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

Abstract

Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

“…On average for each breed, 1.4 M (12%) of the detected variants had small insertions and deletions (InDels, Table 1B). The SNP variants results from Cameroonian cattle were much higher as compared to the 27 M SNPs obtained by Stafuzza et al [23] on Bos indicus Gyr, Girolando, Gruzerat and Bos taurus Holstein cattle breeds from Brazil, whereas our obtained SNP variants were markedly lower as compared to those reported by Kim et al [17] on East African zebu (Boran, Ogaden, Kenana) and Sanga (Ankole, taurine/zebu crossbreeds). The ratio of the number of heterozygous to homozygous SNP variants were different across the cattle breeds.…”

“…Interestingly, a very high proportion of raw reads was mapped ranging from 98.9 % for Namchi up to 99.6 % for Red Fulani (Table 1B). Our mapping rates were even higher than reported by Kim et al [17] from other indigenous East African cattle breeds (Ankole, Boran and Ogaden) and of other cattle re-sequencing studies published [16,17,[21][22][23].…”

“…The density of variants per chromosome was proportional to the chromosome length, except for the X chromosomes which showed a lower number of variants identi ed (Additional le 2 Figure S2). These ndings were expected because the DNA of X chromosomes is subject to an increased natural selection, which leads to less genetic diversity [23].…”

Post-Translational Protein Deimination Signatures in Serum and Serum-Extracellular Vesicles of Bos taurus Reveal Immune, Anti-Pathogenic, Anti-Viral, Metabolic and Cancer-Related Pathways for Deimination

“…Regulation of ECM-receptor interactions via post-translational deimination has recently been identified by our group via enrichment of deiminated proteins in KEGG pathways for ECM-receptor interactions in the fin whale, a long-lived cancer-resistant animal [96], in the alligator, an animal with unusual antibacterial and anti-viral responses [93], in the wandering albatross (Diomedea exulans), also an unusually long-lived bird for an avian species [99], as well as in aggressive brain cancer cells [100]. In the cow, ECM-receptor interactions are amongst other related to depot-specific adipogenesis [195] and found to be over-represented in specific cattle breeds [196]. ECM-receptor interaction pathway has furthermore been identified in Holstein cattle in relation to adaptive immune responses following viral vaccination [197] and in intra-mammary infection with Streptococcus agalactiae [198].…”

Accurate sequence variant genotyping in cattle using variation-aware genome graphs

“…An intersection of 15,901,526 biallelic SNPs was common to all sequence-variant discovery tools evaluated (Figure 2A), i.e., between 85. 51 Table 2 Average number of autosomal variants identified per animal using three sequence variant genotyping methods.…”