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.
addresses of authors have been modified in an obvious way to reduce the possibility
695. Genetics of vannamei growing at low and high density
Genotype by environment interaction for adult body weights of shrimp Penaeus vannamei when grown at low and high densities. 2008. Ibarra, A. M. and R. Famula. Genetics Selection Evolution 40:541-551.
This is a useful paper. Two growout densities were used: low (6/m2) and high (400, later reduced to 50/
m2). The authors found that the genetic correlation between low and high density environments was only around 0.5, which suggests that there may be strong GxE effects.
Many of the genotypes that grow fastest in one of the environments are not the fastest-growing in the other.
Does this mean that you have to develop two separate, specialized strains if you are growing vannamei in low and high-density environments? Not necessarily. The authors advise caution. "... further understanding of genetic correlations between growth and reproductive traits within a given environment is necessary, as there are indications of reduced reproductive fitness for shrimp grown at high densities".
I would say that at the very least, however, you should focus the breeding program to increase selection pressure on genes that are expressed favorably in the environment that most affects the profitability of the farm. Especially if that environment includes growth at very high density. Note that genetic variance and heritability were higher in the high density environment, suggesting that such an approach
to selection might work very well. See Aug 2007 #615 for density-growth interaction in tilapia. aibarra<%>cibnor.mx
694. A 500-year strategy for captive breeding
Sustainable long-term conservation of rare cattle breeds using rotational AI sires. 2008. Colleau, J.-J. and L. Avon. Genetics Selection Evolution 40:415-432.
In the worst-case scenario, habitats of
wild salmonid populations are never adequately restored, and the salmon are forever clinging by their fingernails to the lip of an extinction vortex. If
a society has the will, patience & longevity it can conserve these on-the-edge populations indefinitely by actively managing their breeding and mortality.
This paper explores the control of inbreeding through artificial insemination of females using semen (= milt, in fish) preserved for long periods. "...the results obtained [by simulation] showed that the number of sires should be at least 10-15 and that the same sires should be used during at least 50 years. Simulation based on demographic data from a real population of cattle (27 males, 340 females) showed an inbreeding coefficient of 0.07 after 500 years.
What you need, basically, is a rotational mating scheme (minimal kinship scheme) and large buckets of frozen semen. Inbreeding accumulates in a stepwise fashion with the duration between steps depending on population size and the
milt supply. All of this including population numbers should be technically feasible in salmonids. See Oct 2008 #668 for genetic gain evaluation using cryopreserved sperm. ugencjj<%>@dga2.jouy.inra.fr
693. Do YY tilapia populations have higher growth?
Growth performance of mixed sex, hormonally sex reversed and progeny of YY male tilapia of the GIFT strain, Oreochromis niloticus. 2009. Kamaruzzaman, N., N. H. Nguyen, A. Hamzah and R. W. Ponzoni. Aquaculture Research 40:720-728.
Growth rates in three kinds of tilapia culture, as listed in the title, were compared. The authors conclude that "there were no statistical differences in either body weight or standard length between mixed sex, hormone treated and progeny of YYmale (p<0.05)." This conclusion deserves
careful examination because the practical implications are important.
It is evident from the graphs and tables that males were heavier than females in all three groups and the weight distribution in the group consisting of offspring of YY males is visibly skewed towards the higher size classes. So, why the downbeat conclusion regarding YY tilapia?
There are two potential problems with the statistical analysis.
The first problem is that
everyone expects males to grow faster than females before any tilapia experiment even starts. We also expect the offspring of YYs to have about 50% more males than a mixed-sex control. The result is an expected 10%-12% weight difference between groups, which is commercially important but hard to prove in a small experiment. In the light of this
expectation it is appropriate to use a one-tailed significance test, that is, to test whether YY group is heavier than the control rather than that the groups are equal.
It is unlikely that this
inequality, which is the ordinary rationale for monosex culture and is quite visible in the raw data, would have been rejected.
Inequality is the proper null hypothesis, not equality.
