Influence of porcine genotype on the abundance of thyroid hormones and leptin in sow milk and its impact on growth, metabolism and expression of key adipose tissue genes in offspring

Neonatal mortality is greater in commercial porcine genotypes, compared with the ancient Meishan breed that rapidly lay down adipose tissue; this may be related to hormones, such as triiodothyronine (T3) or leptin. Leptin is present in maternal milk; however, the extent to which this supply provides the neonate with leptin is unknown, but may play a role in growth and development. We investigated whether thyroid hormones and leptin concentrations in maternal milk differed between genotypes; and whether this influenced piglet concentrations or expression of genes involved in adipose tissue regulation. Eight Meishan and six commercial sows were entered into the study and milk samples from the day of parturition to day 4 postpartum was taken daily. The median birth weight piglet in each litter had a daily venous blood sample taken and was euthanised on day 4. Gene expressions of IGF-I, IGF-binding protein 3 (IGFBP-3), peroxisome proliferators activated receptor (PPAR) and glucocorticoid receptor (GR) were measured in adipose tissue using real-time PCR. T3 was increased in Meishan milk, but not in piglet plasma. Milk thyroxine was similar between breeds but commercial piglet levels were significantly higher. Leptin was higher in commercial sow milk throughout the study. Milk leptin was strongly correlated to plasma leptin during the first postnatal days and also to organ and body weight in Meishan piglets that also had significantly higher expression of GR, but not IGF-I, IGFBP-3 or PPAR. In conclusion, we have found a significant disparity in the provision of thyroid hormones in Meishan and commercial sow’s milk. These changes are not always translated to plasma concentrations of hormone in the piglet. Leptin appears to have a stronger role in growth and development in the Meishan genotype compared with commercial; along with the increased GR expression, this may also represent a potential mechanism behind the rapid accumulation of adipose tissue in Meishan piglets.

Effect of species and genotype on the efficiency of enrichment of poultry meat with n-3 polyunsaturated fatty acids

The effect of poultry species (broiler or turkey) and genotype (Wrolstad or BUT T8 turkeys and Ross 308 or Cobb 500 broilers) on the efficiency with which dietary longchain n-3 PUFA were incorporated into poultry meat was determined. Broilers and turkeys of both genotypes were fed one of six diets varying in FA composition (two replicates per genotype x diet interaction). Diets contained 50 g/kg added oil, which was either blended vegetable oil (control), or partially replaced with linseed oil (20 or 40 g/kg diet), fish oil (20 or 40 g/kg diet), or a mixture of the two (20 g linseed oil and 20 g fish oil/kg diet). Feeds and samples of skinless breast and thigh meat were analyzed for FA. Wrolstad dark meat was slightly more responsive than BUT T8 (P = 0.046) to increased dietary 18:3 concentrations (slopes of 0.570 and 0.465, respectively). The Ross 308 was also slightly more responsive than the Cobb 500 (P= 0.002) in this parameter (slopes of 0.557 and 0.449). There were no other significant differences between the genotypes. There was some evidence (based on the estimates of the slopes and their associated standard errors) that white turkey meat was more responsive than white chicken meat to 20:5 (slopes of 0.504 and 0.289 for turkeys and broilers, respectively). There was no relationship between dietary 18:3 n-3 content and meat 20:5 and 22:6 contents. If birds do convert 18:3 to higher FA, these acids are not then deposited in the edible tissues.

The survival, growth and carcase characteristics of crossbred beef cattle in Tanzania

Sires of seven Bos taurus beef breeds were mated with Bos indicus Boran cows at two sites, one near sea level and the other at about 1000 m altitude, and over three years. Purebred Boran calves provided controls for comparisons between sire breeds for growth to 4 years of age, mortality and carcase characteristics in a range environment where all the animals were kept under a similar management regime. Numerous sire breed x site, sire breed x year of birth and site x year of birth interactions were established. Mortality was high, but there was no significant sire breed effect, although purebred Borans had a higher survival than crossbred calves. There was no significant difference between genotypes in birth weight. Generally, Bos taurus cross steers achieved greater live weight gains and heavier carcase weights at 4 years of age than did purebred Borans. Limousin-cross steers had significantly (p<0.05) less fat in the tenth rib sample joint than any of the other genotypes. A productivity index that combined calf survival and carcase weight indicated that the Chianina crosses were more productive than any other genotype at either site. Purebred Borans were more productive than all the Bos taurus crossbreds with the exception of the Chianina crosses at site 1, but were only superior to the Limousin crosses at site 2, which was at the higher altitude. When lean meat yield was introduced into the productivity index, the Boran purebreds were the least productive at site 2.

