Vb6 T-cell receptor elements in artiodactyls: conservation and germline polymorphisms

Prevalence and resistance to gastrointestinal parasites in goats: A review

Gastrointestinal parasitism, particularly nematode infection, is a major health issue affecting goats worldwide, resulting in clinical diseases and productivity loss. Prevalent gastrointestinal parasites (GIPs) affecting goats in South Africa are the Strongyloides papillosus, Eimeria spp., and Strongyles, especially the Haemonchus contortus and Trichostrongylus spp. According to the issues discussed in this paper and by other authors, the prevalence and intensity of various GIPs vary with an animal's location, breed, age, sex, and season. Because GIPs easily develop resistance to chemical treatment, selecting and breeding genetically GIP-resistant animals would be a relatively simple and inexpensive strategy for reducing or eliminating the current reliance on chemotherapy. Potential phenotypic indicators for selecting GIP-resistant goats include parasitological, immunological, and pathological phenotypic markers. Synergistic use of these indicators should be encouraged for a more accurate simplified genotype selection of resistant animals. Genes with Mendelian inheritance, particularly those involved in immunoregulatory mechanisms, have been identified in goats. Exploring this knowledge base to develop cost-effective molecular tools that facilitate enhanced genetic improvement programs is a current challenge. Future statistical and biological models should investigate genetic variations within genomic regions and different candidate genes involved in immunoregulatory mechanisms, as well as the identification of single nucleotide polymorphisms known to affect GIP infection levels.

Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation

Studies in laboratory animals demonstrate important relationships between environment, host traits, and microbiome composition. However, host-microbiome relationships in natural systems are understudied. Here, we investigate metapopulation-scale microbiome variation in a wild mammalian host, the desert bighorn sheep (Ovis canadensis nelsoni). We sought to identify over-represented microbial clades and understand how landscape variables and host traits influence microbiome composition across the host metapopulation. To address these questions, we performed 16S sequencing on fecal DNA samples from thirty-nine bighorn sheep across seven loosely connected populations in the Mojave Desert and assessed relationships between microbiome composition, environmental variation, geographic distribution, and microsatellite-derived host population structure and heterozygosity. We first used a phylogenetically-informed algorithm to identify bacterial clades conserved across the metapopulation. Members of genus Ruminococcaceae, genus Lachnospiraceae, and family Christensenellaceae R7 group were among the clades over-represented across the metapopulation, consistent with their known roles as rumen symbionts in domestic livestock. Additionally, compositional variation among hosts correlated with individual-level geographic and genetic structure, and with population-level differences in genetic heterozygosity. This study identifies microbiome community variation across a mammalian metapopulation, potentially associated with genetic and geographic population structure. Our results imply that microbiome composition may diverge in accordance with landscape-scale environmental and host population characteristics.

Assessing changes in functional connectivity in a desert bighorn sheep metapopulation after two generations

Determining how species move across complex and fragmented landscapes and interact with human-made barriers is a major research focus in conservation. Studies estimating functional connectivity from movement, dispersal or gene flow usually rely on a single study period and rarely consider variation over time. We contrasted genetic structure and gene flow across barriers for a metapopulation of desert bighorn sheep (Ovis canadensis nelsoni) using genotypes collected 2000-2003 and 2013-2015. Based on the recently observed but unexpected spread of a respiratory pathogen across an interstate highway previously identified as a barrier to gene flow, we hypothesized that bighorn sheep changed how they interacted with that barrier, and that shifts in metapopulation structure influenced gene flow, genetic diversity and connectivity. Population assignment tests, genetic structure and genetic recapture demonstrated that bighorn sheep crossed the interstate highway in at least one location in 2013-2015, sharply reducing genetic structure between two populations, but supported conclusions of an earlier study that such crossings were very infrequent or unknown in 2000-2003. A recently expanded population established new links and caused decreases in genetic structure among multiple populations. Genetic diversity showed only slight increases in populations linked by new connections. Genetic structure and assignments revealed other previously undetected changes in movements and distribution, but much was consistent. Thus, we observed changes in both structural and functional connectivity over just two generations, but only in specific locations. Movement patterns of species should be revisited periodically to enable informed management, particularly in dynamic and fragmented systems.

Dissection of the clonal composition of bovine alphabeta T cell responses using T cell receptor Vbeta subfamily-specific PCR and heteroduplex analysis

Although techniques that permit analysis of the clonal composition of T cell populations have been used extensively to provide a better understanding of the mechanisms that influence efficacy of T cell responses in humans and mice, such methods are lacking for other animal species. In this paper we report the establishment and validation of a panel of Vbeta subfamily-specific semi-nested PCR assays, and a CDR3beta heteroduplex technique for analysing the clonal diversity of bovine alphabeta T cell responses. Development of these methods was based on available sequence data for 48 functional Vbeta genes classified within 17 subfamilies. These techniques were used to determine the clonal composition of parasite-reactive CD8(+) T cells obtained from two animals immunised with the protozoan parasite Theileria parva. Analyses of uncloned T cell lines as well as large panels of cloned T cells derived from each of these lines confirmed the specificity and sensitivity of the assays. Specific PCR products were obtained from 96% of the T cell clones examined, indicating that the currently identified Vbeta genes represent most of the functional Vbeta subfamilies in cattle. Heteroduplex analyses, coupled with sequencing of PCR products, identified over 20 clonal expansions within each of the T cell lines, distributed over a large number of Vbeta subfamilies, although a limited number of clonotypes numerically dominated the response in both animals. The development and validation of these methods provides for the first time a generic set of molecular tools that can be used to perform detailed analysis of the TCR diversity and clonal composition of bovine T cell responses.

