Application of DNA parentage analyses for determining relative growth rates of Penaeus japonicus families reared in commercial ponds

The ability to track large numbers of individuals and families is a key determinant of the power and precision of breeding programs, including the capacity to quantify interactions between genotypes and their environment. Until recently, most family based selective breeding programs for shrimp, and other highly fecund aquaculture species, have been restricted by the number of animals that can be physically tagged and individually selected. Advances in the development of molecular markers, such as microsatellite loci, are now providing the means to track large numbers of individuals and families in commercial production systems. In this study microsatellites, coupled with DNA parentage analyses, were used to determine the relative performance of 22 families of R japonicus reared in commercial production ponds. In the experimental design 6000 post-larvae from each of 22 families, whose maternal parents had been genotyped at 8 microsatellite loci, were stocked into each of four I ha ponds. After 6 months the ponds were harvested and a total of 6000 individuals were randomly weighed from each pond. Mean wet weight of the shrimp from one pond was significantly lower than that of the other three ponds demonstrating a possible pond effect on growth rate. The representation of families in the top 10% of each pond's weight distribution was then determined by randomly genotyping up to 300 individuals from this upper weight class. Parentage analyses based on individual genotypic data demonstrated that some families were over-represented in the top 10% in all ponds, while others were under-represented due to slower growth rates. The results also revealed some weak, but significant, male genotype x environment (G x E) interactions in the expression of shrimp growth for some families. This indicates that G x E effects may need to be factored into future R japonicus selective breeding programs. This study demonstrated the utility of DNA parentage analyses for tracking individual family performance in communally stocked shrimp pond populations and, its application to examining G x E effects on trait expression under commercial culture conditions. Crown Copyright (c) 2005 Published by Elsevier B.V. All rights reserved.

The effectiveness of heat, cold and 6-dimethylaminopurine shocks for inducing tetraploidy in the Kuruma shrimp, Marsupenaeus japonicus (Bate)

In this study tetraploid Marsupenaeus japonicus (Bate) embryos were produced by preventing the first division in mitosis. The effectiveness of temperature and chemical shocks for producing tetraploid M. japonicus were assessed when applied at different times postspawning and for different durations. Tetraploid M. japonicus embryos (spawned at 27 degrees C) were produced by heat shocks at 35 degrees C and 36 degrees C in three and eight spawning samples respectively, and a cold shock at 5 degrees C in a single spawning sample. All temperature shocks inducing tetraploidy were applied 18-23 min postspawning for a 5-10 min duration. The percentage of spawnings successfully inducing tetraploid embryos (i.e., frequency of induction) ranged from 33.33% to 66.67% for the 21, 22 and 23 min postspawning heat shock treatment regimes. The percentage of tetraploid embryos within an induction (i.e., induction rate), as determined by flow cytometry, ranged from 8.82% to 98.12% (ave. S.E.) (34.4 +/- 21.4%) for the 35 degrees C shock treatments, from 13.12% to 61.02% (35.0 +/- 5.0%) for the 36 degrees C shock treatments and was 15% for the 5 degrees C cold shock treatment. No tetraploids were produced for spawnings that received heat shocks above 36 degrees C or below 35 degrees C, or for cold shocks above 5 degrees C for any of the tested postspawning treatment and duration times. Chemical shock with 150 mu M 6-dimethylaminopurine did not result in tetraploid M. japonicus embryos at any of the tested postspawning treatment times and durations. Tetraploid M. japonicus embryos were nonviable, with no tetraploid larvae being detected by flow cytometry. Based on our results heat shocking of M. japonicus embryos at 36 degrees C, 23 min postspawning for a 5-10 min duration is the most effective means to produce tetraploids through inhibition of the first mitotic division (taking into consideration the importance of frequency and induction rate equally).

