The accurate identification of conservation units is central to effective management strategies. However, marine environment populations often have large census sizes and few obvious boundaries to gene flow. Poorly understood species in the deep sea are especially at risk of being erroneously managed as a single interbreeding stock (panmictic). However, mistaking cryptic structure for panmixia can have important consequences leading to ineffective management and population decline. Furthermore, characteristics of populations essential for their survival may reflect local adaptation, not evident from surveys using neutral genetic markers. We use genomic methodologies to test hypotheses about potential drivers of cryptic population structure among marine fish populations in the deep sea. In particular, we consider the possibility of isolation by distance along habitat corridors for a species dependent on a specific depth range and test for differentiation at functional loci across potential ecological habitat boundaries. For a species previously understood to be panmictic in the North Atlantic, we reveal neutral genetic differentiation among regional populations isolated by distance along deep‐water channels. We also reveal a distinct pattern of cryptic genetic structure for putative functional loci, despite apparently high levels of gene flow. Synthesis and applications . This example reflects the life history and ecology of a broad range of deep‐sea species currently exploited in intensive fisheries or as bycatch. In many cases where these populations are managed as a single stock, more effective management could be achieved using the methods we describe to identify relevant eco‐evolutionary processes, facilitated by genomic methods, permitting the recognition of cryptic stock structure. This approach also allows managers to more directly promote the essential but elusive conservation of adaptive potential.

Background The role of taste perception in the development and persistence of obesity is currently unclear due to conflicting results from psychophysical and other studies. No study to date has assessed whether there is an underlying fundamental difference in the physiology of taste tissue between lean and obese individuals. Method/subjects We analysed the transcriptomic profile (RNA-seq) of human fungiform taste papillae biopsied from lean ( n = 23) and obese ( n = 13) Caucasian females (age range 18–55) to identify differences in gene expression. Results Obesity status was the major contributor to variance in global gene expression between individuals. A total of 62 genes had significantly different gene expression levels between lean and obese ( P < 0.0002), with the specific taste associated genes phospholipase C beta 2 ( PLCβ2 ) and sonic hedge-hog ( SHH ) having significantly reduced expression in obese group. Genes associated with inflammation and immune response were the top enriched biological pathways differing between the lean and the obese groups. Analysis of a broader gene set having a twofold change in expression (2619 genes) identified three enriched theme groups (sensory perception, cell and synaptic signalling, and immune response). Further, analysis of taste associated genes identified a consistent reduction in the expression of taste-related genes (in particular reduced type II taste cell genes) in the obese compared to the lean group. Conclusion The findings show obesity is associated with altered gene expression in tastebuds. Furthermore, the results suggest the tastebud microenvironment is distinctly different between lean and obese persons and, that changes in sensory gene expression contribute to this altered microenvironment. This research provides new evidence of a link between obesity and altered taste and in the future may help design strategies to combat obesity.

Genome sequences for hundreds of mammalian species are available, but an understanding of their genomic regulatory regions, which control gene expression, is only beginning. A comprehensive prediction of potential active regulatory regions is necessary to functionally study the roles of the majority of genomic variants in evolution, domestication, and animal production. We developed a computational method to predict regulatory DNA sequences (promoters, enhancers and transcription factor binding sites) in production animals (cows and pigs) and extended its broad applicability to other mammals. The method utilizes human regulatory features identified from thousands of tissues, cell lines, and experimental assays to find homologous regions that are conserved in sequences and genome organization and are enriched for regulatory elements in the genome sequences of other mammalian species. Importantly, we developed a filtering strategy, including a machine learning classification method, to utilize a very small number of species-specific experimental datasets available to select for the likely active regulatory regions. The method finds the optimal combination of sensitivity and accuracy to unbiasedly predict regulatory regions in mammalian species. Furthermore, we demonstrated the utility of the predicted regulatory datasets in cattle for prioritizing variants associated with multiple production and climate change adaptation traits, and identifying potential genome editing targets.

