In silico candidate gene mining in livestock species

AbstractThe identification of genes involved in livestock production and disease is a challenge due to the multi-genic, multifactorial nature of the traits and the complexity of integration of information from different studies. Genome-wide techniques such as microarray analysis, SAGE, linkage analysis and linkage disequilibrium analysis have been extensively used in livestock and have often identified a large number of candidate genes. Selection of the most probable candidate genes for further empirical analysis remains a challenge. Novel extensive biological databases (DB) provide an opportunity for candidate gene mining. Bioinformatic methods and tools to prioritize candidate genes underlying pathways or diseases have been presented mostly for application to human disease candidate gene search. These computational methods employ data from a variety of sources to identify the most likely candidate genes from genes sets. The objectives of the study were: 1. to test a set of existing gene prioritization c..

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

status: publishe

Evaluation of Mammalian Interspersed Repeats to investigate the goat genome

Among the repeated sequences present in most eukaryotic genomes, SINEs (Short Interspersed Nuclear Elements) are widely used to investigate evolution in the mammalian order (Buchanan et al., 1999). One family of these repetitive sequences, the MIR (Mammalian Interspersed Repeats; Jurka et al., 1995), is ubiquitous in all mammals.MIR elements are tRNA-derived SINEs and are identifiable by a conserved core region of about 70 nucleotides

Costs of selection schemes in small cattle populations

The objective of this study was to compare selection costs in cattle populations of 1,000 to 15,000 females, with the constraint of 1% of inbreeding per generation. Three selection schemes were analysed: no progeny test, with selection of sires on pedigree index (NPT); progeny test of sires of sires (PT3); classical progeny test of sires of sires and sires of dams (PT4). With the progeny test schemes, bulls were either culled after semen collection for progeny testing, or kept alive. Costs per year increased linearly with population size and showed divergent trends among strategies. PT4 was the most expensive scheme, ranging from 125,700 Euro (1,000 females) to 318,900 Euro (15,000 females) with the alive bull strategy, and from 20,200 Euro to 206,300 Euro with the cull bull strategy. NPT was generally cheaper than PT3 when bulls were culled. Costs per female and per semen dose were also analysed

Use of linked loci as individuals or haplotypes for marker-assisted breed assignement

The objective of this study was to use simulation to evaluate the benefits of considering haplotypes of loci when linked single nucleotide polymorphisms are used for breed assignment. Three breeds of 10 000 females each were simulated under eight scenarios that differed according to the number of generations separating the breeds, size of breed founder populations and recombination rate between linked loci. Molecular genotypes consisted of 20 groups of three linked loci each. Breed assignment was performed in the final generation and was based on the frequency method. Haplotypes were reconstructed using the expectation-maximization algorithm. Accuracy of breed assignment was based on the frequency of correct breed assignment. Assignment accuracy increased as more genotypes (loci or haplotypes) were considered and more animals were used to estimate genotypic frequencies within breed. For most scenarios, use of haplotypes yielded equal or greater accuracies than when loci were considered independent. The advantage of haplotypes tended to increase as linkage disequilibrium between adjacent loci increased. The greatest advantage for using haplotypes was observed when recombination rate was low (0.001), breeds were separated by few generations (100), and a relatively large number of founder animals (110) was used to form new breeds. In this situation, 90% accuracy of breed assignment was achieved using nine to 14 haplotypes (i.e. 27-42 loci) depending on breed, vs. 39-57 individual loci

Analisi del valore culturale delle razze caprine dell\u2019arco alpino italiano

Many livestock local breeds are still today custodian of local traditions. The aim of this work was to analyse the cultural value of ten goat breeds farmed on the Italian Alpine ark: Roccaverano, Valdostana, Vallesana, Verzaschese, Lariana, Ciavenasca, Orobica, Bionda dell\u2019Adamello, Mochena and Passiria. The following aspects were considered: role in maintaining the traditional landscape, role in maintaining the traditional farming systems and the traditional tools for the management of the animals and products making, role in maintaining gastronomy, role in maintaining folklore and handicrafts, presence in forms of artistic expression. The degree of endangerment of these cultural elements was assessed. The contribution of each breeds to the cultural variability of the metapopulation was computed. The parameters used were able to differentiate breeds on the basis of their cultural value. Many of these elements could be used to add economic value to the farming of these local breeds. In addition, the parameters used in this investigation could be used to define conservation priorities