An Optimization Model for the Banana Northern Prawn Fishery

This study presents an optimal control model of the Banana Northern Prawn Fishery, one of the most important fisheries in Australia. The life cycle of this species involves migration between the sea, where the catch takes place, and the estuary, where post-larvae and juveniles develop. The model combines a stage-matrix population dynamics model and an economic model of sustainable catch. The controls involve the amount of effort allowed and the length of the fishing season. Life stages are defined in terms of prawn size, allowing catch revenue to be adjusted to the expected proportion of specific sized classes caught in a particular month of the year, hence providing a more realistic projection of profits when price is influenced by size. The model is calibrated based on 18 years of detailed catch data.fisheries management, Australia, optimal control, profit maximisation, banana prawns., Resource /Energy Economics and Policy,

Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data

BACKGROUND: Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. RESULTS: A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r(2) criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r(2) above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. CONCLUSIONS: A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds

Use of Genetic Polymorphisms to Assess the Genetic Structure and Breed Composition of Crossbred Animals

This thesis explores the accuracy of methods to estimate the breed composition of crossbred animals which have unknown pedigree. Herein I present the use of SNP technologies to estimate the breed composition of small-holder crossbred dairy cattle in developing countries for the first time. Before this could be done there was a need to determine: what are the accuracies of different methods for estimating breed composition? The genetic structure of animals, the design of reference populations, the number of SNP markers and the model selected has possible consequences for estimation of breed composition. Once the effect of the above factors on the accuracy of estimation of breed composition is identified, it is possible to estimate with confidence the breed composition of crossbred animals that have no recorded pedigree. The overall aim of this thesis was to investigate the use of high-density SNP data to understand the livestock breed's population structure and estimate the breed composition of crossbred animals

Towards breed formation by island model divergence in Korean cattle

BACKGROUND: The main cattle breed in Korea is the brown Hanwoo, which has been under artificial selection within a national breeding program for several decades. Varieties of the Hanwoo known as Jeju Black and Chikso were not included in the breeding program and remained isolated from the effects of recent artificial selection advancements. We analysed the Jeju Black and Chikso populations in regards to their genetic variability, state of inbreeding, as well as level of differentiation from the mainland Hanwoo population. RESULTS: Jeju Black and Chikso were found to have small estimated effective population sizes (N(e)) of only 11 and 7, respectively. Despite a small N(e), higher than expected heterozygosity levels were observed (0.303 and 0.306), however, lower allelic richness was found for the two island populations (1.76 and 1.77) compared to the mainland population (1.81). The increase in heterozygosity could be due to environmental disease challenges that promoted maintenance of higher genetic variability; however, no direct proof exists. Increased heterozygosity due to a first generation crossing of genetically different populations is not recorded. The differentiation between the Korean populations had F(ST) values between 0.014 and 0.036 which is not as high as the differentiation within European beef or dairy cattle breeds (0.047–0.111). This suggests that the three populations have not separated into independent breeds. CONCLUSION: Results agree with an island model of speciation where the brown Hanwoo represents the ancestral breed, whilst the Jeju Black and Chikso diverge from this common ancestor, following different evolutionary trajectories. Nevertheless, differences are minor and whether Jeju Black and Chikso cattle will develop into discrete breeds or reintegrate with the main population has to be seen in the future and will largely depend on human management decisions. This offers a rare opportunity to accompany the development of new breeds but also poses challenges on how to preserve these incipient breeds and ensure their long term viability. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0563-2) contains supplementary material, which is available to authorized users

Is Sexual Dimorphism a Practical Selection Objective in Sheep?

