commentaries are not abstracts written by the original authors.
They reflect the opinions of someone else -- usually Roger Doyle. Direct quotations from the papers or
abstracts are marked with inverted commas.
576. Inbreeding mainly affects metabolism- and stress-related genes
Genome-wide analysis on inbreeding effects on gene expression in
Drosophila melanogaster. 2005. Kristensen, T. N., P. Sørensen, M.
Kruhøffer, K. S. Pedersen and V. Loeschcke. Genetics 171:157-167.
This interesting study
shows that inbreeding alters the expression of many genes, especially
those that are known to be involved in energy metabolism and stress
responses. The authors suggest that "effects of different kinds of
stresses (such as inbreeding, aging, and oxidative stress) may bear
similarities, and those genes being differentially expressed under such
conditions may act to maintain homeostasis in organisms exposed to diverse
This makes sense because
it is known that inbreeding depression is magnified under stressful
conditions (e.g. Sept 2006 #538) and that inbreeding, stress and ageing
have somewhat similar effects at the cellular level. But this appears to
be one of the first papers on the effect of inbreeding on the whole
genome. Note that genes expressing anti-bacterial peptides were
upregulated in the inbred lines of Drosophila (See Dec 2003 #453). firstname.lastname@example.org
575. Frankenfishfeed disappears in
genetically modified soybean meal in rainbow trout Oncorhynchus mykiss
diets. 2006. Chainark, P., S. Satoh, T. Hino, V. Kiron, I. Hirono and
T. Aoki. Fisheries Science 72:1072-1078.
long does genetically modified fish feed remain detectable? In this
experiment, trout were fed a diet containing genetically modified soybean
meal. Nested PCR did detect the cauliflower mosaic virus 35S promoter
(from the soybean GMO construct) in the muscle of the fish while they were
on the Frankendiet. But by the fifth day after switching to ordinary
soybean meal the GMO had disappeared. Growth of the fish was, of course,
the same on both diets. email@example.com
574. Mapping colour in the tilapia genome
second-generation genetic linkage map of tilapia (Oreochromis spp.).
2005. Lee, B.-Y., W.-J. Lee, J. T. Streelman, K. L. Carleton, A. E. Howe,
G. Hulata, A. Slettan et al. Genetics 170:237-244.
crosses are good for mapping, and this one involves two well known and
important (for aquaculture) species, Oreochromis niloticus and Oreochromis
A red-coloured niloticus
male was crossed with an ordinary aureus female and the mapping was based
on the segregation of the F2 generation, i.e. the grandchildren of these
two founders. "We detected associations of sex and red color with
markers on linkage group 3." The complicated pattern of genetic sex
determination is generally consistent with previous work; see June 2006
#498, Oct 2003 #435, Mar 2003 #293.
The red phenotype studied
here originated as a mutation in an Egyptian niloticus stock held at
Stirling University in the UK. "Our results show that the mutation
segregates as a single dominant gene. ... Efforts to positionally clone
this gene are underway in our laboratory." The average marker spacing
is now down to 2.4 cM on 24 linkage groups. (There are 22 chromosomes.)
Colour is not a trivial trait in tilapia and we want to understand it. firstname.lastname@example.org
573. Does WSSV switch off a shrimp's immunity genes?
of the genes in response to White Spot Syndrome virus (WSSV) infection in
Fenneropenaeus chinensis through cDNA microarray. 2006. Wang, B., F.
Li, B. Dong, X. Zhang, C. Zhang and J. Xiang. Marine Biotechnology
than 100 elements in arrays constructed from WSSV-infected shrimp showed
changes in expression, relative to non-infected controls. Genes known to
be involved in cell growth and immune function (e.g. heat shock proteins,
ubiquitin) were up-regulated, genes affecting metabolism and homeostasis
(e.g. ATP synthase) were down-regulated. The authors offer an interesting
interpretation: "These findings show that WSSV is able to switch off
or limit the expression of the host’s immune-related genes to facilitate
its own replication in the host." email@example.com
572. Markers can supplement
pedigrees, but not replace them
of the use of pedigree and molecular marker information in conservation
programs. 2005. Fernández, J., B. Villanueva, R. Pong-Wong and M. A.