The second reason to be hesitant is a bit more subtle but
depends on the same logic. The "effect size" for the retrospective power test used in the paper need not have been calculated from the data itself, which is always a questionable procedure. Given the common knowledge that tilapia males grow faster
the effect size could have been estimated a priori from myriad previous observations on the sex ratios and male and female
body weights, including some published by the same authors (Aug 2007 #615, Apr 2008 #652).
The power analysis should have been done with this a priori effect size.
Alternatively, and more usefully, the alternative expectation
(i.e. 10%-12% rather than 0% in YY vs. mixed) could have been used as a prior in a Bayesian analysis, or, as mentioned above, as an alternative null hypothesis in the
frequentist tests actually used.
The authors surprising
but strong recommendation from their grow-out trial is, "monosex culture of all male tilapia would be of no advantage over mixed sex culture for the GIFT strain under conditions of cages suspended in earthen ponds". It
is hard to give a 100% endorsement of this advice. For additional recent information on GIFT see Feb 2007 #580 and Feb 2008 #640, and for GIFT comparisons June 2007 #698, Aug 2007 #615 & #620. See Apr 2000 #39, Feb 2002 #294, Nov 2006 #555 for more powerful designs for
comparing strains. r.ponzoni<%>cgiar.org
692. A useful way to find meaning in spatial
Applications of graph theory to landscape
genetics. 2008. Garroway, C. J., J. Bowman, D. Carr and P. J. Wilson. Evolutionary Applications 1:620-630.
Analysis of directed graphs has a long and honored, but not overwhelming big, presence in biology. Examples are transcriptional regulation networks (molecular genetics), path analysis (population genetics), loop analysis (ecology). This paper uses graph theoretic methods to come up with useful conclusions in the new field of
landscape genetics, conclusions that otherwise might have been hard to make.
Landscape genetics is a still somewhat inchoate field which relies mostly on tried-and-true procedures such as principal component or coordinate analysis. A fine example of the latter is May 2002 #311. The type of network analysis presented here (data on fishers, a type of
boreal mammal related to mink, weasel etc.) should be directly applicable to salmonid population networks.
Genotypes sampled in a single habitat are
treated as network nodes, of which there were 34 in the study, and the network edges (connecting lines) are weighted genetic distances. Analysis proceeds from this straightforward topology.
One of the non-intuitive,
useful findings is that, "redundancy in paths between nodes such that there were alternate short paths through the network .... suggests that genetic connectivity may not be particularly affected by the loss of even well-connected nodes." The authors's practical conclusion, not otherwise obvious in the data, is "[analysis] suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread". For aquatic relevance of this see the discussion of local extirpation in a salmonid metapopulation, Feb. 2004 #464, striped bass July 2006 #512. See also another new tool for landscape genetics in June 2006 #497. colin.garroway<%>gmail.com
691. Rapid diversity loss in P. monodon during domestication
Shifts in genetic diversity during domestication of Black Tiger shrimp, Penaeus monodon, monitored using two multiplexed microsatellite systems. 2008. Dixon, T. J., G. J. Coman, S. J. Arnold, M. J. Sellars, R. E. Lyons, L. Dierens, N. P. Preston et al. Aquaculture 283:1-6.
Five populations of Penaeus monodon were studied (four domesticated and one wild, but all originating from the same site). The domesticated populations had all lost considerable genetic diversity -- one-half or more, depending on the estimator -- and had developed genetic differences among themselves whilst doing so. This study illustrates the rapid loss of genetic diversity and reduction in effective population size that can occur during domestication when rigid genetic management of the stocks is not possible. See Jan 2002 #277 & #283. Tom.Dixon<%>csiro.au
690. Another good use for neutral markers in breeding programs
Increased accuracy of artificial selection by using the realized relationship matrix. 2009. Hayes, B. J., P. M. Visscher and M. E. Goddard. Genetics Research 91:47-60.
