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
Flash! Why domesticated Frankenfish won't grow much faster
Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch). 2009. Devlin, R. H., D. Sakhrani, W. E. Tymchuk, M. L. Rise and B. Goh. Proceedings National Academy of Sciences (US) 106:3047-3052.
Soon after it became possible to
transfer growth hormone genes, it was seen that the resulting increase in growth rate was
less in domesticated than in wild animals of the same species (e.g. salmon Feb 2001 #174, mice Apr 2001 #181). Now
this important paper reports that the reason for this (in salmon) is that transgenesis and domestication selection have similar metabolic effects.
"Genes in many different physiological pathways show modified expression in domestic and GH transgenic strains relative to wild-type, but effects are strongly correlated." A salmon cDNA microarray chip was used to compare expression profiles (see Dec 2003 #441 on microarrays).
One implication is that the steady gain from conventional breeding could make transgenic growth enhancement unnecessary in the long run. However,
conventional selection has its limits, and "modification or creation of alternative pathways, and/or targeting other points in the pathway, which may have become rate limited during domestication, may allow enhancement of phenotype". Furthermore, the relative rate of growth enhancement by selection and transgenesis depends on generation length.
A transgenic program that doesn't make commercial sense in tilapia or shrimp might well do so in
long-generation salmon, halibut or sturgeon.
As the authors point out,
environmental risk assessment of transgenic fish might be affected if
"transgenic and domesticated organisms are being phenotypically altered by substantially similar mechanisms". It is important to note in this connection that the molecular changes during domestication are repeatable and presumably predictable
(see Sept 2006 #540). robert.devlin<%>dfo-mpo.gc.ca
718. Inbreeding lowers tilapia reproductive fitness
Effects of relatedness and inbreeding on reproductive success of Nile tilapia (Oreochromis niloticus). 2009. Fessehaye, Y., H. Bovenhuis, M. A. Rezk, R. Crooijmans, J. A. M. van Arendonk and H. Komen. Aquaculture 294:180-186.
Tilapia were allowed to spawn semi-naturally in groups, and the
spawnings that resulted were studied to find out whether (a) there was any behavioral avoidance of mating among closely-related individuals, and (b) the effect of relatedness and inbreeding on survival and reproductive success. See June 2006 #504 for the microsatellite identification procedures used.
The genetic relatedness (kinship coefficient) between the member of a mating pairs did not have any discernable effect on the reproductive success of males.
There was no discernable choosing of mates to reduce the kinship of the mating pair (that is, no preference for unrelated potential mates), nor did the kinship of parental pairs have any effect on their reproductive success or fecundity.
See June 2007 #611.
When related individuals mated, however, problems
did show up in the next generation because their offspring were more inbred. Inbred males and females
from the free spawnings had lower reproductive individual success and fecundity, respectively. The loss of reproductive fitness in inbred males was higher under more competitive conditions (See Oct 2006 #538), i.e.
when the sex ratio was higher, so the authors suggest that 1:1 sex ratio is appropriate when inbreeding is a concern.
See They also suggest that the reduced fitness may help purge tilapia populations of inbreeding depression
(See Mar 03 #395, Oct 2007 #629). Hans.komen<%>wur.nl
717. Vannamei DNA library will be useful
Construction and characterization of a bacterial artificial chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei. 2009. Zhang, X., Y. Zhang, C. Scheuring, H.-B. Zhang, P. Huan, B. Wang, C. Liu et al. Marine Biotechnology in press.
The authors have succeeded in placing long sections of L. vannamei DNA into a type of modified bacterial plasmid called a bacterial artificial chromosome, or BAC. The inserted sections of genomic DNA overlap so that every location in the genome is
represented about five times, on average.
The resulting population of bacteria carrying the shrimp DNA (called a "BAC library") can be used for many purposes, including "screening of genomic regions of interest candidate genes, gene families, or large-sized synthetic DNA region and promote future works on comparative genomics, physical mapping, and large-scale genome sequencing in the species".