Evolutionary adaptations are occasionally convergent solutions to the same problem. A mutation contributing to a heat tolerance adaptation in Senepol cattle, a New World breed of mostly European descent, results in the distinct phenotype known as slick, where an animal has shorter hair and lower follicle density across its coat than wild type animals. The causal variant, located in the 11th exon of prolactin receptor, produces a frameshift that results in a truncated protein. However, this mutation does not explain all cases of slick coats found in criollo breeds. Here, we obtained genome sequences from slick cattle of a geographically distinct criollo breed, namely Limonero, whose ancestors were originally brought to the Americas by the Spanish. These data were used to identify new causal alleles in the 11th exon of the prolactin receptor, two of which also encode shortened proteins that remove a highly conserved tyrosine residue. These new mutations explained almost 90% of investigated cases of animals that had slick coats, but which also did not carry the Senepol slick allele. These results demonstrate convergent evolution at the molecular level in a trait important to the adaptation of an animal to its environment.

There is sustained growth in the number of tropical cattle, which represent more than half of all cattle worldwide. By and large, most research in tropical areas is still focused on breeds of cattle, their particular advantages or disadvantages in tropical areas, and the tropical forages or feeds that could be usefully fed to them. A consistent issue for adaptation to climate is the heat of tropical environments. Changing the external characteristics of the animal, such as color and coat characteristics, is one way to adapt, and there are several major genes for these traits. However, further improvement in heat tolerance and other adaptation traits will need to use the entire genome and all physical and physiological systems. Apart from the response to heat, climate forcing through methane emission identifies dry season weight loss as an important if somewhat neglected trait in climate adaptation of cattle. The use of genome-estimated breeding values in tropical areas is in its infancy and will be difficult to implement, but will be essential for rapid, coordinated genetic improvement. The difficulty of implementation cannot be exaggerated and may require major improvements in methodology.

The ability of beef cattle to remain productive in tropical environments is largely determined by heat tolerance and tick resistance. In Australia, crossbreeding and composite breeding with Bos indicus cattle have been used to introduce these traits into Bos taurus breed backgrounds. We examined SNP genotyping data and phenotypes for six production traits from a Tropical Composite herd in Central Queensland to test whether the Bos indicus ancestry (Indicus) percentage was able to explain the performance of beef cattle in tropical Australia. Tick count and coat length were significantly linked to Indicus percentage, while live weight, body condition, rectal temperature and scrotal circumference were not influenced by the Indicus content of the genome.

Tuna are large pelagic fish whose populations are close to panmixia. In addition, they are threatened species, so it is important for the maintenance and monitoring of genetic diversity that genetic information at a genome level be obtained. Here we report the draft assembly of the southern bluefin tuna genome and the collection of genome-wide sequence data for five other tuna species. We sampled five tuna species of the genus Thunnus, the northern and southern bluefin, yellowfin, albacore, and bigeye, as well as the skipjack (Katsuwonis pelamis), a tuna-like species. Genome assembly was facilitated at k-mer=25 while k-mer=51 generated assembly artefacts. The estimated size of the southern bluefin tuna genome was 795 Mb. We assembled two southern bluefin tuna individuals independently using both paired end and mate pair sequence. This resulted in scaffolds with N50>174,000 bp and maximum scaffold lengths>1.4 Mb. Our estimate of the size of the assembled genome was the scaffolded sequences in common to both assemblies, which amounted to 721 Mb of the 795 Mb of the southern bluefin tuna genome sequence. Using BLAST, there were matches between 13,039 of 14,341 (91%) refseq mRNA of the zebrafish Danio rerio to the tuna assembly indicating that most of a generic fish transcriptome was covered by the assembly.

Cattle diverged during the Pleistocene into two subspecies, one in temperate and one in tropical environments. Here we have used next generation sequencing of the indicine subspecies of cattle and compared it to the taurine subspecies. Although 23.8 million single nucleotide polymorphisms (SNP) were found, the number of fixed amino acid substitutions between the taurine and indicine subspecies was low and consistent with the Haldane predictions for adaptive selection rather than with Neutral Theory. We noted 33 regions of enhanced divergence of nonsynonymous SNP between the subspecies, which included an increased rate of deleterious variants. Signals of positive selection were found for genes associated with immunity, including the Bovine Major Histocompatibility Complex, which also showed an increased rate of deleterious amino acid variants. The genes important in sensing the environment, especially the olfactory system, showed a network wide signal of positive selection.

