How bioinformatics enables livestock applied sciences in the genomic era

This review paper presents the three main approaches currently used in livestock genomic sciences where the bioinfomatics plays a critical role. They are named as Genomic Selection (GS), Genome Wide Association Study (GWAS) and Signatures of Selection (SS). The subsides for the construction of this article were generated in a current project (started in 2011), so called Zebu Genome Consortium (ZGC), which joins researchers from different institutions and countries, aiming to scientifically explore genomic information of Bos taurus indicus cattle breeds and deliver useful information to breeders and academic community, specially from the tropical regions of the world. © 2012 Springer-Verlag.

Morphological and Genomic Differences Between Cutting and Racing Lines of Quarter Horses

To investigate morphological and genomic differences between cutting and racing lines of Quarter Horses, 120 racing and 68 cutting animals of both sexes, registered at the Brazilian Association of Quarter Horse Breeders, were used. Blood samples were collected, and the following physical traits were measured: weight; height at withers; body length; length of the shank, pastern, rump, head, and neck; and chest, shank, and hoof circumference. For analysis of genomic differences, 54,602 single-nucleotide polymorphisms (SNPs) were genotyped using the Equine SNP50 BeadChip, and the quality of individual and SNP genotype data were evaluated. The fixation index, FST, was used to identify genome regions that were altered in the lines by selection. The results showed significant differences between the lines in all physical traits. Quality control led to the exclusion of four cutting animals with a call rate of <0.95. After filtering, 12,544, 13,815, and 13,370 SNPs were excluded for the whole population (n = 184), the 120 racing animals, and the 64 cutting animals, respectively. The number of informative polymorphisms detected in each line and in the whole population indicated that the Equine SNP50 BeadChip can be used in genetic studies of Quarter Horses. The fixation index, FST, identified 2,558 genome regions that may have been modified by divergent selection. © 2013 Elsevier Inc.

Associação de polimorfismos de nucleotídeo único com características de crescimento e reprodutivas em bovinos Canchim

Pós-graduação em Genética e Melhoramento Animal - FCAV

Estudo de associação genômica e análise de enriquecimento genético da criotolerância espermática em bovinos da raça Nelore

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Seleção genômica para características de carcaça em bovinos da raça Nelore

Pós-graduação em Genética e Melhoramento Animal - FCAV

Prospecting major genes in dairy buffaloes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo genômico da produção de leite e seus constituintes em bovinos da raça Guzerá

Pós-graduação em Genética e Melhoramento Animal - FCAV

Estudo de associação genômica e perfil de expressão gênica de folículos antrais em novilhas das raças nelore e angus, associadas ao fenótipo de alta e baixa população folicular

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.

Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genome-wide scans to uncover loci underlying bovine reproductive biology

Pós-graduação em Medicina Veterinária - FCAV

A genome-wide scan for selection signatures in Nellore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genome-wide methylation and transcriptome analysis in penile carcinoma: uncovering new molecular markers

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genome-wide scan for visceral leishmaniasis in mixed-breed dogs identifies candidate genes involved in T helper cells and macrophage signaling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.