This is good work. Many markers (microsatellite, AFLP, SNP etc) are already known for several shrimp species and medium to coarse grain linkage maps have been constructed with them. A number of kilobase-sized DNA sequences have
also been published. Now we have the long, continuous sequences that are needed to efficiently track down individual genes. The BACs can serve as a scaffold on which the much shorter DNA sequences can be located.
Apparently this has not been
easy. The shrimp genome is very large -- almost two-thirds the size of ours -- and notoriously hard to work with. This BAC library was tested by successfully hybridizing with sequence from eight known immune- and sex-related genes. jhxiang<%>ms.qdio.ac.cn
716. Protecting genetic property rights of
Chinese province crafts pioneering law to thwart biopiracy. 2008. Stone, R. Science 320:732-733.
Farmers in a remote region of SW China have been growing a unique and delicious strain of sticky rice from time
immemorial. They are now beginning to profit from the work of their ancestors as the strain becomes cultivated more widely. The national and provincial governments (Guizhou province) and the Chinese Institute for Indigenous Knowledge and Culture Property at Guizhou University in Guiyang have helped these farmers protect their inheritance.
This was done in several ways: by drafting new legislation to classify indigenous knowledge as intellectual property, by allowing
farmers to trademark the strain and helping them use a new national law on rural development to organize a cooperative for distributing income. Note that "Registering a trademark gave the farmers leverage over companies that wanted to market the
rice..... Of course the companies resisted... but once the Kam [farmers] acquired this right, they could get capital and work with an outside company without being dominated. They had the power to negotiate."
See "Lords of the Harvest", Nov 2001 #251.
Also see Feb 2008 #648, where the conclusion is that a trademark,
backed up by a limited-use contract and willingness to sue for damages, is the only
law-based way to protect genetic intellectual property from piracy.
715. Decrease in fitness and diversity during partial supplementation
Stocking success of local-origin fry and impact of hatchery ancestry: monitoring a new steelhead (Oncorhynchus mykiss) stocking program in a Minnesota tributary to Lake Superior. 2008. Caroffino, D. C., L. M. Miller, A. R. Kapuscinski and J. J. Ostazeski. Can. J. Fish. Aquat. Sci. 65:309-318.
The important feature of this work is that the broodstock used for stocking a river originated in that same
river only one or two generations earlier. Although this is a feature of
many current stocking programs, the authors point out that its success has not been studied as often as it should be.
The majority of studies have looked at alien and/or domesticated
Here, the survival of fry from hatchery-spawned females was lower, but the production of age-2 juveniles was higher, than that of wild-spawned females. The authors's overall conclusion is that hatchery programs are usefully for increasing numbers but
need to be watched carefully to prevent genetic changes resulting from even one generation of domestication selection and from drift if small numbers of wild-caught spawners are used every generation. See Apr 2008 #664 for a study of the same phenomenon using a different analytical procedure.
Note that Oct 2008 #667 reports a case in which genetic diversity has been maintained for many generations of supplementation even though allele richness was usually higher in the wild-spawned than in the hatchery-spawned component of each generation. See also Apr 2004 #479. lmm<&>umn.edu
714. Effects of pedigree errors on the efficiency of conservation decisions
Effects of pedigree errors on the efficiency of conservation decisions. 2009. Oliehoek, P. A. and P. Bijma. Genetics Selection Evolution 41: on-line.
The errors considered here include mistakes in parentage assignment from marker data as well as inaccurate paper records. Errors do cause problems when the breeding objective is to conserve genetic diversity using optimal contribution / minimal kinship mating schemes (see, for example, Feb 2004 #455, Aug 2007 #624, Oct 2007 #632, ).
"When the percentage of wrong parent information is above 15%, the population structure and type of errors, should be taken into account before applying optimal contributions."
