16
isoenzymes, microsatellites, AFLP, SNPs; see Box 1.1) are genes or portions of the
genome that do not have expression on the phenotype and therefore are not susceptible to selection; therefore they are defined as selectively neutral. The latter, on the
other hand, are phenotypic characters (i.e., morphological, physiological, phenological, growth; see Box 1.2) and therefore potentially adaptive, measured in provenance, progeny, or clonal trials. The two sources of information are valuable and
complementary. Genetic markers will allow us to identify differences between and
within populations due to past demo-stochastic processes (fundamentally genetic
drift and gene flow processes modeled by demographic fluctuations in populations),
while variation in quantitative traits of individuals with known kindship relationships will allow us to recognize differences due to processes of adaptation to current
or modern conditions.
Box 1.1: Characteristics of the Main Genetic Markers Used in the Study
of Forest Trees
A genetic marker is a gene or a fragment of DNA sequence with a specific
location on a chromosome that is associated with a gene or a trait, shows
polymorphism, and allows the distinction of different individuals. There
are three conceptually different classes of genetic markers: protein variants
(isozymes), DNA sequence polymorphism, and DNA repeat variation
(Schlötterer 2004). Isozymes were the first markers used in studies of forest
trees, back in the 1970s (Bergmann 1971). With the advent of techniques that
allowed the screening of the DNA molecule, more powerful DNA markers
became available which allowed detecting higher levels of variability. Some
of the most used markers in forest tree species are described below:
Isozymes: Are isoforms of an enzyme, encoded by one or several genes, having the same function, which can be separated through gel electrophoresis.
Variants that are coded by alleles at the same locus are called allozymes.
Their main advantage as genetic markers relies upon their Mendelian
inheritance with codominant expression of the alleles. Given the degenerated condition of the genetic code and the fact that some mutations result
in the same net charge of the molecule, many mutations are not detectable.
The level of polymorphism is therefore moderated to low.
RAPD (random amplified polymorphic DNA): Is a PCR-based technic that
uses aleatory primers to amplify non-specific DNA fragments. It is costeffective and produces highly polymorphic markers, but the main disadvantages are its dominant expression and its low repeatability.
AFLP (amplified fragment length polymorphisms): Is a DNA fingerprinting
method that uses restriction enzyme digestion followed by selective amplification of a subset of fragments. The main advantage is the hypervariable
level of diversity; the main disadvantage is the dominant expression.
Nuclear microsatellites or SSRs (simple sequence repeats): Microsatellites
are tandemly repeated DNA motifs (from one to six nucleotides), distribM. J. Pastorino
isoenzymes, microsatellites, AFLP, SNPs; see Box 1.1) are genes or portions of the
genome that do not have expression on the phenotype and therefore are not susceptible to selection; therefore they are defined as selectively neutral. The latter, on the
other hand, are phenotypic characters (i.e., morphological, physiological, phenological, growth; see Box 1.2) and therefore potentially adaptive, measured in provenance, progeny, or clonal trials. The two sources of information are valuable and
complementary. Genetic markers will allow us to identify differences between and
within populations due to past demo-stochastic processes (fundamentally genetic
drift and gene flow processes modeled by demographic fluctuations in populations),
while variation in quantitative traits of individuals with known kindship relationships will allow us to recognize differences due to processes of adaptation to current
or modern conditions.
Box 1.1: Characteristics of the Main Genetic Markers Used in the Study
of Forest Trees
A genetic marker is a gene or a fragment of DNA sequence with a specific
location on a chromosome that is associated with a gene or a trait, shows
polymorphism, and allows the distinction of different individuals. There
are three conceptually different classes of genetic markers: protein variants
(isozymes), DNA sequence polymorphism, and DNA repeat variation
(Schlötterer 2004). Isozymes were the first markers used in studies of forest
trees, back in the 1970s (Bergmann 1971). With the advent of techniques that
allowed the screening of the DNA molecule, more powerful DNA markers
became available which allowed detecting higher levels of variability. Some
of the most used markers in forest tree species are described below:
Isozymes: Are isoforms of an enzyme, encoded by one or several genes, having the same function, which can be separated through gel electrophoresis.
Variants that are coded by alleles at the same locus are called allozymes.
Their main advantage as genetic markers relies upon their Mendelian
inheritance with codominant expression of the alleles. Given the degenerated condition of the genetic code and the fact that some mutations result
in the same net charge of the molecule, many mutations are not detectable.
The level of polymorphism is therefore moderated to low.
RAPD (random amplified polymorphic DNA): Is a PCR-based technic that
uses aleatory primers to amplify non-specific DNA fragments. It is costeffective and produces highly polymorphic markers, but the main disadvantages are its dominant expression and its low repeatability.
AFLP (amplified fragment length polymorphisms): Is a DNA fingerprinting
method that uses restriction enzyme digestion followed by selective amplification of a subset of fragments. The main advantage is the hypervariable
level of diversity; the main disadvantage is the dominant expression.
Nuclear microsatellites or SSRs (simple sequence repeats): Microsatellites
are tandemly repeated DNA motifs (from one to six nucleotides), distribM. J. Pastorino