A model of seed dormancy in wild oats (Avena fatua) for investigating genotype x environment interactions

Dormancy is an adaptive trait in seed populations that helps ensure that seed germination is distributed over time and occurs in environmental conditions suitable for seedling growth. Several genes.. associated with seed dormancy in various plant species, have been integrated into a hypothetical dormancy model for Avena fatua L. (wild oats). Generally, the synthesis of, and sensitivity to, abscisic acid (ABA) during imbibition determines whether genes similar to those during maturation are expressed leading to a maintenance of dormancy during extended imbibition. Alternatively, there may be a shift towards expression of genes associated with gibberellins leading to germination. Environmental factors during maturation, after-ripening and imbibition are likely to interact with the genotype to affect gene expression and hence whether or not a seed germinates. In spite of the difficulties of working on a hexaploid species, A. fatua was selected for study because of its worldwide importance as a weed. Dormant and non-dormant genotypes of this species were also available. Gene expression studies are being carried out on three A.fatua genotypes produced tinder different environmental conditions to investigate the role of specific genes in dormancy and genotype X environment interactions in relation to dormancy.

A novel transcriptomic approach to identify candidate genes for grain quality traits in wheat

A novel methodology is described in which transcriptomics is combined with the measurement of bread-making quality and other agronomic traits for wheat genotypes grown in different environments (wet and cool or hot and dry conditions) to identify transcripts associated with these traits. Seven doubled haploid lines from the Spark x Rialto mapping population were selected to be matched for development and known alleles affecting quality. These were grown in polytunnels with different environments applied 14 days post-anthesis, and the whole experiment was repeated over 2 years. Transcriptomics using the wheat Affymetrix chip was carried out on whole caryopsis samples at two stages during grain filling. Transcript abundance was correlated with the traits for approximately 400 transcripts. About 30 of these were selected as being of most interest, and markers were derived from them and mapped using the population. Expression was identified as being under cis control for 11 of these and under trans control for 18. These transcripts are candidates for involvement in the biological processes which underlie genotypic variation in these traits.

Tolerance traits and the stability of mutualism

Identifying factors which allow the evolution and persistence of cooperative interactions between species is a fundamental issue in evolutionary ecology. Various hypotheses have been suggested which generally focus on mechanisms that allow cooperative genotypes in different species to maintain interactions over space and time. Here, we emphasise the fact that even within mutualisms (interactions with net positive fitness effects for both partners), there may still be inherent costs, such as the occasional predation by ants upon aphids. Individuals engaged in mutualisms benefit from minimising these costs as long as it is not at the expense of breaking the interspecific interaction, which offers a net positive benefit. The most common and obvious defence traits to minimise interspecific interaction costs are resistance traits, which act to reduce encounter rate between two organisms. Tolerance traits, in contrast, minimise fitness costs to the actor, but without reducing encounter rate. Given that, by definition, it is beneficial to remain in mutualistic interactions, the only viable traits to minimise costs are tolerance-based 'defence' strategies. Thus, we propose that tolerance traits are an important factor promoting stability in mutualisms. Furthermore, because resistance traits tend to propagate coevolutionary arms races between antagonists, whilst tolerance traits do not, we also suggest that tolerance-based defence strategies may be important in facilitating the transition from antagonistic interactions into mutualisms. For example, the mutualism between ants and aphids has been suggested to have evolved from parasitism. We describe how phenotypic plasticity in honeydew production may be a tolerance trait that has prevented escalation into an antagonistic arms race and instead led to mutualistic coevolution.

Action following the discovery of a global association between the whole genome and adverse event risk in a clinical drug-development programme

Observation of adverse drug reactions during drug development can cause closure of the whole programme. However, if association between the genotype and the risk of an adverse event is discovered, then it might suffice to exclude patients of certain genotypes from future recruitment. Various sequential and non-sequential procedures are available to identify an association between the whole genome, or at least a portion of it, and the incidence of adverse events. In this paper we start with a suspected association between the genotype and the risk of an adverse event and suppose that the genetic subgroups with elevated risk can be identified. Our focus is determination of whether the patients identified as being at risk should be excluded from further studies of the drug. We propose using a utility function to? determine the appropriate action, taking into account the relative costs of suffering an adverse reaction and of failing to alleviate the patient's disease. Two illustrative examples are presented, one comparing patients who suffer from an adverse event with contemporary patients who do not, and the other making use of a reference control group. We also illustrate two classification methods, LASSO and CART, for identifying patients at risk, but we stress that any appropriate classification method could be used in conjunction with the proposed utility function. Our emphasis is on determining the action to take rather than on providing definitive evidence of an association. Copyright (C) 2008 John Wiley & Sons, Ltd.