It appears to be most important to know which animals are true founders (e.g. from the wild) and not merely animals with unidentified parents. Mistakes are more consequential near the beginning of the pedigree. If the error rate is larger than 35%, simulation suggests, the optimal contribution breeding schemes may be less effective that equal-contribution breeding schemes... Free electronic access
713. Frankenfeed DNA is found in tilapia muscle etc.
Detection of transgenic DNA in tilapias (Oreochromis niloticus, GIFT strain) fed genetically modified soybeans (Roundup Ready). 2009. Ran, T., L. Mei, W. Lei, L. Aihua, H. Ru and S. Jie. Aquaculture Research 40:1350-1357.
DNA from Roundup Ready modified soybean was found in tilapia fed with
GM feed in China. The RR gene was found in the intestines, as one would
expect, but also in heart, liver, stomach, gonads, brain, gills, spleen, gall bladder and muscle. The authors do not know whether
this exogenous DNA is absorbed only into the blood of the fish or whether it actually penetrates the cells of
the organs (somewhat unlikely, in my view). Traces of GM DNA were also found in more than 90% of the commercial fish feeds the authors sampled in China. A sensitive two-stage PCR technique was used, and
the primer sequences for recognizing the Roundup Ready genes are published
in this paper. liumei<%>ms.qdio.ac.cn
712. Salmon genetic diversity retained through stock collapse
Genetic diversity and effective size of the Atlantic salmon Salmo salar L. inhabiting the River Eo (Spain) following a stock collapse. 2008. Ribeiro, Â., P. Morán and A. Caballero. Journal of Fish Biology 72:1933-1944.
Here is a riverine population that declined dramatically during the past two decades but nevertheless "exhibits a high level of genetic diversity, similar to that from other populations, and almost unchanged during the period of
study". Diversity held up despite census numbers and some genetic indication that a bottleneck occurred throughout the 1990s. (Genetic tests included allele frequency distributions and range of sizes, plus heterozygosity excess.)
"The recent growing number of salmon... relatively large estimates of the ratio Ne/N... and the high levels of diversity found suggest that the population has not been greatly affected by the historical census declines." The authors discuss several aspects of local and general salmon biology that helped maintain diversity through the critical period. "The Eo salmon population is unlikely to be heavily influenced by random genetic processes in the near future and a potentially satisfactory recovery may be expected."
This is a story that should encourage conservationists everywhere. See Apr 2007 #598 for a
relaed account of high salmon diversity on the Iberian peninsula. paloma<%>uvigo.es
711. How juvenile monodon escape vibriosis
Expression of immune-related genes in the digestive organ of shrimp, Penaeus monodon, after an oral infection by Vibrio harveyi. 2009. Soonthornchai, W., W. Rungrassamee, N. Karoonuthaisiri, P. Jarayabhun, S. Klinbunga, K. Söderhäll and P. Jiravanichpaisal. Developmental and Comparative Immunology: in press.
Infection with Vibrio harveyi
normally kills P. monodon at the PL stage, but juveniles and adults generally survive. How do they do it? The authors of this paper tried to find out by immersing the shrimp in the pathogen (so all the normal defense mechanisms of juvenile monodon would be challenged) and then looked at the expression of fifteen immune-related genes,
in the intestine. These included genes for lectins and other antimicrobial peptides. (See Dec 2003 #453, Nov 2006 #558 for lectins and also Aug 2009 #707 for a review of shrimp immunity.)
Although the expression of some of these genes did change as a result of infection the actual defense mechanism was local and had a histological basis. Sections of the gut wall were rapidly and severely damaged by the pathogen, as a result of which "necrotic and massive hemocyte infiltration occurred underneath the affected tissue to combat the infection". If the bacteria were cleared out the shrimp survived. Some of the changing gene expression was functionally associated with this process.
