An assessment of the AFLP method for investigating population structure in the red alga Chondrus crispus Stackhouse (Gigartinales, Florideophyceae) |
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Authors: | Sylva L Donaldson Thierry Chopin Gary W Saunders |
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Institution: | (1) Department of Biology, University of New Brunswick, Fredericton, NB, Canada, E3B 5A3;(2) Present address: Botany Department, University of Toronto –, Scarborough Campus, 1265 Military Trail, Scarborough, Ontario, Canada, M1C 1A4;(3) Centre for Coastal Studies and Aquaculture, University of New Brunswick, Saint John, NB, Canada, E2L 4L5 |
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Abstract: | The appropriateness of the Amplified Fragment Length Polymorphism (AFLP) technique for investigating Chondrus crispus Stackhouse populations in the Maritime Provinces of Canada was assessed. The AFLP procedure was first subjected to reproducibility
testing and three shortcomings were noted: 1) failure to reproduce band intensity between replicate runs for the same individual
and primer pair; 2) failure of some bands to replicate; 3) lack of reproducibility for complete replicate runs for some individuals
and primer pairs. In the last-mentioned case, the lack of reproducibility resulted in characteristic electropherograms indicative
of weak reactions. These weak runs can be attributed to poor restriction digest/ligation reactions and/or substandard PCR,
these failures ultimately resulting from low and inconsistent DNA quality. We recommend that reproducibility testing should
be completed routinely in studies using the AFLP technique. In the current work, only fragments and individuals that gave
reproducible results were used in subsequent analyses. The AFLP method resulted in highly variable markers within and between
the populations of C. crispus included in this investigation, which prevented successful resolution of population structure. This situation could result
from a lack of suitability for AFLP markers in population genetic studies, and/or too extensive genetic variation for C. crispus populations to be discerned by the AFLP technique. These two possible explanations are discussed.
This revised version was published online in August 2006 with corrections to the Cover Date. |
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Keywords: | AFLP Chondrus Florideophyceae genetic markers population Rhodophyta |
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