ONeSAMP: a program to estimate effective population size using approximate Bayesian computation

The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web-based program, ONeSAMP that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. ONeSAMP requires an input file of sampled individuals' microsatellite genotypes along with information about several sampling and biological parameters. ONeSAMP provides an estimate of effective population size, along with 95% credible limits. We illustrate the use of ONeSAMP with an example data set from a re-introduced population of ibex Capra ibex.

Diversity, phylogeny and distribution of bean rhizobia in salt-affected soils of North-West Morocco

Different molecular methods: BOX-PCR fingerprinting, R-FLP-PCR and sequencing of the 16S rDNA as well as the symbiotic genes nodC and nifH, were used to study the genetic diversity within a collection of nodulating bean rhizobia isolated from five soils of North-West Morocco. BOX fingerprints analysis of 241 isolates revealed 19 different BOX profiles. According to the PFLP-PCR and sequencing of 16S rDNA carried out on 45 representative isolates, 5 genotypes were obtained corresponding to the species Rhizobium etli, R. tropici, R. gallicum, R. leguminosarum and Sinorhizobium meliloti. The most abundant species were R. etli and R. tropici (61% and 24%, respectively). A high intraspecific diversity was observed among the R. etli isolates, while the R. tropici group was homogeneous. Most of the rhizobia studied belong to species known to nodulate common bean, while 2 species were unconventional microsymbionts: R. leguminosarum biovar viciae and S. meliloti. Our results, especially the nodulation promiscuity of common bean and the relation between the predominance of some species of rhizobia in particular soils and the salt content of these soils, indicate that there is a real need for a better understanding of the distribution of common bean rhizobia species in the soils of Morocco before any inoculation attempt.

Adventitious root formation in anacardium occidentale L. in response to phytohormones and removal of roots

Despite advances in tissue culture techniques, propagation by leafy, softwood cuttings is the preferred, practical system for vegetative reproduction of many tree and shrub species. Species are frequently defined as 'difficult'- or 'easy-to-root' when propagated by conventional cuttings. Speed of rooting is often linked with ease of propagation, and slow-to-root species may be 'difficult' precisely because tissues deteriorate prior to the formation of adventitious roots. Even when roots form, limited development of these may impair the establishment of a cutting. In this study we used softwood cuttings of cashew (Anacardium occidentale), a species considered as 'difficult-to-root'. We aimed to test the hypothesis that speed, and extent of early rooting, is critical in determining success with this species; and that the potential to form adventitious roots will decrease with time in the propagation environment. Using two genotypes, initial rooting rates were examined in the presence or absence of exogenous auxin. In cuttings that formed adventitious roots, either entire roots or root tips were removed, to determine if further root formation/development was feasible. To investigate if subsequent root responses were linked to phytohormone action, a number of cuttings were also treated with either exogenous auxin (indole-3-butyric acid-IBA) or cytokinin (zeatin). Despite the reputation of Anacardium as being 'difficult-to-root', we found high rooting rates in two genotypes (AC 10 and CCP 1001). Removing adventitious roots from cuttings and returning them to the propagation environment, resulted in subsequent re-rooting. Indeed, individual cuttings could develop new adventitious roots on four to five separate occasions over a 9 week period. Data showed that rooting potential increased, not decreased with time in the propagation environment and that cutting viability was unaffected. Root expression was faster (8-15 days) after the removal of previous roots compared to when the cuttings were first stuck (21 days). Exposing cuttings to IBA at the time of preparation, improved initial rooting in AC 10, but not in CCP 1001. Application of IBA once roots had formed had little effect on subsequent development, but zeatin reduced root length and promoted root number and dry matter accumulation. These results challenge our hypothesis, and indicate that rooting potential remains high in Anacardium. The precise mechanisms that regulate the number of adventitious roots expressed, remain to be determined. Nevertheless, results indicate that rooting potential can be high in 'difficult-to-root' species, and suggest that providing supportive environments is the key to expressing this potential. (c) 2006 Elsevier B.V. All rights reserved.

The population genetic structure of clonal organisms generated by exponentially bounded and fat-tailed dispersal

Long distance dispersal (LDD) plays an important role in many population processes like colonization, range expansion, and epidemics. LDD of small particles like fungal spores is often a result of turbulent wind dispersal and is best described by functions with power-law behavior in the tails ("fat tailed"). The influence of fat-tailed LDD on population genetic structure is reported in this article. In computer simulations, the population structure generated by power-law dispersal with exponents in the range of -2 to -1, in distinct contrast to that generated by exponential dispersal, has a fractal structure. As the power-law exponent becomes smaller, the distribution of individual genotypes becomes more self-similar at different scales. Common statistics like G(ST) are not well suited to summarizing differences between the population genetic structures. Instead, fractal and self-similarity statistics demonstrated differences in structure arising from fat-tailed and exponential dispersal. When dispersal is fat tailed, a log-log plot of the Simpson index against distance between subpopulations has an approximately constant gradient over a large range of spatial scales. The fractal dimension D-2 is linearly inversely related to the power-law exponent, with a slope of similar to -2. In a large simulation arena, fat-tailed LDD allows colonization of the entire space by all genotypes whereas exponentially bounded dispersal eventually confines all descendants of a single clonal lineage to a relatively small area.

