![]() ![]() Two recent studies have reported the analysis of whole genome sequencing of cattle (Fleckevieh and Kuchinoshima-Ushi bulls) focussing on SNP discovery. This catalogue will help researchers to efficiently associate genomic information with productivity traits and improve disease resistance to achieve breeding goals. Therefore, cattle research initiatives similar to the human 1000 Genomes and Personal Genome projects are of paramount importance in order to obtain a complete catalogue of genomic variation in this species. The increasing cost efficiency of sequencing technologies has enabled large scale sequencing of individual genomes, which has dramatically increased of the catalogue of genomic sequences and structural variants detected and filled some of the earlier gaps in resources that were biased towards common sequence variants. ![]() Despite their known functional importance in humans, so far only a few small-scale studies have probed the extent of structural variants, mainly copy number variation (CNV), in cattle. In contrast, whole genome sequencing of single individuals removes the polymorphism ascertainment bias, detects rare putative functional variants and also retrieves structural variants, an important category of genomic variation that only recently has become fully appreciated. ![]() The identification of rare causal mutations might be complicated due to failure to detect the disequilibrium between causal mutations and genotyped SNPs. For example, an ascertainment bias derived from the fact that the SNPs used are chosen to have a minimum "rare" allele frequency as well as to segregate in multiple breeds is sometimes introduced. ĭespite the fact that SNP genotyping technology has enabled successful genome-wide association studies (GWAS) in humans and in livestock species, it has known disadvantages. Furthermore, the integration of population-wide genotype information with phenotypic registrations generated in the dairy and beef industry provides an important resource for uncovering genes associated with complex production traits. The recent publication of the cattle genome assembly and the insights into sequence and structural variations identified in the bovine HapMap project has sparked the full potential of cattle genomic research, expanding our knowledge of mammalian evolution and biology. Being phylogenetically distant from primates and rodents and with a drastically different biology, cattle serve a significant role as animal model for studies of evolution, metabolism, reproduction, and disease. The domestic cow ( Bos taurus) is a ruminant that belongs to the Cetartiodactyl order of eutherian mammals. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants. CNV discovery was affected dramatically by platform resolution and coverage biases. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. This requires an accurate identification of the different types of variation in individual genomes. Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. ![]()
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