Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

Abstract

BackgroundIntegration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes.ResultsWe 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. 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. 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. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays.ConclusionsOur 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. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. 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.

Genetic variants and signatures of selective sweep of Hanwoo population (Korean native cattle)

“…This exception corresponds to LINEs around 2,000 bp. This effect has also been identified in humans and cattle using the same method as used in this study and with other methods, respectively (18,19). These findings indicated that the exception is not due to the analysis method or sample population.…”

Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds

“…Zhan et al [15] identified enrichment bias for this pathway when re-sequencing a Holstein Friesian bull and performing an enrichment analysis for genes with nonsynonymous SNVs. Do et al [40] reported that the olfactory transduction pathway is associated with residual feed intake in pigs.…”

Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome1

“…A total of 790 CNVRs were identified in this study, and only 4 CNVRs from our set were found to be overlapping. In the NGS study of Zhan et al (2011), 520 CNVRs were identified on the genome of one Holstein-Friesian bull when comparing the sequence reads against a Fleckvieh bull. A total of 7 of our CNVRs overlapped with this set.…”

“…Cattle CNVs have been reported using a variety of platforms, including comparative genomic hybridization arrays (Liu et al, 2008, 2010; Fadista et al, 2010), the Illumina BovineHD BeadChip (Hou et al, 2012a; Wu et al, 2015; Aguilar et al, 2016; Prinsen et al, 2016; Xu et al, 2016), the Illumina BovineSNP50 BeadChip (Matukumalli et al, 2009; Bae et al, 2010; Hou et al, 2011, 2012b; Jiang et al, 2012; Bagnato et al, 2015; Ben Sassi et al, 2016), and next-generation sequencing (NGS) (Stothard et al, 2011; Zhan et al, 2011; Bickhart et al, 2012; Choi et al, 2013; Keel et al, 2016; Ben Sassi et al, 2016). In these studies, it is reported that copy number variable regions comprise ~2–7% of the cattle genome.…”