Abstract
Molecular markers, to be used in the population genetics of forest trees, should ideally allow easy and fast genotyping, be codominant, reproducible over time and space, be fully transferable among labs and have a high information content. None of the available molecular marker systems fully meets all these requirements. We decided to focus on Simple Sequence Repeats (SSRs or microsatellites) because they are codominant, reproducible, highly informative and easy to exchange even though they have high development costs. We isolated AC/GT and AG/CT SSRs from the Norway spruce (Picea abies K.) nuclear genome. Based on hybridization data we estimate that there is one AC SSR every 500–600 kb and one AG SSR every 200–300 kb. Given the genome size of spruce (30–40 pg) this corresponds to an extremely large number of SSRs available for analysis. We isolated several hundreds positive clones from a small-insert genomic library and following sequence analysis we designed primers for 36 of them, 24 containing AG and 12 AC SSRs. Twenty-two percent of the primer pairs produced a single-locus hypervariable pattern, with the remaining ones giving either a single monomorphic product (22%) or very poor amplification (19%) or amplification of multiple bands (37%). Mendelian segregation was demonstrated for all the loci amplified with the primer pairs giving a simple variable pattern. We screened a panel of 18 spruce trees at these loci. The average number of alleles per locus was 14 and expected heterozygosity 0.80, with up to 23 alleles per locus and heterozygosities exceeding 0.94. This shows that nuclear SSRs can be very useful markers for the population genetics of conifers even though the overall efficiency of the marker identification process is quite low due to the high complexity of the spruce genome.
We recently extended the use of SSR markers to the chloroplast genome. We demonstrated that mononucleotide poly(A/T) stretches are frequent in the chloroplast genomes of plants and show high levels of between and within population variation. This makes them ideal tools for cytoplasmic population genetics and overcomes the difficulties in finding within species variation that are frequently encountered when analysing the cpDNA molecule by RFLPs or PCR-RFLPs. We identified a set of 20 cpSSRs for the analysis of pine species and will discuss the possible applications of such markers for studying gene flow, plant population dynamics and history and for paternity analysis.
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Morgante, M. et al. (1996). Polymorphic Simple Sequence Repeats in Nuclear and Chloroplast Genomes: Applications to the Population Genetics of Trees. In: Ahuja, M.R., Boerjan, W., Neale, D.B. (eds) Somatic Cell Genetics and Molecular Genetics of Trees. Forestry Sciences, vol 49. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-3983-0_32
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DOI: https://doi.org/10.1007/978-94-011-3983-0_32
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