The accuracy of breeding value estimates, e.g. for selection, can potentially be increased by using marker information rather than pedigree information. That is, by estimating
EBVs from the observed distribution of markers in the breeding population instead of a relationship matrix predicted from pedigrees. (See May 02 #320, Aug 2007 #614, Oct 2007#632)
The realized relationship among individuals that have the same predicted relationship varies at every locus because of Mendelian sampling of parental genomes during gametogenesis. The marker method can compensate for this if the marker density is high enough to provide tight linkage with QTLs. (Note that this use of markers is not the same as their use in parentage assignment, e.g. Aug 06 #528. Nor is it marker assisted selection, since no QTLs are identified.)
Realized relationship matrices will also be useful in predicting the breeding values of animals for which there are no phenotypic records, e.g. in disease challenge test situations, straying and return rates in salmon, etc. The downside is that thousands of markers are required, which probably means SNP gene array technology (Dec 2003 #441, June 2006 #503). Large numbers of individuals must be screened and it helps if the effective population size is small and the genome is "short" (fewer independently segregating chromosome segments). Nevertheless, the numbers are feasible and benefits could outweigh the costs in some high-value aquaculture for traits that are expensive to measure, sex limited or can only be measured on
689. Finding tilapia markers by homology with sticklebacks
Linking the genomes of nonmodel teleosts through comparative genomics. 2008. Sarropoulou, E., D. Nousdili, A. Magoulas and G. Kotoulas. Marine Biotechnology 10:227-233.
This analysis of publicly available marker data shows that the general organization of the genomes of important aquacultural species including Oreochromis niloticus (tilapia) and Sparus aurata (gilthead sea bream) is remarkably similar to that of several "model" fish species
that have been completely sequenced, especially Gasterosteus aculateus (stickleback). That is, the physical position of the markers on chromosomes is similar in these species, some of which last shared a common ancestor more than 100 million years ago.
The authors use trios of species, e.g. tilapia + sea bream + stickleback to help anchor homologous chromosomes and chromosome locations. A variety of comparative genomics tricks are used and the paper makes interesting reading. To my knowledge this is the first comparative genomics paper in aquaculture. The major practical importance, for now,
may be that "comparison of low coverage gene maps of aquacultured fish species against fully sequenced fish species will enhance the efficiency of candidate genes identification projected for quantitative trait loci (QTL) scans for traits of commercial interest".
688. QTL designs for mass spawners, super high fecundity etc.
QTL mapping designs for aquaculture. 2008. Massault, C., H. Bovenhuis, C. Haley and D.-J. Koning. Aquaculture 285:23-29.
This review of breeding designs is especially useful because it includes mass spawning species, where control over mating is poor and pedigree information may be limited. The paper discusses three experimental designs with varying levels of control over mating: hierarchical (e.g. salmon), mass spawning (e.g. sea bass), large full-sib families (e.g. oysters). "For each of the systems studied, it is possible to design an experiment that would have an 80% power to detect a QTL of moderate effect (explaining between 1.5 and 5% of the trait variation) by genotyping 1000 or fewer individuals". Cecile.massault<%>roslin.ed.ac.uk
687. Mechanisms of hybrid disgenesis and outbreeding depression
Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. 2009. Michalak, P. Heredity 102:45-50.
Many people were interested in the possible aquacultural and conservation implication of the recent papers on near-species-level divergence in P. monodon (April 2009 #678) in relation to the F2 hybrid breakdown in Tigropius (April 2009 #682). Outbreeding depression is of general concern.
A lot of new mechanisms of hybrid disgenesis are coming to light including interference with DNA methylation, release of mobile elements, small RNA molecules etc. etc. associated with higher-level hybridization. This brief review "focuses on a broad class of genetic processes related to maternal effects, epigenetic changes, activity of transposable elements and small RNAs in interspecies hybrids." And: "[it]... offers a handful of glimpses into these complex dynamics." It also provides a useful entry point into the literature on other major mechanisms of disgenesis such as interactions between proteins. michalak<%>uta.edu
686. Genetic architecture of GM Frankengene escape
Impact of transgene inheritance on the mitigation of gene flow between crops and their wild relatives: the example of foxtail millet. 2008. Shi, Y., T. Y. Wang, Y. Li and H. Darmency. Genetics 180:969-975.
