ArticlePloS one2011
Haplotype analysis improved evidence for candidate genes for intramuscular fat percentage from a genome wide association study of cattle.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Haplotype GWAS in Swedish warmblood horses for conformation and jumping traits.Journal of animal science · 2026Article
- Genomic-based genetic parameters and genome-wide association studies for productive and reproductive traits in Beef-on-Dairy crossbreds.Frontiers in genetics · 2025Article
- SNP-Based and Kmer-Based eQTL Analysis Using Transcriptome Data.Animals : an open access journal from MDPI · 2024Article
- A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population.Animal bioscience · 2024Article
- The PPARGC1A Is the Gene Responsible for Thrifty Metabolism Related Metabolic Diseases: A Scoping Review.Genes · 2022Article
- Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days.Animals : an open access journal from MDPI · 2022Article
- Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds.Animal genetics · 2021Article
- Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits.Animals : an open access journal from MDPI · 2020Article
- A TOMM40/APOE allele encoding APOE-E3 predicts high likelihood of late-onset Alzheimer's disease in autopsy cases.Molecular genetics & genomic medicine · 2020Article
- Article
- Evolutionary Pattern of Interferon Alpha Genes in Bovidae and Genetic Diversity of IFNAA in the Bovine Genome.Frontiers in immunology · 2020Article
- Article
- Exploring effective approaches for haplotype block phasing.BMC bioinformatics · 2019Article
- Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Animals : an open access journal from MDPI · 2019Article
- Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle.BMC genetics · 2019Article
- Article
- Lack of UGT polymorphism association with idasanutlin pharmacokinetics in solid tumor patients.Cancer chemotherapy and pharmacology · 2019Article
- Identification of polymorphisms inAsian-Australasian journal of animal sciences · 2018Article
- Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins.PloS one · 2018Article
- Increased expression of thyroid hormone responsive protein (THRSP) is the result but not the cause of higher intramuscular fat content in cattle.International journal of biological sciences · 2017Article
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1 author.
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Abstract
In genome wide association studies (GWAS), haplotype analyses of SNP data are neglected in favour of single point analysis of associations. In a recent GWAS, we found that none of the known candidate genes for intramuscular fat (IMF) had been identified. In this study, data from the GWAS for these candidate genes were re-analysed as haplotypes. First, we confirmed that the methodology would find evidence for association between haplotypes in candidate genes of the calpain-calpastatin complex and musculus longissimus lumborum peak force (LLPF), because these genes had been confirmed through single point analysis in the GWAS. Then, for intramuscular fat percent (IMF), we found significant partial haplotype substitution effects for the genes ADIPOQ and CXCR4, as well as suggestive associations to the genes CEBPA, FASN, and CAPN1. Haplotypes for these genes explained 80% more of the phenotypic variance compared to the best single SNP. For some genes the analyses suggested that there was more than one causative mutation in some genes, or confirmed that some causative mutations are limited to particular subgroups of a species. Fitting the SNPs and their interactions simultaneously explained a similar amount of the phenotypic variance compared to haplotype analyses. Haplotype analysis is a neglected part of the suite of tools used to analyse GWAS data, would be a useful method to extract more information from these data sets, and may contribute to reducing the missing heritability problem.
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