Selection for muscle fat content and triploidy affect flesh quality in pan-size rainbow trout, Oncorhynchus mykiss

A lean muscle line (L) and a fat muscle line (F) of rainbow trout were established (Quillet et al., 2005) by a two-way selection for muscle lipid content performed on pan-size rainbow trout using a non-destructive measurement of muscle lipid content (Distell Fish Fat Meter®). The aim of the present study was to evaluate the consequences of this selective breeding on flesh quality of pan size (290 g) diploid and triploid trout after three generations of selection. Instrumental evaluations of fillet color and pH measurement were performed at slaughter. Flesh color, pH, dry matter content and mechanical resistance were measured at 48 h and 96 h postmortem on raw and cooked flesh, respectively. A sensorial profile analysis was performed on cooked fillets. Fillets from the selected fatty muscle line (F) had a higher dry matter content and were more colorful for both raw and cooked fillets. Mechanical evaluation indicated a tendency of raw flesh from F fish to be less firm, but this was not confirmed after cooking, neither instrumentally or by sensory analysis. The sensory analysis revealed higher fat loss, higher intensity of flavor of cooked potato, higher exudation, higher moisture content and a more fatty film left on the tongue for flesh from F fish. Triploid fish had mechanically softer raw and cooked fillets, but the difference was not perceived by the sensorial panel. The sensorial evaluation also revealed a lower global intensity of odor, more exudation and a higher moisture content in the fillets from triploid fish. These differences in quality parameters among groups of fish were associated with larger white muscle fibers in F fish and in triploid fish. The data provide additional information about the relationship between muscle fat content, muscle cellularity and flesh quality.