Analysis of T-cell receptor BV gene sequences in cattle reveals extensive duplication within the BV9 and BV20 subgroups

We investigated the repertoire of functional T-cell receptor beta-chain variable genes (TRBV genes) in cattle by analysing the nucleotide sequences and predicted amino acid sequences of a set of cDNA clones isolated from lymph node T cells. Thirty-nine distinct TRBV sequences were identified, bringing the total number of recognised bovine TRBV gene segments to more than 40. Sixteen TRBV subgroups were defined based on their sequence homology to each other and to human TRBV genes. All of the main phylogenetic lineages of BV gene subgroups described in humans and mice were represented. Eight of the subgroups were found to contain more than one member. The most striking feature of the results was the large number of sequences (more than half of the sequenced clones) in the BV9 and BV20 subgroups, which were found to contain 12 and 8 distinct sequences, respectively. In contrast, the corresponding human TRBV subfamilies contain a single member. The results indicate that, as in humans, there has been extensive gene duplication within the TRBV locus during evolution. However, duplication of different BV subgroups in cattle has resulted in a TRBV gene repertoire distinct from that found in other species.

Increased heterozygosity and allele variants are seen in Texel compared to Suffolk sheep

In this study, the Suffolk and Texel sheep breeds were compared for microsatellite marker heterozygosity throughout seven chromosomal regions in the sheep genome. A total of 623 Texel animals and 489 Suffolk animals in five and three half-sib families, respectively, were genotyped for microsatellite markers across the seven different chromosomes. Using the observed allele frequencies, the expected levels of heterozygosity were calculated for each family. The expected levels of heterozygosity did not significantly differ between the breeds across all regions studied. However, levels of expected heterozygosity were 32% higher in Texel animals on chromosome 4 due to a region of increased heterozygosity between BMS648 and BM3212. The number of allelic variants significantly differed between the breeds, solely due to a region of increased number of alleles on chromosome 20. This region of higher numbers of allele variants in the Texel breed extended from the MHC to c. 15 cM distal to the MHC region incorporating markers OMHC1, CSRD226, TGLA387 and BM1818, which had 3.30, 7.02, 3.09 and 6.75 more alleles in Texel than in Suffolk animals, respectively. No difference was observed in the variance of allele frequency between the two breeds. It is proposed that previous selective sweeps may have reduced numbers of alleles and levels of heterozygosity in the Suffolk breed.

Exonic MHC-DRB polymorphisms and intronic simple repeat sequences: Janus' faces of DNA sequence evolution

The evolution of highly polymorphic gene loci is following routes that cannot be extrapolated from the existing knowledge of single copy genes. In addition, interpreting the evolution of the most polymorphic loci in vertebrates requires a plethora of data from different taxa. We evaluate here the rules for the evolution of Major Histocompatibility Complex (MHC-)DRB genes recently established in humans and other primates on the basis of sequences from several artiodactyl species. MHC genes encode essential molecules for self/altered-self/non-self discrimination in the interaction of the organism with its environment. The necessity to effectively present various different antigens to immunocompetent cells causes positive selection pressure on the variability of these genes in the population. Artiodactyls represent the third mammalian order in which this phenomenon was evidence independently. A further incentive to investigate also the surroundings of MHC-DRB loci was the presence of a particular repetitive sequence stretch in the vicinity of the polymorphic exon--in addition to the evolutionarily old alleles, ancient polymorphisms and the mechanisms for their generation and/or maintenance. Besides their utility for indirect gene diagnosis (MHC-DRB typing), the closely linked stretches of simple repetitive DNA in the neighborhood of the highly polymorphic MHC-DRB genes are also interesting remains of the evolutionary history. Evolutionary development is different in genetically inert intronic DNA compared to the exonic counterparts, despite their close vicinity. The persistence of these simple repeats over nearly 100 million years in one location preserving the same basic motif structure is startling. Indirect evidence is weighed that biological meaning should be considered for these elements. The combined analysis of the polymorphic DRB genes and the (highly variable but persistent) simple repeat stretches deepen our understanding of the complexities within a unique genomic compartment encoding essential molecules for self/non-self differentiation in the interaction of the organism with its environment.

The analysis of simple repeat loci as applied in evolutionary and behavioral sciences

This chapter describes several aspects of tandemly organized, simple repetitive DNA sequences and their usefulness for genetic relationship analyses. After introducing the structure, the evolution and the biological meaning of such target sequences in a particularly well-studied gene, we discuss oligonucleotide probes for generating individual specific multilocus banding patterns. Thus, oligonucleotide fingerprinting allows to approach novel problems in behavioral sciences. Here, we use a passerine bird, the great tit (Parus major) as an example. Finally, genomic fingerprinting is compared to sensitive amplification methods requiring less DNA. Advantages and shortcomings of these techniques need to be evaluated in the context of the biological question(s) asked and, above all, the quality and quantity of the starting material.