The rate of flow of transgenes from a genetically engineered organism to its wild relatives depended on the genetic architecture of the gene, this
Herbicide-resistance transgenes which were either (a) nuclear recessive or (b) nuclear dominant flowed from transgenic millet to neighboring wild plants in a ratio of 60:1 or 190:1 relative to flow of transgenes which were (c) plastid (chloroplast) maternally inherited. "Because the recessive gene was not expressed in the first-generation hybrids, it should be more effective than dominant genes in reducing gene flow under normal agricultural conditions where herbicides are sprayed because interspecific hybrids cannot gain from beneficial genes."
The point is, spraying the whole area with weed killer will wipe out the first-generation transgenic hybrids before they can send the gene on to future generations. This is conceivably applicable to
aquaculture. A hypothetical transgene for WSSV resistance, for instance, would be less likely to spread beyond the farm in a WSSV-prone area if the transgene were recessive. See May 2001 #198, June 2004 #487 for spread of deleterious Frankengenes that cause a mating advantage. darmency<%>dijon.inra.fr
685. Prince Charles eats organic Frankenfish?
Organic and GM—Why Not? 2008. Tester, M. Science 322:1190-1191.
This is a review of a recent book entitled Tomorrow's Table: Organic Farming, Genetics, and the Future of Food, by P.C. Ronald and R.W. Adamchak. Oxford University Press, New York, 2008. ISBN 9780195301755.
Quotes from the review: "The organic movement's opposition to genetically modified (GM) crops is causing it to miss an opportunity. Like agriculture across the planet, organic farming needs all the technological help it can get to be both sustainable and high-yielding.... [In the book reviewed here] we now have the positive aspects of both organic and GM approaches discussed logically and clearly....The marriage is long overdue.....delightfully constructive book ....thesis that GM technologies and organic agriculture are quite compatible ... .highlights the superficial nature of much of the GM debate, in which both sides make oversimplifications that support unnecessarily polarized standpoints....All proponents of organic agriculture, especially the noisier ones such as Prince Charles, should read Tomorrow's Table....".
684. Social interaction increases response to selection
Response to domestication and selection for growth in the European sea bass (Dicentrarchus labrax) in separate and mixed tanks. 2009. Vandeputte, M., M. Dupont-Nivet, P. Haffray, H. Chavanne, S. Cenadelli, K. Parati, M.-O. Vidal et al. Aquaculture 286:20-27.
Experiments on the effect of social interaction on growth rate have become
more interesting in light of the discovery that it constitutes a large, potentially usable, reservoirs of heritable variation
in growth (Oct 2003 #427, Apr 2007 #600 & #597, Apr 2008 #659, Oct 2008 # 669).
This paper reports on families of European sea bass grown in common tanks (the usual practice, where heritability of growth is normally fairly high) and as separated individuals. The male parents had one of four different histories: "wild", one generation of domestication, mass selection or individual (within-group) selection. In other words it was a realized-response-to-selection experiment, with a control.
It is important to note that selection took place in the generation prior to the growth treatments.
Also, animals in the selected generation appear to have been reared in large groups. So it is the
expression, or realization, of genetic gain in different environments which is being examined, not the effect of social interaction on selection itself.
Response to selection was higher when fish were reared together, i.e. in a social environment similar to the one where selection took place, rather than separately. The authors suggest this is because genetic variance is magnified by competition. If by this they mean that different genes are expressed, or expressed differently, in an interactive environment the interpretation is consistent with the papers cited above. The response decreased somewhat as the fish grew larger, which the authors attribute to a nuisance effect of density and a size X environment interaction involving density. The decrease is not very large. marc.vandeputte<%>jouy.inra.fr