Acute phase proteins and biomarkers for health in chickens

Acute phase proteins (APPs) are proteins synthesised predominantly in the liver, whose plasma concentrations increase (positive APP) or decrease (negative APP) as a result of infection, inflammation, trauma and tissue injury. They also change as a result of the introduction of immunogens such as bacterial lipopolysaccharide (LPS), turpentine and vaccination. While publications on APPs in chickens are numerous, the limited availability of anti-sera and commercial ELISAs has resulted in a lot of information on only a few APPs. Disease is a threat to the poultry industry, as pathogens have the potential to evolve, spread and cause rapid onset of disease that is detrimental to the welfare of birds. Low level, sub-acute disease with non-specific, often undiagnosed causes can greatly affect bird health and growth and impact greatly on productivity and profitability. Developing and validating methods to measure and characterise APPs in chickens will allow these proteins to be used diagnostically for monitoring flock health. Using immune parameters such as APPs that correlate with disease resistance or improvements in production and welfare will allow the use of APPs as selection parameters for breeding to be evaluated. For APPs to be useful parameters on which to evaluate chicken health, information on normal APP concentrations is required. Ceruloplasmin (Cp) and PIT54 concentrations were found to be much lower in healthy birds form commercial production farms than the reported normal values obtained from the literature. These APPs were found to be significantly higher in culled birds from a commercial farm and Cp, PIT54 and ovotransferrin (Ovt) were significantly higher in birds classified as having obvious gait defects. Using quantitative shotgun proteomics to identify the differentially abundant proteins between three pools: highly acute phase (HAP), acute phase (AP) and non-acute phase (NAP), generated data from which a selection of proteins, based on the fold difference between the three pools was made. These proteins were targeted on a individual samples alongside proteins known to be APPs in chickens or other species: serum amyloid A (SAA), C-reactive protein (CRP), Ovt, apolipoprotein A-I (apo-AI), transthyretin (Ttn), haemopexin (Hpx) and PIT54. Together with immunoassay data for SAA, Ovt, alpha-1-acid glycoprotein (AGP) and Cp the results of this research reveal that SAA is the only major APP in chickens. Ovotransferrin and AGP behave as moderate APPs while PIT54 and Cp are minor APPs. Haemopexin was not significantly different between the three acute phase groups. Apolipoprotein AI and Ttn were significantly lower in the HAP and AP groups and as such can be classed as negative APPs. In an effort to identify CRP, multiple anti-sera cross reacting with CRP from other species were used and a phosphorylcholine column known to affinity purify CRP were used. Enriched fractions containing low molecular weight proteins, elutions from the affinity column together with HAP, AP and NAP pooled samples were applied to a Q-Exactive Hybrid Quadrupole–Orbitrap mass spectrometer (Thermo Scientific) for Shotgun analysis and CRP was not identified. It would appear that CRP is not present as a plasma protein constitutively or during an APR in chickens and as such is not an APP in this species. Of the proteins targeted as possible novel biomarkers of the APR in chickens mannan binding lectin associated serine protease-2, α-2-HS-glycoprotein (fetuin) and major facilitator superfamily domain-containing protein 10 were reduced in abundance in the HAP group, behaving as negative biomarkers. Myeloid protein and putative ISG(12)2 were positively associated with the acute phase being significantly higher in the HAP and AP groups. The protein cathepsin D was significantly higher in both HAP and AP compared to the NAP indicating that of all the proteins targeted, this appears to have the most potential as a biomarker of the acute phase, as it was significantly increased in the AP as well as the HAP group. To evaluate APPs and investigate biomarkers of intestinal health, a study using re-used poultry litter was undertaken. The introduction of litter at 12 days of age did not significantly increase any APPs measured using immunoassays and quantitative proteomics at 3, 6 and 10 days post introduction. While no APP was found to be significantly different between the challenged and control groups at anytime point, the APPs AGP, SAA and Hpx did increase over time in all birds. The protein apolipoprotein AIV (apo-AIV) was targeted as a possible APP and because of its reported role in controlling satiety. An ELISA was developed, successfully validated and used to measure apo-AIV in this study. While no significant differences in apo-AIV plasma concentrations between challenged and control groups were identified apo-AIV plasma concentrations did change significantly between certain time points in challenged and control groups. Apoliporotein AIV does not appear to behave as an APP in chickens, as it was not significantly different between acute phase groups. The actin associated proteins villin and gelsolin were investigated as possible biomarkers of intestinal health. Villin was found not to be present in the plasma of chickens and as such not a biomarker target. Gelsolin was found not to be differentially expressed during the acute phase or as a result of intestinal challenge. Finally a proteomic approach was undertaken to investigate gastrocnemius tendon (GT) rupture in broiler chickens with a view of elucidating to and identify proteins associated with risk of rupture. A number of proteins were found to be differentially expressed between tendon pools and further work would enable further detailing of these findings. In conclusion this work has made a number of novel findings and addressed a number of data poor areas. The area of chicken APPs research has stagnated over the last 15 years with publications becoming repetitive and reliant on a small number of immunoassays. This work has sought to characterise the classic APPs in chickens, and use a quantitative proteomic approach to measure and categorise them. This method was also used to take a fresh approach to biomarker identification for both the APR and intestinal health. The development and validation of assays for Ovt and apo-AIV and the shotgun data mean that these proteins can be further characterised in chickens with a view of applying their measurement to diagnostics and selective breeding programs.

Polynesian pearls

Black-lip pearl oyster culture in French Polynesia is still based on natural spat collection from wild stocks, but new developments in hatchery technology and selective breeding are bringing substantive change to the sector.

Growth of native trees in two agroforestry systems.

Agroforestry systems with eucalyptus prevail in Central and Southeast Brazil, and little information is available about systems using native trees. The aim of the present study was to evaluate the development of seven native tree species grown under two agroforestry systems. The experiment was conducted starting in 2007 in 12-hectare area in the municipality of São Carlos, São Paulo state, Brazil. The tree species planted in the two systems (a silvopastoral system and an agrisilvicultural system) were: 'capixingui' (Croton floribundus) and 'mutambo' (Guazuma ulmifolia) (tutors), 'jequitibá-branco' (Cariniana estrellensis), 'canafistula' (Peltophorum dubium) and 'ipê felpudo' (Zeyheria tuberculosa) (timber trees), and 'angico-branco' (Anadenanthera colubrina) and 'pau-jacaré' (Piptadenia gonoacantha) (N-fixing trees). Data were collected for 48 months. The results show differences among tree development, which was evaluated as growth in height and diameter, as well as sensitivity to insect and disease damage. The overall results show that the agrisilvicultural system allowed better tree development. The species with best performance in the two systems were capixingui, mutambo and canafístula. Ipê-felpudo and jequitibá-branco showed the worst results. The high variability among individuals of the same species indicates the possibility of high production advances with selective breeding of these species.

Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Mud-packing frog: A novel breeding behaviour and parental care in a stream dwelling new species of Nyctibatrachus (Amphibia, Anura, Nyctibatrachidae)

Reproductive modes are diverse and unique in anurans. Selective pressures of evolution, ecology and environment are attributed to such diverse reproductive modes. Globally forty different reproductive modes in anurans have been described to date. The genus Nyctibatrachus has been recently revised and belongs to an ancient lineage of frog families in the Western Ghats of India. Species of this genus are known to exhibit mountain associated clade endemism and novel breeding behaviours. The purpose of this study is to present unique reproductive behaviour, oviposition and parental care in a new species Nyctibatrachus kumbara sp. nov. which is described in the paper. Nyctibatrachus kumbara sp. nov. is a medium sized stream dwelling frog. It is distinct from the congeners based on a suite of morphological characters and substantially divergent in DNA sequences of the mitochondrial 16S rRNA gene. Males exhibit parental care by mud packing the egg clutch. Such parental care has so far not been described from any other frog species worldwide. Besides this, we emphasize that three co-occurring congeneric species of Nyctibatrachus, namely N. jog, N. kempholeyensis and Nyctibatrachus kumbara sp. nov. from the study site differ in breeding behaviour, which could represent a case of reproductive character displacement. These three species are distinct in their size, call pattern, reproductive behaviour, maximum number of eggs in a clutch, oviposition and parental care, which was evident from the statistical analysis. The study throws light on the reproductive behaviour of Nyctibatrachus kumbara sp. nov. and associated species to understand the evolution and adaptation of reproductive modes of anurans in general, and Nyctibatrachus in particular from the Western Ghats.

Polychlorinated Biphenyl DDT And Dieldrin Residues In Grey Seal (Halichoerus-Grypus) Males Females And Mother-Foetus Pairs Sampled At The Farne Islands England During The Breeding-Season

PCB, DDT, DDE, dieldrin and total non-polar organohalogen residues have been determined in the blubber-lipid of grey seals (Halichoerus grypus) sampled during the 1972 breeding season (November) at the Farne Islands off the north eastern coast of England. PCBs were analysed by gas-liquid chromatography linked to a chlorine- and carbon-selective microwave plasma detector and total organohalogen residues were determined by microcoulometry. Total organohalogen residues were negatively correlated with blubber thickness and positively correlated with age in males (aged 1 to 24 y) and females (aged 5 to 38 y). However, the correlation of blubber-lipid residue with age in males depended upon the inclusion of immature (aged < 6 y) animals, and in females reflected only a small residue increment. The mean blubber organohalogen concentration of the males was significantly greater than that of the females. PCB and DDT group residue concentrations were significantly correlated. PCB, DDT, DDE and dieldrin were detected in the liver of mother/foetus pairs demonstrating transplacental movement of these residues. The possibility of the condition of the seals at breeding time influencing residue levels and of these residues influencing the health of the population is discussed.

