Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage

Abstract

Background: Genome-and population-wide re-sequencing would allow for most efficient detection of causal trait variants. However, despite a strong decrease of costs for next-generation sequencing in the last few years, resequencing of large numbers of individuals is not yet affordable. We therefore resorted to re-sequencing of a limited number of bovine animals selected to explain a major proportion of the population's genomic variation, so called key animals, in order to provide a catalogue of functional variants and a substrate for population-and genome-wide imputation of variable sites. Results: Forty-three animals accounting for about 69 percent of the genetic diversity of the Fleckvieh population, a cattle breed of Southern Germany and Austria, were sequenced with coverages ranging from 4.17 to 24.98 and averaging 7.46. After alignment to the reference genome (UMD3.1) and multi-sample variant calling, more than 17 million variant positions were identified, about 90 percent biallelic single nucleotide variants (SNVs) and 10 percent short insertions and deletions (InDels). The comparison with high-density chip data revealed a sensitivity of at least 92 percent and a specificity of 81 percent for sequencing based genotyping, and 97 percent and 93 percent when a imputation step was included. There are 91,733 variants in coding regions of 18,444 genes, 46 percent being nonsynonymous exchanges, of which 575 variants are predicted to cause premature stop codons. Three variants are listed in the OMIA database as causal for specific phenotypes.

A nonsense mutation in PLD4 is associated with a zinc deficiency-like syndrome in Fleckvieh cattle

“…Given the relatively low fold sequence coverage, some variants might have been wrongly called and lost, respectively. However, multi-sample variant calling followed by population-based genotype imputation as applied in the present study provides high quality genotypes even for lowly covered sites [14]. The p.W125X-mutation was perfectly associated in a panel of 3,650 animals, further substantiating our suspicion of causality.…”

“…In a next attempt to identify the causal mutation, one of the affected calves (id = 58953) and one of the unaffected homozygous animals (id = 58952) were re-sequenced together with 41 animals of the FV population [14]. Multi-sample variant calling yielded genotypes for 7,660 polymorphic sites within the 1,032 kb disease-associated segment at the distal end of BTA 21.…”

“…Sequencing on Illumina GA IIX and Hiseq 2000 instruments was performed as detailed by Jansen et al [14]. Paired-end reads were obtained and mapped to the bovine reference sequence (see above) using the Burrows-Wheeler Aligner ( BWA ) [47].…”

“…Beagle phasing and imputation was applied to improve the primary genotype calls. A detailed overview of the entire variant calling pipeline and all obtained variants is presented in Jansen et al [14]. Of 17.17 million sites, 7,086 SNPs and 574 InDels were located within the 1,023 kb segment (70,550,045 bp – 71,573,501 bp) of extended homozygosity on BTA 21.…”

Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation

“…Whole-genome sequencing of key ancestors provides a catalog of annotated variants segregating within and across cattle populations (Jansen et al, 2013;Daetwyler et al, 2014). The sequence-derived genotypes enable rapid assessment of the frequency of trait-associated variants in populations different from the mapping population.…”