Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection.

The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform.

Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis.

Background: Regenerative capacity differs greatly between animals. In vertebrates regenerative abilities are highly limited and tissue or organ specific. However the closest related chordate to the vertebrate clade, Botrylloides leachi, can undergo whole body regeneration (WBR).

Broad-scale genetic patterns of New Zealand abalone, Haliotis iris, across a distribution spanning 13° latitude and major oceanic water masses.

The New Zealand black-foot abalone, Haliotis iris, or pāua, is endemic to the rocky reefs surrounding New Zealand, whose main land mass spans 13° of latitude and separates the Tasman Sea from the Pacific Ocean. In this study, we examined the population genetic structure of this important commercial, cultural and recreational species by genotyping nine microsatellite loci in 485 pāua from 27 locations distributed across mainland New Zealand and the Chatham Islands. We found low, but significant, levels of genetic differentiation.

Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle.

The reproductive performance of bulls has a high impact on the beef cattle industry. Scrotal circumference (SC) is the most recorded reproductive trait in beef herds, and is used as a major selection criterion to improve precocity and fertility. The characterization of genomic regions affecting SC can contribute to the identification of diagnostic markers for reproductive performance and uncover molecular mechanisms underlying complex aspects of bovine reproductive biology.

Accuracy of genotype imputation in Nelore cattle.

Background: Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Bos indicus cattle (e.

The Trojan female technique: a novel, effective and humane approach for pest population control.

Humankind's ongoing battle with pest species spans millennia. Pests cause or carry disease, damage or consume food crops and other resources, and drive global environmental change. Conventional approaches to pest management usually involve lethal control, but such approaches are costly, of varying efficiency and often have ethical issues.

Effects of immunization against androstenedione or bone morphogenetic protein 15 (BMP15) on reproductive performance in sheep.

Partial neutralization of bone morphogenetic protein 15 (BMP15) bioactivity by immunization is known to increase ovulation rate in sheep. However, it remains uncertain whether BMP15 vaccination would be a suitable procedure for increasing lambing rate. The aim of this study was to compare the efficacy of a BMP15 vaccination treatment on lamb production to that of commercially-available androstenedione-based vaccines that are used for this purpose.

Using sheep lines with mutations in single genes to better understand ovarian function.

Livestock populations have been subjected to strong selection pressure to improve reproductive success, and this has led to the identification of lines of animals with increased fecundity. These animals provide a rich biological resource for discovery of genes and regulatory mechanisms that underpin improved reproductive success. To date, three genes, all related to the transforming growth factor β pathway, have been identified as having mutations that lead to alterations in ovulation in sheep.

Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.

Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure.

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection.

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic.

Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements.

Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene's promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation.

Changes in methylation patterns of kiss1 and kiss1r gene promoters across puberty.

The initiation of mammalian puberty is underpinned by an increase in Kisspeptin (Kiss1) signaling via its receptor (Kiss1r/GPR54) on gonadotropin-releasing hormone (GnRH) neurons. Animals and humans with loss-of-function mutations in Kiss1 or Kiss1r fail to go through puberty. The timing of puberty is dependent on environmental factors, and malleability in puberty timing suggests a mechanism that can translate environmental signals into patterns of Kiss1/Kiss1r gene expression.

Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model.

Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome.

Are old males still good males and can females tell the difference? Do hidden advantages of mating with old males off-set costs related to fertility, or are we missing something else?

Sperm function generally declines with male age. Paradoxically, females of many species still choose to mate with old males rather than young males. Females choosing old mates may suffer reduced fertilization rates and an increased incidence of birth defects in offspring, lowering fitness which may in turn lead to conflict between the sexes.

Effects of immunizing ewes against bone morphogenetic protein 15 on their responses to exogenous gonadotrophins to induce multiple ovulations.

Sheep with a heterozygous inactivating mutation in the bone morphogenetic protein 15 (BMP15) gene experience an increased ovulation rate during either a natural oestrous cycle or a cycle in which exogenous FSH and eCG (gonadotrophins) are given to induce multiple ovulations. The primary aim of these studies was to determine whether ewes immunised against BMP15 would also show an improved superovulation rate following exogenous gonadotrophin treatment. A secondary aim was to determine the effects of BMP15 immunisation on ovarian follicular characteristics.

Seasonal changes in morphology and steroid receptor expression in the prostate of the brushtail possum (Trichosurus vulpecula): an animal model for the study of prostate growth?

The prostate of the brushtail possum undergoes growth and regression during the year. The present study investigated the morphological changes and expression of androgen and oestrogen receptors during the breeding and non-breeding seasons. Prostate tissue was collected from adult possums at 2-monthly intervals.

Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora.

Understanding genetic variation responsible for phenotypic differences in natural populations is significantly hampered by a lack of genomic data for many species. Levels of variation can, however, be estimated using microsatellite markers, which may be useful for relating individual fitness to genetic diversity. Prior studies have demonstrated correlations between heterozygosity and individual fitness in some species.

Identification of a line of sheep carrying a putative autosomal gene increasing ovulation rate in sheep that does not appear to interact with mutations in the transforming growth factor beta superfamily.

Sheep lines with mutations in single genes that have major effects on ovulation rate have been very useful in gaining a better understanding of pathways important in controlling follicular development and ovulation rate. To date however, all known mutations are in the transforming growth factor beta (TGFB) superfamily. Ovulation rates were measured in 720 progeny of 20 rams that were descendants of a single prolific ewe.

Aptamer-based regionally protected PCR for protein detection.

Background: DNA aptamers are single-stranded nucleotide sequences that bind specifically to target molecules. By combining the advantages of PCR for amplifying specific DNA sequences and aptamer technology, we have developed a new strategy to detect target molecules such as proteins.

Methods: Ovine follicle-stimulating hormone alpha subunit (oFSHalpha) was used as the model protein to generate a specific DNA aptamer via an in vitro evolutionary process.