Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

Abstract

BackgroundOne of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or genomic regions with phenotypes. The completion of the bovine genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of the genetic variations present in cattle. Here we describe the whole-genome resequencing of two Bos taurus bulls from distinct breeds for the purpose of identifying and annotating novel forms of genetic variation in cattle.ResultsThe genomes of a Black Angus bull and a Holstein bull were sequenced to 22-fold and 19-fold coverage, respectively, using the ABI SOLiD system. Comparisons of the sequences with the Btau4.0 reference assembly yielded 7 million single nucleotide polymorphisms (SNPs), 24% of which were identified in both animals. Of the total SNPs found in Holstein, Black Angus, and in both animals, 81%, 81%, and 75% respectively are novel. In-depth annotations of the data identified more than 16 thousand distinct non-synonymous SNPs (85% novel) between the two datasets. Alignments between the SNP-altered proteins and orthologues from numerous species indicate that many of the SNPs alter well-conserved amino acids. Several SNPs predicted to create or remove stop codons were also found. A comparison between the sequencing SNPs and genotyping results from the BovineHD high-density genotyping chip indicates a detection rate of 91% for homozygous SNPs and 81% for heterozygous SNPs. The false positive rate is estimated to be about 2% for both the Black Angus and Holstein SNP sets, based on follow-up genotyping of 422 and 427 SNPs, respectively. Comparisons of read depth between the two bulls along the reference assembly identified 790 putative copy-number variations (CNVs). Ten randomly selected CNVs, five genic and five non-genic, were successfully validated using quantitative real-time PCR. The CNVs are enriched for immune system genes and include genes that may contribute to lactation capacity. The majority of the CNVs (69%) were detected as regions with higher abundance in the Holstein bull.ConclusionsSubstantial genetic differences exist between the Black Angus and Holstein animals sequenced in this work and the Hereford reference sequence, and some of this variation is predicted to affect evolutionarily conserved amino acids or gene copy number. The deeply annotated SNPs and CNVs identified in this resequencing study can serve as useful genetic tools, and as candidates in searches for phenotype-altering DNA differences.

BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection1–3

“…The SNP on these arrays, primarily selected using spacing along the genome and allele frequency (Matukumalli et al, 2009;Ramos et al, 2009), are ef- Table 6. Genetic correlations between genomic EBV trained by GPE Cycle VII shear force measurements, using whole-genome and sets selected by functional annotation and association with phenotype, and 14-d slice shear force measured on steers from Cycle VIII and continuous GPE 1 (Cánovas et al, 2010;Stothard et al, 2011;Larkin et al, 2012). Categorizing these variants according to expected effect on annotated protein coding genes may reveal the variants most infl uential to gene function (McLaren et al, 2010;Cingolani et al, 2012).…”

Adaptation to abiotic stress in the oyster Crassostrea angulata relays on genetic polymorphisms

“…However, it could also be related to differences between C. angulata and C. gigas genomes, that may reflect the finding that C. angulata is evolutionarily more distant from the reference genome (C. gigas) than is usually thought [37e39]. On the other hand, the average mapping depth presents lower values than those observed in the wild C. gigas oyster (50-fold) [3] and Korean cattle (45.6-fold) [40] but higher than those previously reported in whole-genome re-sequenced carried out in cattle of the Black Angus and Holstein breed (9.8-fold and 10.8-fold, respectively) [41] or Japanese native cattle (15.8-fold) [42]. So, in spite of the large number of scaffolds existing in the reference genome, ranging between 100 bp and 1.9 millions bp in size (Supplementary file 1), both the coverage of reads and the mapping depth obtained (83.36% and 29.34-fold respectively) are in the range of optimal values required for the analysis of the genome of C. angulata by a whole-genome re-sequencing approach.…”

The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility

“…The libraries were prepared using the reagents and protocols provided by Applied Biosystems, and as reported in previous studies. 29 Sequence reads were mapped to the Btau4.0 bovine genome assembly using the Bioscope 1.0 software suite (Life Technologies Corporation). A list of putative SNPs was generated for each animal from the mapped reads, using the diBayes SNP Detection module (with the "med-coverage" stringency setting) included with Bioscope.…”

“…Transcript sequences from liver, hypothalamus, muscle, adipose, duodenum, kidney, lung blood, cortex and Peyer's patch were evaluated to identify SNPs in each of the 89 candidate genes mapped to the 57 regions of the bovine genome thought to be related to BSE susceptibility. Whole-genome sequences from a Holstein bull and a Black Angus bull 29 were also used to identify structural variation within candidate genes. Non-synonymous mutations were selected when available as were SNPs predicted to introduce a stop codon or splice variation.…”