122
T.F. Cross et al.
Box 4.1 (continued)
proteins), which can be localised and amplified by PCR from tiny tissue samples. At variable (polymorphic) loci, the different alleles vary in repeat number,
with mutations increasing or decreasing the number of repeats. Most loci
appear to be “neutral” (not affected by natural selection) and so are ideal as
population markers. However, a minority of microsatellite loci are tightly
linked to functional genes and can be used as markers of these genes in
adaptational studies (see Box 4.2 on MHC). Using several polymorphic
microsatellites and appropriate statistics, an individual can be assigned to its
population or strain of origin. Progeny can also be assigned to parents and
thus microsatellites have high utility when dealing with interactions.
A more recently developed marker is the so-called single nucleotide
polymorphism (SNP), which usually consists of a point mutation at a given
site, commonly with just two alternative bases and thus alleles. SNPs are
much more common in the genome than microsatellites (at least one per
1,000 bp) and have the great advantage of transferability between laboratories,
so complex and expensive intercalibration is not required. In any species
where there has been considerable genome work using several individuals,
very large numbers of SNPs (and their exact genome location) will be known.
A number of different techniques can be used to identify alleles (nucleotide)
and genotypes. The only current problem with SNPs is that there is no single/cheap technique for their detection. Once this is resolved they may supplant microsatellites as the “marker of choice” though it is recognised that it
will be necessary to screen larger numbers of loci since most SNP loci are
bialleic (whereas microsatellites typically have over 10 alleles). With PCR, it
is possible to isolate large quantities of specific DNA fragments for sequencing. While initially very expensive, sequencing has now become a very rapid
and cheap process, in the wake of the human and other genome projects.
Thus, it may shortly be economical to identify large suites of SNPs for novel
species, rapidly.
DNA sequencing (using automated techniques and the di-dedoxy method
(Sanger et al. 1977), is also being increasingly used to investigate functional
genes (those coding for proteins) usually be isolating mRNA and producing
cDNA, using reverse transcriptase. Such functional genes, if polymorphic,
will be of great importance in future interactions studies, since captive
breeding will often change allele frequencies at these loci, potentially reducing
fitness in the wild.
Functional genomics are also starting to be applied to studies of reared
strains and wild populations. Using microarray technology to study multiple
gene expression, Roberge et al. (2006) have shown that many of the same
genes are up- or down regulated in entirely separate reared Atlantic salmon
strains compared with native wild populations, in both Norway and Canada.
T.F. Cross et al.
Box 4.1 (continued)
proteins), which can be localised and amplified by PCR from tiny tissue samples. At variable (polymorphic) loci, the different alleles vary in repeat number,
with mutations increasing or decreasing the number of repeats. Most loci
appear to be “neutral” (not affected by natural selection) and so are ideal as
population markers. However, a minority of microsatellite loci are tightly
linked to functional genes and can be used as markers of these genes in
adaptational studies (see Box 4.2 on MHC). Using several polymorphic
microsatellites and appropriate statistics, an individual can be assigned to its
population or strain of origin. Progeny can also be assigned to parents and
thus microsatellites have high utility when dealing with interactions.
A more recently developed marker is the so-called single nucleotide
polymorphism (SNP), which usually consists of a point mutation at a given
site, commonly with just two alternative bases and thus alleles. SNPs are
much more common in the genome than microsatellites (at least one per
1,000 bp) and have the great advantage of transferability between laboratories,
so complex and expensive intercalibration is not required. In any species
where there has been considerable genome work using several individuals,
very large numbers of SNPs (and their exact genome location) will be known.
A number of different techniques can be used to identify alleles (nucleotide)
and genotypes. The only current problem with SNPs is that there is no single/cheap technique for their detection. Once this is resolved they may supplant microsatellites as the “marker of choice” though it is recognised that it
will be necessary to screen larger numbers of loci since most SNP loci are
bialleic (whereas microsatellites typically have over 10 alleles). With PCR, it
is possible to isolate large quantities of specific DNA fragments for sequencing. While initially very expensive, sequencing has now become a very rapid
and cheap process, in the wake of the human and other genome projects.
Thus, it may shortly be economical to identify large suites of SNPs for novel
species, rapidly.
DNA sequencing (using automated techniques and the di-dedoxy method
(Sanger et al. 1977), is also being increasingly used to investigate functional
genes (those coding for proteins) usually be isolating mRNA and producing
cDNA, using reverse transcriptase. Such functional genes, if polymorphic,
will be of great importance in future interactions studies, since captive
breeding will often change allele frequencies at these loci, potentially reducing
fitness in the wild.
Functional genomics are also starting to be applied to studies of reared
strains and wild populations. Using microarray technology to study multiple
gene expression, Roberge et al. (2006) have shown that many of the same
genes are up- or down regulated in entirely separate reared Atlantic salmon
strains compared with native wild populations, in both Norway and Canada.