection of overlapping clonesCurrent Genetics, 1991
- The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome.Proceedings of the National Academy of Sciences, 1990
- Hypervariability of simple sequences as a general source for polymorphic DNA markersNucleic Acids Research, 1989
- Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.Proceedings of the National Academy of Sciences, 1987
- A comprehensive set of sequence analysis programs for the VAXNucleic Acids Research, 1984
- CONSTRUCTION OF A GENETIC-LINKAGE MAP IN MAN USING RESTRICTION FRAGMENT LENGTH POLYMORPHISMS1980
- Analysis of Gene Diversity in Subdivided PopulationsProceedings of the National Academy of Sciences, 1973