Although for most traits, there is a difference between phenotypic expression in ewes versus rams, they have been traditionally treated equally in breeding programs. This thesis has investigated whether there is any variation between them in how they inherit growth and whether there are any benefits to be gained from divergent selection objectives. A bioeconomic model was used to show that divergent selection for growth in ewes and rams could increase the feed efficiency and profitability of a self-replacing production system. The magnitude of the increase was found to be influenced by the age structure of the flock, fertility, base weight (average of both sexes) and the annual feed availability and price cycles. To test whether divergent selection for growth is possible, sex specific genetic parameters and genetic correlations between ewes and rams were estimated. Accordingly, a series of univariate, multivariate and random regression models using combinations of direct additive genetic, maternal additive genetic, maternal permanent environmental and direct permanent environmental effects were fitted. The results from these analyses revealed that ewes have larger heritability and smaller phenotypic variances than rams and that the intersex genetic correlations were less than unity and decreased with age (range 0.59 to 0.97). Furthermore, the phenotypic and BLUP selection responses predicted using these parameters revealed that rams had higher selection responses than ewes. The results for fat depth (corrected for live weight) were the sole exception to these results. Fat in ewes was deeper and had a lower heritability and higher phenotypic variances than rams. Little variation in sexual dimorphism was observed between the breeds used in this study despite variation in selection history/objectives and founder effects in each breed. In conclusion, these results reveal that it is useful to select for divergent weight, fat and eye muscle depth objectives in ewes and rams and that sexual dimorphism can have a positive effect on the feed efficiency and profitability of a self-replacing flock. Other potential uses of sexual dimorphism in livestock breeding including in species other than sheep, single sex production systems (using sexed semen), reducing product diversity (equal ewes and rams) and the influence of recording/selecting a single sex were also discussed

Detection of genomic regions underlying resistance to gastrointestinal parasites in Australian sheep

International audienceAbstractBackgroundThis study aimed at identifying genomic regions that underlie genetic variation of worm egg count, as an indicator trait for parasite resistance in a large population of Australian sheep, which was genotyped with the high-density 600 K Ovine single nucleotide polymorphism array. This study included 7539 sheep from different locations across Australia that underwent a field challenge with mixed gastrointestinal parasite species. Faecal samples were collected and worm egg counts for three strongyle species, i.e. Teladorsagia circumcincta, Haemonchus contortus and Trichostrongylus colubriformis were determined. Data were analysed using genome-wide association studies (GWAS) and regional heritability mapping (RHM).ResultsBoth RHM and GWAS detected a region on Ovis aries (OAR) chromosome 2 that was highly significantly associated with parasite resistance at a genome-wise false discovery rate of 5%. RHM revealed additional significant regions on OAR6, 18, and 24. Pathway analysis revealed 13 genes within these significant regions (SH3RF1, HERC2, MAP3K, CYFIP1, PTPN1, BIN1, HERC3, HERC5, HERC6, IBSP, SPP1, ISG20, and DET1), which have various roles in innate and acquired immune response mechanisms, as well as cytokine signalling. Other genes involved in haemostasis regulation and mucosal defence were also detected, which are important for protection of sheep against invading parasites.ConclusionsThis study identified significant genomic regions on OAR2, 6, 18, and 24 that are associated with parasite resistance in sheep. RHM was more powerful in detecting regions that affect parasite resistance than GWAS. Our results support the hypothesis that parasite resistance is a complex trait and is determined by a large number of genes with small effects, rather than by a few major genes with large effects

The Genetic Architecture of Complex Traits in Sheep

Many important traits in biology, medicine and agriculture are complex and quantitative in that they exhibit continuous variation and non-trivial patterns of genetic inheritance. They are largely polygenic and influenced by factors such as gene-gene and gene-environment interactions. Important reasons to study complex traits include trying to understand how the genetic components operate on their own and how they relate to each other, quantification of the contributions of these elements to trait variation, and elucidation of the underlying genetic architecture behind a trait. An understanding of the sources and consequences of variation in complex traits and identification of the genes involved provides us with a handle to manipulate biological systems, which can have direct applications in medicine and agricultural production. From an agricultural standpoint there are huge economic benefits to be achieved by a better understanding and exploitation of the genetic architecture of complex production traits such as milk yield in dairy animals and meat quality in e.g. sheep or cattle. This thesis is centred on making some inroads to better understand the genetic architecture of complex traits in sheep. The thesis progresses through a characterization of genetic structure and variability in Australian sheep populations, followed by a genome-wide association study for weight. Then a novel approach to improve estimates of genomic breeding values is discussed. Lastly, the inheritance and partitioning of gene expression variance is studied. A more detailed breakdown of the thesis follows

Analysis of social interactions in group-housed animals using dyadic linear models