Inbreeding has the potential to negatively impact on animal performance. Strategies to monitor and mitigate inbreeding depression require that it can be estimated accurately. Here, we use genome-wide SNP data to produce three alternative estimates of inbreeding: proportion of heterozygous SNP, diagonal elements of the genomic relationship matrix and runs of homozygosity. We focus on Brahman (N = 2,112) versus Tropical Composite (N = 2,550) cattle which have been genotyped by a 74K Indicine chip and phenotyped for 10 traits of commercial importance to tropical adaptation. While the summary statistics for the Brahman and Tropical Composite populations are remarkably similar, the relationships of the inbreeding coefficients to the various phenotypes are different. In both populations, the proportion of heterozygous SNP was positively correlated with body condition score and negatively correlated with yearling weight. A possible explanation relating to the content of the Indicine SNP chip is briefly discussed.

Background: The success of genomic selection in animal breeding hinges on the availability of a large reference population on which genomic-based predictions of additive genetic or breeding values are built. Here, we explore the benefit of combining two unrelated populations into a single reference population.Methods: The datasets consisted of 1829 Brahman and 1973 Tropical Composite cattle with measurements on five phenotypes relevant to tropical adaptation and genotypes for 71,726 genome-wide single nucleotide polymorphisms (SNPs). The underlying genomic correlation for the same phenotype across the two breeds was explored on the basis of consistent linkage disequilibrium (LD) phase and marker effects in both breeds.Results: The proportion of genetic variance explained by the entire set of SNPs ranged from 37.5 to 57.6 %. Estimated genomic correlations were drastically affected by the process used to select SNPs and went from near 0 to more than 0.80 for most traits when using the set of SNPs with significant effects and the same LD phase in the two breeds. We found that, by carefully selecting the subset of SNPs, the missing heritability can be largely recovered and accuracies in genomic predictions can be improved six-fold. However, the increases in accuracy might come at the expense of large biases.Conclusions: Our results offer hope for the effective implementation of genomic selection schemes in situations where the number of breeds is large, the sample size within any single breed is small and the breeding objective includes many phenotypes.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'-polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.

BACKGROUND:A better understanding of non-additive variance could lead to increased knowledge on the genetic control and physiology of quantitative traits, and to improved prediction of the genetic value and phenotype of individuals. Genome-wide panels of single nucleotide polymorphisms (SNPs) have been mainly used to map additive effects for quantitative traits, but they can also be used to investigate non-additive effects. We estimated dominance and epistatic effects of SNPs on various traits in beef cattle and the variance explained by dominance, and quantified the increase in accuracy of phenotype prediction by including dominance deviations in its estimation.METHODS:Genotype data (729 068 real or imputed SNPs) and phenotypes on up to 16 traits of 10 191 individuals from Bos taurus, Bos indicus and composite breeds were used. A genome-wide association study was performed by fitting the additive and dominance effects of single SNPs. The dominance variance was estimated by fitting a dominance relationship matrix constructed from the 729 068 SNPs. The accuracy of predicted phenotypic values was evaluated by best linear unbiased prediction using the additive and dominance relationship matrices. Epistatic interactions (additive × additive) were tested between each of the 28 SNPs that are known to have additive effects on multiple traits, and each of the other remaining 729 067 SNPs.RESULTS:The number of significant dominance effects was greater than expected by chance and most of them were in the direction that is presumed to increase fitness and in the opposite direction to inbreeding depression. Estimates of dominance variance explained by SNPs varied widely between traits, but had large standard errors. The median dominance variance across the 16 traits was equal to 5% of the phenotypic variance. Including a dominance deviation in the prediction did not significantly increase its accuracy for any of the phenotypes. The number of additive × additive epistatic effects that were statistically significant was greater than expected by chance.CONCLUSIONS:Significant dominance and epistatic effects occur for growth, carcass and fertility traits in beef cattle but they are difficult to estimate precisely and including them in phenotype prediction does not increase its accuracy.