Toro. Genetics 170:1313-1321.
speaking, the best way to conserve genetic diversity in a managed
population is to choose breeders and arrange matings, each generation, so
as to minimize the global coancestry of the offspring. (Apr 2004 #473, Feb
2004#455, Nov 2001 #261).
ideal can be reached quite closely if you know the pedigrees. It can be
approximated if you have marker (i.e. microsatellite) relatedness
estimates on parents, offspring or both (Apr 2004 #473, Feb 2004#455, Nov
2001 #261). How good is the approximation?
very good, in this this simulation study. Measures of simulated genetic
diversity included heterozygosity, allele diversity and inbreeding.
"The amount and degree of polymorphism of markers to be used to
compute molecular coancestry had to be high to mimic the performance of
the strategy relying on pedigree, especially in the short term (for
example, >10 markers per chromosome with 10 alleles each were needed if
only the parents' genotype was available)." The authors conclude that
"in realistic situations (i.e., species with large genomes and a limited number of available markers), probably it would be more
efficient to allocate the available resources to the enlargement of the
population or to a better control of pedigree and restrict the use of
markers to more specific tasks such as solving pedigree
See April 2004 #469 for a
paper that reaches similar conclusions and #571, below, for a paper which
shows that you can in fact get useful results in a wild salmon population. firstname.lastname@example.org
Inferring salmon families for genetic conservation
first-generation pedigrees in wild endangered salmon populations using
molecular genetic markers. 2006. Herbinger, C. M., P. T. O'Reilly and
E. Verspoor. Molecular Ecology 15:2261-2275.
markers be used to infer family structure in real-world, wild salmon
populations when there is no data whatsoever from the parental generation?
Can family structure be used to maximise diversity of a broodstock at the
start of a captive breeding program?
The essence of this paper
is identification of kinship groups of wild Atlantic salmon (that is,
groups of related individuals which comprise one or more full-sib
families), in several eastern Canadian rivers. Marker-based family
inferences are inherently ambiguous because of the random effects of
Mendelian segregation in a small set of marker loci. This paper provides an especially insightful discussion of this
basic problem and the relative success of various statistical approaches
(and computer programs) in overcoming them. Their program PEDIGREE for
inferring kinship groups from marker data is free and web-based; sign on
at http://herbinger.biology.dal.ca:5080/Pedigree. The authors also make
use of J. Wang's program
COLONY http://www.zoo.cam.ac.uk/ioz/software.htm#COLONY. Both programs
tolerate null alleles and various kinds of procedural error.
conclusion of the paper is that random samples of broodstock from a wild
population -- such as those commonly taken to found a captive broodstock
-- will lose a large proportion of the kinship groups even when the sample
is moderately large. "On the other hand, using results from the
analysis presented here, an informed sampling of 100 individuals would
ensure that one, and in most instances two, representatives from all kin
groupings would be retained." The analysis is based on nine
microsatellite markers. See Jan 2002 #283 and #572, above. email@example.com
Fitness improves when "new blood" is added
rescue of an insular population of large mammals. 2006. Hogg, J. T.,
S. H. Forbes, M. M. Steele and G. Luikart. Proceedings of the Royal
Society B: Biological Sciences 273:1491-1499.
always nice to see evidence that bringing new genes into a small,
endangered population can do some good. The beneficiary in this case is a
group of bighorn sheep that was founded with only 12 individuals and
maintained in isolation for 10 to 12 generations at an average population
number of 42 animals. Starting twenty years ago, immigrants were added.
"We detected marked improvements in reproduction, survival and
five fitness-related traits among descendants of the 15 recent migrants.
Trait values were increased by 23–257% in maximally outbred
individuals." The authors comment that "This is the first
demonstration, to our knowledge, of increased male and female fitness
attributable to outbreeding realized in a fully competitive natural
See Jan 2001#158 for the beneficial genetic effects (on effective
population size, not components of fitness) of coho salmon supplementation
in the Sacramento river. See Oct 2006 #546 for other instances of genetic
High heritabilities of commercial traits in cod
variation and genotype by location interaction in body weight, spinal
deformity and sexual maturity in Atlantic cod (Gadus morhua) reared at
different locations off Norway. 2006. Kolstad, K., I. Thorland, T.