Understanding factors affecting social interactions among animals is important for applied animal behavior research. Thus, there is a need to elicit statistical models to analyze data collected from pairwise behavioral interactions. In this study, we propose treating social interaction data as dyadic observations and propose a statistical model for their analysis. We performed posterior predictive checks of the model through different validation strategies: stratified 5-fold random cross-validation, block-by-social-group cross-validation, and block-by-focal-animals validation. The proposed model was applied to a pig behavior dataset collected from 797 growing pigs freshly remixed into 59 social groups that resulted in 10,032 records of directional dyadic interactions. The response variable was the duration in seconds that each animal spent delivering attacks on another group mate. Generalized linear mixed models were fitted. Fixed effects included sex, individual weight, prior nursery mate experience, and prior littermate experience of the two pigs in the dyad. Random effects included aggression giver, aggression receiver, dyad, and social group. A Bayesian framework was utilized for parameter estimation and posterior predictive model checking. Prior nursery mate experience was the only significant fixed effect. In addition, a weak but significant correlation between the random giver effect and the random receiver effect was obtained when analyzing the attacking duration. The predictive performance of the model varied depending on the validation strategy, with substantially lower performance from the block-by-social-group strategy than other validation strategies. Collectively, this paper demonstrates a statistical model to analyze interactive animal behaviors, particularly dyadic interactions

Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and Bos taurus cattle

Background: Rhipicephalus (Boophilus) microplus is an obligate blood feeder which is host specific to cattle. Existing knowledge pertaining to the host or host breed effects on tick transcript expression profiles during the tick - host interaction is poor. Results: Global analysis of gene expression changes in whole R. microplus ticks during larval, pre-attachment and early adult stages feeding on Bos indicus and Bos taurus cattle were compared using gene expression microarray analysis. Among the 13,601 R. microplus transcripts from BmiGI Version 2 we identified 297 high and 17 low expressed transcripts that were significantly differentially expressed between R. microplus feeding on tick resistant cattle [Bos indicus (Brahman)] compared to R. microplus feeding on tick susceptible cattle [Bos taurus (Holstein-Friesian)] (p <= 0.001). These include genes encoding enzymes involved in primary metabolism, and genes related to stress, defence, cell wall modification, cellular signaling, receptor, and cuticle formation. Microarrays were validated by qRT-PCR analysis of selected transcripts using three housekeeping genes as normalization controls. Conclusion: The analysis of all tick stages under survey suggested a coordinated regulation of defence proteins, proteases and protease inhibitors to achieve successful attachment and survival of R. microplus on different host breeds, particularly Bos indicus cattle. R. microplus ticks demonstrate different transcript expression patterns when they encounter tick resistant and susceptible breeds of cattle. In this study we provide the first transcriptome evidence demonstrating the influence of tick resistant and susceptible cattle breeds on transcript expression patterns and the molecular physiology of ticks during host attachment and feeding

A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development

Background: The developmental transition between the late fetus and a newborn animal is associated with profound changes in skeletal muscle function as it adapts to the new physiological demands of locomotion and postural support against gravity. The mechanisms underpinning this adaption process are unclear but are likely to be initiated by changes in hormone levels. We tested the hypothesis that this developmental transition is associated with large coordinated changes in the transcription of skeletal muscle genes.Results: Using an ovine model, transcriptional profiling was performed on Longissimus dorsi skeletal muscle taken at three fetal developmental time points (80, 100 and 120 d of fetal development) and two postnatal time points, one approximately 3 days postpartum and a second at 3 months of age. The developmental time course was dominated by large changes in expression of 2,471 genes during the interval between late fetal development (120 d fetal development) and 1-3 days postpartum. Analysis of the functions of genes that were uniquely up-regulated in this interval showed strong enrichment for oxidative metabolism and the tricarboxylic acid cycle indicating enhanced mitochondrial activity. Histological examination of tissues from these developmental time points directly confirmed a marked increase in mitochondrial activity between the late fetal and early postnatal samples. The promoters of genes that were up-regulated during this fetal to neonatal transition were enriched for estrogen receptor 1 and estrogen related receptor alpha cis-regulatory motifs. The genes down-regulated during this interval highlighted de-emphasis of an array of functions including Wnt signaling, cell adhesion and differentiation. There were also changes in gene expression prior to this late fetal - postnatal transition and between the two postnatal time points. The former genes were enriched for functions involving the extracellular matrix and immune response while the latter principally involved functions associated with transcriptional regulation of metabolic processes.Conclusions: It is concluded that during late skeletal muscle development there are substantial and coordinated changes in the transcription of a large number of genes many of which are probably triggered by increased estrogen levels. These changes probably underpin the adaption of muscle to new physiological demands in the postnatal environment