Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants.

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations.

Livestock Genomics for Developing Countries - African Examples in Practice.

African livestock breeds are numerous and diverse, and typically well adapted to the harsh environment conditions under which they perform. They have been used over centuries to provide livelihoods as well as food and nutritional security. However, African livestock systems are dynamic, with many small- and medium-scale systems transforming, to varying degrees, to become more profitable.

Sex-biased inbreeding effects on reproductive success and home range size of the critically endangered black rhinoceros.

A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically endangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring).

Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus.

Background: The rising demand for pork has resulted in a massive expansion of pig production in Uganda. This has resulted in increased contact between humans and pigs. Pigs can act as reservoirs for emerging infectious diseases.

Patterns of genetic divergence among populations of the common dormouse, Muscardinus avellanarius in the UK.

Quantitative descriptions of population genetic structure allows the delineation of population units and is therefore of primary importance in population management and wildlife conservation. Yet, predicting factors that influence the gene flow patterns in populations particularly at landscape scales remains a major challenge in evolutionary biology. Here we report a population genetic study of the common dormouse, Muscardinus avellanarius, a species that is seriously threatened due to anthropogenic factors, in two regions, Bontuchel (Denbighshire) and Afonwen (Gwynedd), both in Wales, UK.

Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection.

African bovine trypanosomiasis caused by Trypanosoma sp., is a major constraint on cattle productivity in sub-Saharan Africa. Some African Bos taurus breeds are highly tolerant of infection, but the potentially more productive Bos indicus zebu breeds are much more susceptible.

A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice.

Background: African trypanosomes are protozoan parasites that cause "sleeping sickness" in humans and a similar disease in livestock. Trypanosomes also infect laboratory mice and three major quantitative trait loci (QTL) that regulate survival time after infection with T. congolense have been identified in two independent crosses between susceptible A/J and BALB/c mice, and the resistant C57BL/6.

Divergent antimicrobial peptide (AMP) and acute phase protein (APP) responses to Trypanosoma congolense infection in trypanotolerant and trypanosusceptible cattle.

African animal trypanosomiasis (AAT) is endemic across Sub-Saharan African and is a major constraint to livestock production. The ability of certain cattle breeds to remain productive despite infection is known as trypanotolerance; however, the underlying immune mechanisms contributing to this trait remain poorly understood. Antimicrobial peptides (AMPs) and acute phase proteins (APPs) are evolutionarily conserved effector molecules of the innate immune system that have important roles in the resolution of infection and activation of the adaptive immune response.

Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility.

Background: African animal trypanosomiasis (AAT) caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC) gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds.

Isolation and characterization of 10 microsatellite loci in the common dormouse Muscardinus avellanarius.

To assess the level and spatial pattern of genetic diversity of the common dormouse, Muscardinus avellanarius, we developed polymorphic microsatellite loci from partial genomic libraries enriched for microsatellite motifs. Ten dinucleotide polymorphic microsatellites were isolated and levels of genetic diversity were assessed in 139 individuals from Bontuchel, (Denbighshire, Wales). We observed high levels of heterozygosity (mean H(O)  = 0.

Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays.

Background: Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations. Sequence mismatches between probe and target strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays.

Effective population sizes and migration rates in fragmented populations of an endangered insect (Coenagrion mercuriale: Odonata).

1. Effective population sizes (N(e)) and migration rates (m) are critical evolutionary parameters that impact on population survival and determine the relative influence of selection and genetic drift. While the parameter m is well-studied in animal populations, N(e) remains challenging to measure and consequently is only rarely estimated, particularly in insect taxa.

Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of 'neighbourhood size' using a more precise estimator.

Genetic and demographic estimates of dispersal are often thought to be inconsistent. In this study, we use the damselfly Coenagrion mercuriale (Odonata: Zygoptera) as a model to evaluate directly the relationship between estimates of dispersal rate measured during capture-mark-recapture fieldwork with those made from the spatial pattern of genetic markers in linear and two-dimensional habitats. We estimate the 'neighbourhood size' (Nb) - the product of the mean axial dispersal rate between parent and offspring and the population density - by a previously described technique, here called the regression method.

Cytokine mRNA profiling of peripheral blood mononuclear cells from trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense.

To examine differences in cytokine profiles that may confer tolerance/susceptibility to bovine African trypanosomiasis, N'Dama (trypanotolerant, n = 8) and Boran (trypanosusceptible, n = 8) cattle were experimentally challenged with Trypanosoma congolense. Blood samples were collected over a 34-day period, and RNA was extracted from peripheral blood mononuclear cells. The expression levels of a panel of 14 cytokines were profiled over the time course of infection and between breeds.

High resolution mapping of chromosomal regions controlling resistance to gastrointestinal nematode infections in an advanced intercross line of mice.

Fine mapping of quantitative trait loci (QTL) associated with resistance to the gastrointestinal parasite Heligmosomoides polygyrus was achieved on F(6)/F(7) offspring (1076 mice) from resistant (SWR) and susceptible (CBA) mouse strains by selective genotyping (top and bottom 20% selected on total worm count in week 6). Fecal egg counts were recorded at weeks 2, 4, and 6, and the average was also analyzed. Blood packed cell volume in weeks 3 and 6 and five immunological traits (mucosal mast cell protease 1, granuloma score, IgG1 against adult worm, IgG1, and IgE to L4 antigen) were also recorded.

Controlling malaria and African trypanosomiasis: the role of the mouse.

Malaria and trypanosomiasis are vector-borne protozoal diseases which disproportionately affect the poor. Both give rise to immense human suffering; malaria exerts its effect directly on human health, while trypanosomiasis causes damage largely though its effect on the health and productivity of the livestock on which so many poor people depend. These diseases both have multifaceted and poorly understood mechanisms of pathogenesis, combined with relatively complex life cycles characterised by multiple stages in both insect vector and mammalian host.

Male sex pheromones and the phylogeographic structure of the Lutzomyia longipalpis species complex (Diptera: Psychodidae) from Brazil and Venezuela.

Lutzomyia longipalpis, a sibling complex, is the main vector of Leishmania chagasi/infantum. Discriminating between siblings is important as they may differ in vectorial capacity. Lutzomyia longipalpis populations display distinct male sex pheromone chemotypes.

There are high levels of functional and genetic diversity in Oxyrrhis marina.

Oxyrrhis marina, a widely distributed marine protist, is used to model heterotrophic flagellate responses in microbial food webs. Although clonal variability occurs in protists, assessments of intraspecific diversity are rare; such assessments are critical, particularly where species are used as models in ecological studies. To address the extent of intraspecific variation within O.

Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics.

African bovine trypanosomiasis, caused by the protozoan parasite Trypanosoma congolense, is endemic throughout sub-Saharan Africa and is a major constraint on livestock production. A promising approach to disease control is to understand and exploit naturally evolved trypanotolerance. We describe the first attempt to investigate the transcriptional response of susceptible Boran (Bos indicus) cattle to trypanosome infection via a functional genomics approach using a bovine total leukocyte (BOTL) cDNA microarray platform.

Responses of bovine chimaeras combining trypanosomosis resistant and susceptible genotypes to experimental infection with Trypanosoma congolense.

West African N'Dama cattle have developed a genetic capacity to survive, reproduce and remain productive under trypanosomosis risk. The cellular and molecular bases of this so-called trypanotolerance are not known, but the trait is manifested by the N'Dama's greater capacity to control parasitaemia and anaemia development during an infection. In order to examine the role of the haematopoietic system in trypanotolerance, we have exploited the tendency for the placentas of bovine twin embryos to fuse.