Comparative genomic identification and validation of ß-defensin genes in the Ovis aries genome.

BACKGROUND: ß-defensins are small, cationic, antimicrobial peptides found in species across the plant and animal kingdoms. In addition to microbiocidal activity, roles in immunity as well as reproduction have more recently been documented. ß-defensin genes in Ovis aries (domestic sheep) have been poorly annotated, having been identified only by automatic gene prediction algorithms. The objective of this study was to use a comparative genomics approach to identify and characterise the ß-defensin gene repertoire in sheep using the bovine genome as the primary reference. RESULTS: All 57 currently predicted bovine ß-defensin genes were used to find orthologous sequences in the most recent version of the sheep genome (OAR v4.0). Forty three genes were found to have close genomic matches (>70% similarity) between sheep and cattle. The orthologous genes were located in four clusters across the genome, with 4 genes on chromosome 2, 19 genes on chromosome 13, 5 genes on chromosome 20 and 15 genes on chromosome 26. Conserved gene order for the ß-defensin genes was apparent in the two smaller clusters, although gene order was reversed on chromosome 2, suggesting an inversion between sheep and cattle. Complete conservation of gene order was also observed for chromosome 13 ß-defensin orthologs. More structural differences were apparent between chromosome 26 genes and the orthologous region in the bovine reference genome, which is known to be copy-number variable. In this cluster, the Defensin-beta 1 (DEFB1) gene matched to eleven Bovine Neutrophil beta-Defensin (BNBD) genes on chromosome 27 with almost uniform similarity, as well as to tracheal, enteric and lingual anti-microbial peptides (TAP, EAP and LAP), suggesting that annotation of the bovine reference sequence is still incomplete. qPCR was used to profile the expression of 34 ß-defensin genes, representing each of the four clusters, in the ram reproductive tract. Distinct site-specific and differential expression profiles were detected across the reproductive tract of mature rams with preferential ß-defensin gene expression in the epididymis, recapitulating observations for orthologous genes in other species. CONCLUSIONS: This is the first comprehensive analysis of ß-defensin genes encoded by the ovine reference sequence, and the first report of an expanded repertoire of ß-defensin genes in this species. The preferential expression of these genes in the epididymis suggests a role in fertility, possibly providing immunoprotection for sperm within the female reproductive tract.

Genetic diversity in farm animals--a review.

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.

Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations.

Mitochondrial DNA has been the traditional marker for the study of animal domestication, as its high mutation rate allows for the accumulation of molecular diversity within the time frame of domestic history. Additionally, it is exclusively maternally inherited and haplotypes become part of the domestic gene pool via actual capture of a female animal rather than by interbreeding with wild populations. Initial studies of British aurochs identified a haplogroup, designated P, which was found to be highly divergent from all known domestic haplotypes over the most variable portion of the D-loop. Additional analysis of a large and geographically representative sample of aurochs from northern and central Europe found an additional, separate aurochs haplotype, E. Until recently, the European aurochs appeared to have no matrilinear descendants among the publicly available modern cattle control regions sequenced; if aurochs mtDNA was incorporated into the domestic population, aurochs either formed a very small proportion of modern diversity or had been subsequently lost. However, a haplogroup P sequence has recently been found in a modern sample, along with a new divergent haplogroup called Q. Here we confirm the outlying status of the novel Q and E haplogroups and the modern P haplogroup sequence as a descendent of European aurochs, by retrieval and analysis of cytochrome b sequence data from twenty ancient wild and domesticated cattle archaeological samples.

Bayesian inference of population expansions in domestic bovines.

The past population dynamics of four domestic and one wild species of bovine were estimated using Bayesian skyline plots, a coalescent Markov chain Monte Carlo method that does not require an assumed parametric model of demographic history. Four domestic species share a recent rapid population expansion not visible in the wild African buffalo (Syncerus caffer). The estimated timings of the expansions are consistent with the archaeological records of domestication.