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Genetics Section

Horning, Matthew [1], Huber, M. Sue [1], Cronn, RC [1].

Fluorescent length polymorphism (FLP) scanning is an efficient tool for identifying intraspecific chloroplast DNA variation.

The genomes of cytoplasmic organelles are attractive markers for population genetic and phylogeographic studies because they are non-recombinant, uniparentally inherited, and frequently achieve high rates of fixation relative to nuclear markers. Organellar markers have an important benefit of being haploid, a feature that permits genetic comparisons among taxa that exhibit chromosome number or ploidy variation. In plants, chloroplast markers are widely used in population genetic and phylogeographic studies, even though studies at intraspecific levels are frequently challenged by the conservative rate of chloroplast evolution and the paucity of characters present. In this presentation, we show how a notable feature of chloroplast genome evolution – the common accumulation of insertions and deletions – can be used as an efficient, inexpensive screen of haplotype variation. Fluorescent length polymorphism (FLP) screening of a minimum of four non-coding regions from diverse angiosperm taxa (Calamagrostis breweri [Poaceae], Lilium philadelphicum [Liliaceae]; Lupinus argenteus [Fabaceae], Purshia tridendata [Rosaceae]) reveals as many haplotypes as direct nucleotide sequencing from the same genic regions. For example, direct sequencing of seven non-coding chloroplast regions (~5,000 bp) from geographically divergent Purshia tridentata samples reveals 12 mutations (four substitutions, 8 insertion-deletion events) and nine haplotypes. All of these haplotypes are identifiable by FLP variation alone. Because this pattern holds true across diverse and unrelated taxa, FLP appears to provide an efficient and cost-effective way to identify unique cytoplasmic haplotypes in intraspecific studies. o­nce identified, FLP variants can be treated as classical haplotypic markers in population genetic studies, or they can be sequenced as is required by phylogenetically explicit methods.

1 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331-4401, USA

length polymorphism scanning
population genetic diversity
Purshia tridentata
Calamagrostis breweri
Lilium philadelphicum.

Presentation Type: Paper
Session: 53-1
Location: Peruvian (Cliff Lodge)
Date: Wednesday, August 4th, 2004
Time: 1:00 PM
Abstract ID:688

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