Comparison of RAPDs, AFLPs and SSR markers for the genetic ...

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Fig. 1. Patterns of amplified DNA obtained with nine S. cerevisiae
strains,in reactions with primer OPC-01. Lane M: Size marker f 174
DNA, Hae III. Polymorphic bands are indicated by arrows.
between loci ranged from 7% at locus ScAAT6 to 67%
at locus ScAAT1. Duplicate analysis of random strains
resulted in identical profiles.
Information content,measured as IDavp,was higher
for the SSR analysis (0.62),although Ai was highest
using AFLP analysis (4.0),followed by the SSR method
(3.4) and finally RAPDs (2.1). Values obtained for the
average ENA avp were greatest using SSR analysis at 3.4,
with the extremes measuring 1.16 and 6.08. Values
obtained using AFLP and RAPD analysis were lower,
averaging 1.6 and 1.3,respectively.
3.2. Genetic similarity
A summary of genetic similarity estimates,calculated
for each marker system,is recorded in Table 3. Average
estimates obtained using RAPD and AFLP analysis
were both high (higher than 0.981),with a small range in
variation. Estimates obtained from the SSR analysis
were significantly lower,with a mean value of 0.437 and
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F. Javier Gallego et al. / Food Microbiology 22 (2005) 561–568
Table 2
Level of polymorphism detected and comparison of informativeness obtained with RAPD,AFLP,and SSR methods in the 27 Sacharomyces
cerevisiae strains studied
variation ranging from 0.000 to 1.000. The correlation
among similarity matrices derived for each method
(Table 4) was very low in all cases,with AFLP/SSR
correlation (0.43) being the greatest.
Genetic similarity trees for each marker type individually,and
as a whole,are presented in Figs. 4a–d.
Cophenetic correlations (Table 4) indicate the extent to
which the dendrograms derived from the different
techniques accurately represent estimates of the original
similarity matrices. High cophenetic correlations were
obtained for RAPD (0.81) and AFLP marker types
(0.81),with SSR markers achieving an even higher
correlation of 0.91. Nevertheless,low correlations were
observed among the different dendrograms (Table 4),
topping out at 0.56 for the AFLP/SSR correlation.
4. Discussion
RAPDs AFLPs SSRs
Number of assay units 32 6 6
Average number of bands per assay unit 4.8 22.8 6.5
Polymorphic bands (%) 8.38 10.94 100
Number of loci 155 137 6
Average number of alleles per locus 1.08 1.10 6.5
Number of strains discriminated 13 19 20
Number of assay units necessary to achieve the highest discrimination of the strains 7 4 3
DI avp 0.20 0.35 0.62
ENA avp 1.3 1.6 3.4
Ne 16.9 24.0 20.4
Ai 2.1 4.0 3.4/10.2
DIavp: diversity index per polymorphic locus.ENAavp: effective number of alleles per polymorphic locus.Ne: number of effective alleles per
polymorphic locus.Ai: assay efficiency index.
All three techniques employed in this study (RAPD,
AFLP and SSR analysis) resulted in sufficient resolution
to detect differences between the genetic profiles of
various strains of the same species (S. cerevisiae). While
the use of these methods may overcome certain
limitations associated with classical taxonomic methods,
differences between them exist with regards to the level
of polymorphism detected,discriminatory power,effectiveness,and
speed of use.
AFLP analysis generated the greatest number of
bands per assay unit,due to the high number of loci
identified per assay. The most polymorphic bands,
however,were obtained by microsatellite analysis
(100%). Based on the small size of the S. cerevisiae
genome and the number of amplification products
obtained in this work,primers containing fewer selective
bases will be used in order to increase the number of
bands per assay unit.