Characterization and PCR multiplexing of polymorphic microsatellite loci in cashew (Anacardium occidentale L.) and their cross-species utilization

Cashew (Anacardium occidentale L.) is the most economically important tropical nut crop in the world, and yet there are no sequence tagged site (STS) markers available for its study. Here we use an automated, high-throughput system to isolate cashew microsatellites from a non-enriched genomic library blotted onto membranes at high density for screening. Sixty-five sequences contained a microsatellite array, of which 21 proved polymorphic among a closely related seed garden population of 49 genotypes. Twelve markers were suitable for multiplex analysis. Of these, 10 amplified in all three related tropical tree species tested: Anacardium microcarpum, Anacardium pumilum and Anacardium nanum.

Evaluation of cacao (Theobroma cacao L.) clones against seven Colombian isolates of Moniliophthora roreri (Cif.) Evans et al., representing four major genetic groupings of the pathogen in cacao

Artificial pod inoculation was used to compare the relative aggressiveness of seven Colombian isolates of Moniliophthora roreri (the causal agent of moniliasis or frosty pod disease), representing four major genetic groupings of the pathogen in cacao (cocoa), when applied to five diverse cacao genotypes (ICS-1, ICS-95, TSH-565, SCC-61 and CAP-34) at La Suiza Experimental Farm, Santander Department, Colombia. The following variables were evaluated 9 weeks after inoculation of 2- to 3-month-old pods with spore suspensions (1.2 x 10(5) spores mL(-1)): (i) disease incidence (DI); (ii) external severity (ES); and (iii) internal severity (IS). IS was found to be of greatest value in classifying the reaction of the host genotype against M. roreri. Genetic variation reported between isolates and cacao genotypes was not matched by similar diversity in their aggressiveness. All isolates were generally highly aggressive against most cacao genotypes, with only two isolates showing reduced IS and ES reactions. There was considerable variation between clones in the IS and ES scores, but one cultivated clone (ICS-95) displayed a significant level of resistance against all seven isolates. This clone may be useful in cacao breeding initiatives for resistance to moniliasis of cacao.

Cryopreservation of cocoa (Theobroma cacao L.) somatic embryos for long-term germplasm storage

Cryopreservation using encapsulation-dehydration was developed for the long-term conservation of cocoa (Theobroma cacao L.) germplasm. Survival of individually encapsulated somatic embryos after desiccation and cryopreservation was achieved through optimization of cryoprotectants (abscisic acid (ABA) and sugar), duration of osmotic and evaporative dehydration, and embryo development stage. Up to 63% of the genotype SPA4 early-cotyledonary somatic embryos survived cryopreservation following 7 days preculture with 1 M sucrose and 4 h silica exposure (16% moisture content in bead). This optimized protocol was successfully applied to three other genotypes, e.g. EET272, IMC14 and AMAZ12, with recovery frequencies of 25, 40 and 72%, respectively (but the latter two genotypes using 0.75 M sucrose). Recovered SPA4 somatic embryos converted to plants at a rate of 33% and the regenerated plants were phenotypically comparable to non-cryopreserved somatic embryo-derived plants.

Evidence for a residual postglacial founder effect in a highly dispersive freshwater invertebrate

In the northern hemisphere, glacial periods have had profound and lasting effects on the population genetics of numerous species, with founder effects often persisting for many generations in formerly glaciated regions. We found an unusual example of this in the freshwater bryozoan Cristatella mucedo, which showed regional differences in haplotype diversity with relatively low levels of haplotype diversity in northern Europe compared to central/southern Europe despite previous evidence for frequent dispersal between C. mucedo populations. Such contradictions between high dispersal and low gene flow have now been reported in several other freshwater taxa and may be attributed to persistent founder effects following colonization of sites by a few individuals whose efficient reproduction leads to rapid population growth. Alternatively, selection may determine which genotypes can thrive in northerly locations, or it may be that C. mucedo has undergone cryptic speciation. Future work on adaptive genomic regions is required before we can understand how gene flow, local adaptation, and speciation influence the current distribution patterns of bryozoans and other freshwater invertebrates.