17
uted throughout the genome. Their main advantages are the codominant
expression and the high level of polymorphism detected. The need to know
the flanked sequences to design the primers was the main disadvantage for
their use, although with the advance of massive sequencing methods their
development became easier and cheaper.
Organelle DNA markers (chloroplast and mitochondrial DNA): They consist
in the amplification and sequencing of non-coding regions of the organelle
genomes. Due to the uniparental and clonal inheritance of these genomes,
they show moderate to low levels of polymorphism, allowing phylogeographic and phylogenetic reconstructions.
SNPs (single nucleotide polymorphisms): Are loci with alleles that differ in a
single base, with the rarer allele having a frequency of at least 1% in a set
of individuals. SNPs can occur in coding or non-coding regions and are
highly frequent in the genomes of plants and animals and codominantly
expressed.
Box 1.2: The Quantitative Perspective of Genetic Variation Patterns
Because the phenotype is the expression of the genotype modulated by environmental conditions, the analysis of the variation between individuals in
phenotypic characters allows us to gain knowledge about the gene pools that
determine them. For this, it is necessary to set up a trial in which the environmental effect can be controlled. Essentially, this trial seeks to raise the different genetic entities (i.e., provenances, families, clones) under the same
environmental condition (common garden experiment), with the expectation
that the differences that appear in the phenotype are the reflection of the
genetic variations. These trials will have an experimental design defined by
the environmental conditions and the entities to be tested, and their conclusions will be valid for the trial conditions.
The variables to consider can be of different kinds, some measured simply
with a ruler (e.g., seedling height) and others with sophisticated devices such
as a spectrophotometer (e.g., chlorophyll concentration). Some variables are
of greater productive importance, while others will provide information particularly on adaptability. In this sense, juvenile characters may be the most
relevant when the main interest is to ensure post-plantation survival.
The main statistical method to analyze the variation in quantitative characters is the analysis of variance (ANOVA), which can be applied to additive
linear models of fixed effects, random effects, or mixed effects. A typical test
in a low-intensity breeding program is the comparison of different provenances of a species and, within them, open-pollinated families. Such a trial
can be set up by collecting seeds from 10 to 30 trees in each of about 20 populations of interest. All plants obtained with the seeds of one of the trees will
be an open-pollinated family, and the kindship relationship between them will
1 Native Forests Claim for Breeding in Argentina: General Concepts and Their State
uted throughout the genome. Their main advantages are the codominant
expression and the high level of polymorphism detected. The need to know
the flanked sequences to design the primers was the main disadvantage for
their use, although with the advance of massive sequencing methods their
development became easier and cheaper.
Organelle DNA markers (chloroplast and mitochondrial DNA): They consist
in the amplification and sequencing of non-coding regions of the organelle
genomes. Due to the uniparental and clonal inheritance of these genomes,
they show moderate to low levels of polymorphism, allowing phylogeographic and phylogenetic reconstructions.
SNPs (single nucleotide polymorphisms): Are loci with alleles that differ in a
single base, with the rarer allele having a frequency of at least 1% in a set
of individuals. SNPs can occur in coding or non-coding regions and are
highly frequent in the genomes of plants and animals and codominantly
expressed.
Box 1.2: The Quantitative Perspective of Genetic Variation Patterns
Because the phenotype is the expression of the genotype modulated by environmental conditions, the analysis of the variation between individuals in
phenotypic characters allows us to gain knowledge about the gene pools that
determine them. For this, it is necessary to set up a trial in which the environmental effect can be controlled. Essentially, this trial seeks to raise the different genetic entities (i.e., provenances, families, clones) under the same
environmental condition (common garden experiment), with the expectation
that the differences that appear in the phenotype are the reflection of the
genetic variations. These trials will have an experimental design defined by
the environmental conditions and the entities to be tested, and their conclusions will be valid for the trial conditions.
The variables to consider can be of different kinds, some measured simply
with a ruler (e.g., seedling height) and others with sophisticated devices such
as a spectrophotometer (e.g., chlorophyll concentration). Some variables are
of greater productive importance, while others will provide information particularly on adaptability. In this sense, juvenile characters may be the most
relevant when the main interest is to ensure post-plantation survival.
The main statistical method to analyze the variation in quantitative characters is the analysis of variance (ANOVA), which can be applied to additive
linear models of fixed effects, random effects, or mixed effects. A typical test
in a low-intensity breeding program is the comparison of different provenances of a species and, within them, open-pollinated families. Such a trial
can be set up by collecting seeds from 10 to 30 trees in each of about 20 populations of interest. All plants obtained with the seeds of one of the trees will
be an open-pollinated family, and the kindship relationship between them will
1 Native Forests Claim for Breeding in Argentina: General Concepts and Their State