These aquaculture- and conservation-oriented 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 stresses".
         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). torsten.nygaard@agrsci.dk 

575.  Frankenfishfeed disappears in five days
         Availability of 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.
         How 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. ssatoh@s.kaiyodai.ac.jp 

574.  Mapping colour in the tilapia genome
         A 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.
         Wide crosses are good for mapping, and this one involves two well known and important (for aquaculture) species, Oreochromis niloticus and Oreochromis aureus.
         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. tom.kocher@unh.edu

573.  Does WSSV switch off a shrimp's immunity genes?
         Discovery 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 8:1436-2228.
         More 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." jhxiang@ms.qdio.ac 

572.  Markers can supplement pedigrees, but not replace them
         Efficiency 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.
         Generally 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).
         This 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?
         Not 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 uncertainties".
         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. jmj@inia.es 

571.  Inferring salmon families for genetic conservation
         Unraveling 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.
         Can 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.
         The 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. christophe.herbinger@dal.ca 

570.  Fitness improves when "new blood" is added
         Genetic 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.
         It's 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 setting".
         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 rescue. jthogg@montana.com 

569.  High heritabilities of commercial traits in cod
         Genetic 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.
         Heritability 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. kari.kolstad@akvaforsk.nlh.no 

568.  Recognize tilapia hybrids by their fins
         The 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.
         Tilapia 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. nobahceline@yahoo.fr 

567.  Benchmark genetic diversities for wild vannamei
         Population 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.
         Data 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 F_ST values between locations and total F_ST 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. rperez@cibnor.mx 

566.  Domesticated Atlantic salmon have lost half their genetic diversity
         Genetic 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.
         This 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. withlerr@pac.dfo-mpo.gc.ca

565.  Correlation between parasite resistance and general fitness: a lesson for shrimp
         Evidence from simultaneous quantitative trait loci mapping for resistance and fitness in Tribolium castaneum. 2005. Zhong, D., A. Pai and G. Yan. Genetics 169:2127-2135.
         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. gyan@buffalo.edu