ArticlePloS one2017
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 89 citations in OpenAlex.
- Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results.Journal of animal science · 2018Pooled it
- Morphological indicators of puberty in 3/4 and 5/8 Girolando heifers.Tropical animal health and production · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Sequence-based genome-wide association study reveals genetic and metabolic mechanisms underlying feed efficiency-related traits in beef cattle.Journal of animal science and biotechnology · 2026Article
- Whole-genome sequencing GWAS reveals bovine genomic effects on enteric methane emissions in beef cattle.Scientific reports · 2025Article
- Genomic analysis for cattle breeding improvement, progress and future perspectives in Peru: a review.Animal biotechnology · 2025Review
- Genome-Wide Identification and Characterization of SNPs and InDels ofPlants (Basel, Switzerland) · 2024Article
- Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India.Animal biotechnology · 2024Article
- Genome-wide identification and annotation of SNPs for economically important traits in Frieswal™, newly evolved crossbred cattle of India.3 Biotech · 2023Article
- Unlocking the secrets of ABEs: the molecular mechanism behind their specificity.Biochemical Society transactions · 2023Review
- Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia.Frontiers in genetics · 2023Article
- Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences.PloS one · 2022Article
- Assessing Bos taurus introgression in the UOA Bos indicus assembly.Genetics, selection, evolution : GSE · 2021Article
- Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr.Tropical animal health and production · 2021Article
- Deleterious protein-coding variants in diverse cattle breeds of the world.Genetics, selection, evolution : GSE · 2021Article
- Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review.Animals : an open access journal from MDPI · 2021Review
- Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle.Tropical animal health and production · 2020Article
- Article
- Post-Translational Protein Deimination Signatures in Serum and Serum-Extracellular Vesicles ofInternational journal of molecular sciences · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.