ArticleJournal of applied genetics2016
Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle.
Article in Journal of applied genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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
32 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Relationship between theAnimal biotechnology · 2025Article
- Transcriptome-wide association studies identify candidate genes for carcass and meat traits in meat rabbits.Frontiers in veterinary science · 2024Article
- Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows.Animals : an open access journal from MDPI · 2023Article
- Whole genome sequencing of simmental cattle for SNP and CNV discovery.BMC genomics · 2023Article
- Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle.BMC genomics · 2022Article
- Copy Number Variation of theAnimals : an open access journal from MDPI · 2022Article
- Comparison of Growth Performance, Immunity, Antioxidant Capacity, and Liver Transcriptome of Calves between Whole Milk and Plant Protein-Based Milk Replacer under the Same Energy and Protein Levels.Antioxidants (Basel, Switzerland) · 2022Article
- Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems.Frontiers in genetics · 2022Article
- An Overview of Waste Milk Feeding Effect on Growth Performance, Metabolism, Antioxidant Status and Immunity of Dairy Calves.Frontiers in veterinary science · 2022Review
- Genome-wide detection of CNVs and their association with performance traits in broilers.BMC genomics · 2021Article
- High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data.Scientific reports · 2020Article
- Article
- Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits.Frontiers in genetics · 2020Article
- Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak.Animals : an open access journal from MDPI · 2019Article
- Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.BMC genomics · 2019Article
- A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive.BMC genomics · 2019Article
- Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle.Scientific reports · 2019Article
- Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins.BMC genomics · 2019Article
- Metabolomics Profile and Targeted Lipidomics in Multiple Tissues Associated with Feed Efficiency in Beef Steers.ACS omega · 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
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.
Indexed as
Identifiers
27001052What 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.