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

Polymorphisms that affect complex traits or quantitative trait loci (QTL) often affect multiple traits. We describe two novel methods (1) for finding single nucleotide polymorphisms (SNPs) significantly associated with one or more traits using a multi-trait, meta-analysis, and (2) for distinguishing between a single pleiotropic QTL and multiple linked QTL. The meta-analysis uses the effect of each SNP on each of n traits, estimated in single trait genome wide association studies (GWAS). These effects are expressed as a vector of signed t-values (t) and the error covariance matrix of these t values is approximated by the correlation matrix of t-values among the traits calculated across the SNP (V). Consequently, t'V-1t is approximately distributed as a chi-squared with n degrees of freedom. An attractive feature of the meta-analysis is that it uses estimated effects of SNPs from single trait GWAS, so it can be applied to published data where individual records are not available. We demonstrate that the multi-trait method can be used to increase the power (numbers of SNPs validated in an independent population) of GWAS in a beef cattle data set including 10,191 animals genotyped for 729,068 SNPs with 32 traits recorded, including growth and reproduction traits. We can distinguish between a single pleiotropic QTL and multiple linked QTL because multiple SNPs tagging the same QTL show the same pattern of effects across traits. We confirm this finding by demonstrating that when one SNP is included in the statistical model the other SNPs have a non-significant effect. In the beef cattle data set, cluster analysis yielded four groups of QTL with similar patterns of effects across traits within a group. A linear index was used to validate SNPs having effects on multiple traits and to identify additional SNPs belonging to these four groups.

BACKGROUND:Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69-77 and 81-92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped.RESULTS:To further characterise these regions, a bioinformatic approach was undertaken to identify novel non-synonymous SNP within the QTL regions of interest in Brahman cattle. After SNP discovery, we used conventional molecular assay technologies to perform studies of two candidate genes in both breeds. Non-synonymous SNP mapped to Testis-expressed gene 11 (Tex11) were associated (P < 0.001) with scrotal circumference in both breeds, and associations with percentage of normal sperm cells were also observed (P < 0.05). Evidence for recent selection was found as Tex11 SNP form a haplotype segment of Bos taurus origin that is retained within Brahman and Tropical Composite cattle with greatest reproductive potential.CONCLUSIONS:Association of non-synonymous SNP presented here are a first step to functional genetic studies. Bovine species may serve as a model for studying the role of Tex11 in male fertility, warranting further in-depth molecular characterisation.

Custom-built single-nucleotide-polymorphism (SNP) marker systems that are compatible with Sequenom® chemistry are compared with a general purpose microsatellite marker system in their ability to accurately assign Black Tiger shrimp parentage. The microsatellite system consisted of 13 markers, while the SNP systems comprised of 63 (SNPa), 59 (SNPb) or 122 markers (SNPab). Comparisons were made using animals from commercial breeding lines with thresholds for assignment derived using simulated genotypes. Pedigree assignment for commercial lines was highest when panel SNPab was used. Panel SNPa, panel SNPb and Msat functioned with an overall similar level of power for pedigree assignment, however, for some families, the Msat panel was not as powerful. Pedigree assignment for the simulated diploid genotypes was higher for all SNP panels compared with Msat. Overall the three SNP panels provided parentage assignment rates suitable for commercial shrimp breeding programs with assignment rates in the simulated genotypes greater than 96.8% and correct assignments greater than 99.3%. Compared with the microsatellite panel, custom-built SNP panels, whether they operate as single panels, or as a combined panel, have improved power to perform dam and sire assignment to progeny and provide faster turnaround time as they are compatible with Sequenom® chemistry.

Humans hunt or raise a wide variety of animals for meat, which vary from free-range to intensively reared. These animals form a valuable part of human nutrition. Their tissues, including the fat, contain vitamin and other essential nutrients necessary for health. However, animal fat from ruminants and other land mammals is usually regarded as saturated. The purpose of this review is partly to examine the basis for the saturated fat hypothesis of cardiovascular disease given more recent research, to examine the human health effects of animal fats, and partly to draw into one place the diverse knowledge about animal fat and the effects of fat on metabolism. Mechanistic understanding of the initiation of the fatty streak and atherosclerosis calls into question the avoidance of ruminant or porcine fat. Due to high levels of oleic acid, a low n-6 : n-3 fatty acid ratio in some groups, and the presence of specific micronutrients including vitamins and essential fatty acids, animal fats are of benefit in human nutrition. Animal fats can be obtained in minimally processed form making them a convenient source of energy and micronutrients.