ArticleGenetics, selection, evolution : GSE2014
Recombination locations and rates in beef cattle assessed from parent-offspring pairs.
Article in Genetics, selection, evolution : GSE, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 63 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
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- A comparative study on recombination activity in cattle.Genetics, selection, evolution : GSE · 2026Article
- An Increase in Male Recombination Rate With Age in Dairy Cattle Is Heritable and Polygenic.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Genome landscape and genetic architecture of recombination in domestic goats (Capra hircus).Genetics, selection, evolution : GSE · 2025Article
- Genetics of recombination rate variation within and between species.Journal of evolutionary biology · 2025Article
- Exploring Meiotic Recombination and Its Potential Benefits in South African Beef Cattle: A Review.Veterinary sciences · 2025Review
- A vision of how low-coverage sequence data should contribute to genetic evaluation in the future.Journal of animal science · 2025Article
- Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations.Nature communications · 2024Article
- Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation.PloS one · 2024Article
- SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2023Article
- Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes.Plant biotechnology journal · 2022Article
- Predicting the genomic resolution of bulk segregant analysis.G3 (Bethesda, Md.) · 2022Article
- Article
- Genetic variation in recombination rate in the pig.Genetics, selection, evolution : GSE · 2021Article
- Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle.Frontiers in genetics · 2021Article
- Article
- Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle.Frontiers in genetics · 2020Article
- Bos taurus-indicus hybridization correlates with intralocus sexual-conflict effects of PRDM9 on male and female fertility in Holstein cattle.BMC genetics · 2019Article
- Evaluation of fecal samples as a valid source of DNA by comparing paired blood and fecal samples from American bison (Bison bison).BMC genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecombination events tend to occur in hotspots and vary in number among individuals. The presence of recombination influences the accuracy of haplotype phasing and the imputation of missing genotypes. Genes that influence genome-wide recombination rate have been discovered in mammals, yeast, and plants. Our aim was to investigate the influence of recombination on haplotype phasing, locate recombination hotspots, scan the genome for Quantitative Trait Loci (QTL) and identify candidate genes that influence recombination, and quantify the impact of recombination on the accuracy of genotype imputation in beef cattle.
methods2775 Angus and 1485 Limousin parent-verified sire/offspring pairs were genotyped with the Illumina BovineSNP50 chip. Haplotype phasing was performed with DAGPHASE and BEAGLE using UMD3.1 assembly SNP (single nucleotide polymorphism) coordinates. Recombination events were detected by comparing the two reconstructed chromosomal haplotypes inherited by each offspring with those of their sires. Expected crossover probabilities were estimated assuming no interference and a binomial distribution for the frequency of crossovers. The BayesB approach for genome-wide association analysis implemented in the GenSel software was used to identify genomic regions harboring QTL with large effects on recombination. BEAGLE was used to impute Angus genotypes from a 7K subset to the 50K chip.
resultsDAGPHASE was superior to BEAGLE in haplotype phasing, which indicates that linkage information from relatives can improve its accuracy. The estimated genetic length of the 29 bovine autosomes was 3097 cM, with a genome-wide recombination distance averaging 1.23 cM/Mb. 427 and 348 windows containing recombination hotspots were detected in Angus and Limousin, respectively, of which 166 were in common. Several significant SNPs and candidate genes, which influence genome-wide recombination were localized in QTL regions detected in the two breeds. High-recombination rates hinder the accuracy of haplotype phasing and genotype imputation.
conclusionsSmall population sizes, inadequate half-sib family sizes, recombination, gene conversion, genotyping errors, and map errors reduce the accuracy of haplotype phasing and genotype imputation. Candidate regions associated with recombination were identified in both breeds. Recombination analysis may improve the accuracy of haplotype phasing and genotype imputation from low- to high-density SNP panels.
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.