Size-Dependent Selective Mechanisms on Males and Females and the Evolution of Sexual Size Dimorphism in Frogs

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mothers adjust egg size to helper number in a cooperatively breeding cichlid

Mothers should adjust the size of propagules to the selective forces to which these offspring will be exposed. Usually, a larger propagule size is favored when young are exposed to high mortality risk or conspecific competition. Here we test 2 predictions on how egg size should vary with these selective agents. When offspring are cared for by parents and/or alloparents, protection may reduce the predation risk to young, which may allow mothers to invest less per single offspring. In the cooperatively breeding cichlid Neolamprologus pulcher, brood care helpers protect group offspring and reduce the latters' mortality rate. Therefore, females are expected to reduce their investment per egg when more helpers are present. In a first experiment, we tested this prediction by manipulating the helper number. In N. pulcher, helpers compete for dispersal opportunities with similar-sized individuals of neighboring groups. If the expected future competition pressure on young is high, females should increase their investment per offspring to give them a head start. In a second experiment, we tested whether females produce larger eggs when perceived neighbor density is high. Females indeed reduced egg size with increasing helper number. However, we did not detect an effect of local density on egg size, although females took longer to produce the next clutch when local density was high. We argue that females can use the energy saved by adjusting egg size to reduced predation risk to enhance future reproductive output. Adaptive adjustment of offspring size to helper number may be an important, as yet unrecognized, strategy of cooperative breeders.

Genetic effect of domestication selective pressures on Pacific oyster at larval stage

Among bivalve species, the Pacific oyster, Crassostrea gigas, is the most economically important bivalve production over the world. Today, C. gigas is subject to an important production effort that leads to an intensive artificial selection. Larval stage is relatively unknown, specifically in a domestication context. Genetic consequence of artificial selection is still at a preliminary study. We aimed to tackle the consequence of inconscient domestication on the variance reproductive success focusing on larval stage, keystone of the life cycle. We studied two kinds of specific selective processes that common hatchery rearing practices exert : the effect of discarding the smallest larvae on genetic diversity and the artificial environment rearing effect via the temperature providing a contrast resembling wild versus hatchery conditions (20 and 26°C). In order to monitor the effect of the selection of fast growing larvae by sieving, growth variability and genetic diversity in a larval population descended from a factorial breeding was studied. We used a mixed-family approach to reduce potentially confounding environmental biais. The retrospective assignment of individuals to family groups has been performed using a three microsatellite markers set. Two different rearing were carried out in parallel. For three (replicates) 50-l tanks, the smallest larvae were progressively discarded by selective sieving, whereas for the three others no selective sieving was performed. The intensity of selective sieving was adjusted so as to discard 50% of the larvae over the whole rearing period in a progressive manner. As soon as the larvae reached the pediveliger stage, ready to settle larvae were sampled for genetic analysis. Regarding the artificial environment rearing effect via the temperature, we used a similar mixed-family approach. The progeny from a factorial breeding design was divided as follows: three (replicates) 50-l tanks were dedicaced to a rearing at 26°C versus 20°C for three others 50-l tanks. The whole size variability was preserved for this experiment. Individual growth measurements for larvae genetically identified have been performed at days 22 and 30 after fertilization for both conditions. In a same way, we collected individual measurements for genotyped juvenile oysters (80 days after fertilization). At a phenotypic scale, relative survival and settlement success for larvae with sieving were higher. Sieving appears as a time-saving process associated with a better relative survival ratio. But in the same time, our results confirm that a significant genetic variability exist for early developmental traits in the Pacific oyster. This is congruent with the results already obtained that investigated genetic variability and genetic correlations in early life-history traits of Crassostrea gigas. Discarding around 50% of the smallest larvae can lead to significant selection at the larval stage.

Role of corporate governance in mitigating the selective disclosure of executive stock option information

We examine the nature and extent of statutory executive stock option (ESO) disclosures by Australian listed companies over the 2001 to 2004 period, and the influence of corporate governance mechanisms on these disclosures. Our results show a progressive increase in overall compliance from 2001 to 2004. However, despite the improved compliance, the results reveal managements’ continued reluctance to disclose more sensitive ESO information. Factors associated with good internal governance, including board independence, audit committee independence and effectiveness, and compensation committee independence and effectiveness are found to contribute to improved compliance. Similarly, certain external governance factors are associated with improved disclosure, including external auditor quality, shareholder activism (as proxied by companies identified as poor performers by the Australian Shareholders’ Association), and regulatory intervention.