"Among the examined genes, only the C-lectin was continuously increased until the end of the experiment (48 h after a bacterial challenge)." See May 2000 #55 for a patent for generating transgenic catfish and carp (koi) containing a silk moth gene which produces cecropin-B, a lectin molecule which can function as a built-in fungicide and bactericide. pikul.jir<%>biotec.or.th
710. Fitness traits do have lower additive genetic variance.
R A Fisher finally wins.
Heritability of fitness components in a wild bird population. 2009. Teplitsky, C., J. A. Mills, J. W. Yarrall and J. Merilä. Evolution 63:716-726.
Fisher's fundamental theorem of natural selection leads us to expect that traits closely associated with fitness (fecundity, survival) should have lower genetic variance than other traits because, at the time of observation, they will have evolved about as far as far as they can go under strong directional selection.
Field observations do often show that fitness traits have lower heritability (h2 = ratio of additive genetic to total variance).
This is rarely because additive genetic variance is reduced. Heritability
appears to be lower because other sources of variation (the denominator of
the ratio) are higher in fitness traits.
This paper found
something different and more in line with Fisherian expectation. A large number of fitness and non-fitness traits were studied in seven generations of data from a population of gulls in New Zealand.
"In contrast to earlier findings... we found that reduced heritabilities of fitness traits were not only due to increased residual variance, but also due to a decreased additive genetic variance per se".
Part of what makes this interesting on a technical level is the inclusion of terms for common-environment effects in the animal
model. These were female identity and where possible individual identity, both terms unlinked to the pedigree. Also,
the authors normalized the analysis by using coefficients of variation to scale the variance relative to the mean, in an attempt to provide sensible comparisons of variance components.
The thorough presentation of the model and discussion of issues in interpretation makes this study essential reading for everyone working on the quantitative genetics of wild or semi-wild populations. The authors caution that such studies are still very few and that their own results should not be generalized too far, but "at least in the case of additive genetic variance in this study, all used measures returned a consistent and clear suggestion that life-history traits exhibit lower heritabilities and less additive genetic variance than morphological traits. teplitsky<%>mnhn.fr
709. Software for using markers to estimate REML BLUPs
Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood. 2007. Zhang, Z., R. J. Todhunter, E. S. Buckler and L. D. Vleck. Journal of Animal Science 85:881-886.
Here we have a useful addition to the MTDFREML program for estimating multiple-trait breeding values and variance components. Marker data can
now be used instead of pedigree data in MTDFREML. Those who have used the
program know that it consists of several linked programs that are run sequentially. The job of the first program in the sequence is to calculate the inverse of the relationship matrix, using pedigree data as input. This paper
introduces a new first program, MTDFARM, in which you input the relationship matrix itself to produce the same output as the original first program. The coefficients of the matrix can be estimated from marker data (see e.g. Apr 2008 #651). The FORTRAN code for MTDFREML is available from lvanvleck<%>unlnotes.unl.edu and MTDFARM from zz19<%>cornell.edu.
I haven't tried MTDFARM
yet myself but it seems straightforward and the paper is clearly written. lvanvleck<%>unlnotes.unl.edu
708. Estimate breeders from offspring microsatellites
in aquaculture and conservation
Nb_HetEx: A program to estimate the effective number of breeders. 2008. Zhdanova, O. L. and A. I. Pudovkin. Journal of Heredity 99:694-695.
The estimation procedure
described in this paper will be useful for one-pass appraisals of aquaculture breeding programs as well as appraisals of endangered wild populations. It is based on the fact that when there are only a few breeders an excess of heterozygotes in the offspring can be detected and used to count the effective number of parents. The authors say that 200 offspring should be sampled and that the total number of independent alleles must exceed 80. Apparently the effective number of breeders can be as high as 30 or so when mating is random and perhaps 20 when breeding is more structured.
The program is available at ftp://ftp.dvo.ru/pub/Personal/NB-Estimator . It also estimates Ne by Waples's temporal method if two samples are available. (See also Nov 2006 #553 for Waples's single sample method based on linkage disequilibrium.). axanka<%>iacp.dvo.ru