Refstie and B. Gjerde. Aquaculture 259:66-73.
for body weight was high in this experiment, 0.64, which bodes well for
selection programs, as does the significant but not excessively large
estimate of site X genotype interaction. The genetic correlation was high
between body weight at 2 years, around the time the fish are sexually
mature, and their weight at harvest, suggesting that selection might be
done at 2 years. This would presumably speed up as well as simplify a
selection program. Spinal deformity also had a very high estimated
heritability, around 0.7. firstname.lastname@example.org
568. Recognize tilapia hybrids by
colour pattern of the caudal fin, a useful criterion for identification of
two species of Tilapia and their hybrids. 2006. Nobah, C. S. K., E. P.
Kouamelan, V. N'Douba, J. Snoeks, G. G. Teugels, G. Goore-Bi, T. Kone et
al. Journal of Fish Biology 69:698-707.
zillii and T. guineensis are two species of West African origin which have
been greatly affected by dam construction in their native watersheds.
Morphologically, the hybrids are intermediate and standard morphometric
analysis (meristic and truss morphometrics) does not clearly differentiate
them from the parents. The color and spotting pattern of the caudal fin
was diagnostic, however. This will be useful to those working on field
biology of this hybrid, which has become an important component of the
artisanal and subsistence fishery in Côte d'Ivoire and surrounding areas.
Those working on other
cichlid hybrids might also take a closer look at their caudal fins. They
are used in behavioral displays and could be under strong,
species-specific genetic control. email@example.com
567. Benchmark genetic diversities
for wild vannamei
genetic structure of Pacific white shrimp (Litopenaeus vannamei) from
Mexico to Panama: microsatellite DNA variation. 2004. Valles-Jimenez,
R., P. Cruz and R. Perez-Enriquez. Marine Biotechnology 6:475-484.
from five loci at four geographical locations along the west coast of the
Americas were analysed. "The genetic diversity between populations
was indicated by the mean number of alleles per locus and mean observed
heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388,
respectively.... Significant pairwise FST values between
locations and total FST showed that the white shrimp population
is structured into subpopulations." This information will be useful
both for conservation and for aquaculturists monitoring the genetic health
of their broodstocks. firstname.lastname@example.org
566. Domesticated Atlantic salmon
have lost half their genetic diversity
variation within and among domesticated Atlantic salmon broodstocks in
British Columbia, Canada. 2005. Withler, R. E., K. J. Supernault and
K. M. Miller. Animal Genetics 36:43-50.
useful paper describes the general state of genetic diversity within domesticated Atlantic salmon stocks on the Canadian Pacific coast. It appears that British Columbian aquacultural stocks have lost
around half of their genetic diversity, as measured by the number of
alleles. Allele number (richness, diversity) averages about 11 in domestic
stocks and about 20 in wild (Atlantic) populations.
The cup should be
considered half full, not half empty, because there is lots of diversity
left, assuming that microsatellite diversity correlates with scope for
selection. Atlantic salmon in British Columbia are conventionally
attributed to two European sources (Scotland and Norway) and one Canadian
source (Gaspé peninsula).
Generalizations about the
history of broodstock management are made in the paper. There has been
some introgression of Canadian genes into the European broodstocks. The
genetic distance between different domestic stocks (i.e. aquaculture
companies) which attribute their stocks to the same source is surprisingly
large. All stocks originating from Scotland under the same name are not
the same genetically, and may be very different. The same is true of the
Norwegian stock. This will not surprise anyone familiar with the industry. email@example.com
565. Correlation between parasite
resistance and general fitness: a lesson for shrimp
from simultaneous quantitative trait loci mapping for resistance and
fitness in Tribolium castaneum. 2005. Zhong, D., A. Pai and G. Yan.
A lot less is known about the genetics of shrimp than the genetics of
some other arthropods, and it can be instructive for aquaculturists to
look beyond the genus Litopenaeus.
This experiment on the flour
beetle Tribolium castaneum found three quantitative trait loci (QTL) that
accounted for around 50% of the variance in resistance to a tapeworm
parasite. The QTL were closely associated with, or possibly identical to,
QTL that accounted for around 50% of variance in two major components of
fitness. "The genome regions that contain the QTL for parasite
resistance explained the majority of the variance in fecundity and
egg-to-adult viability in the mapping populations".
The authors point out
that this association could be caused by multiple effects of the same
genes or by tight linkage between genes that affect resistance, fecundity
and viability. Whatever the explanation, the observation is a useful
reminder that there is likely to be strong genetic correlation -- negative
or positive -- among traits that are significant in aquaculture. It is
also evident from the paper that the correlations are likely to vary
considerably among populations and environments. firstname.lastname@example.org