ArticleBMC genetics2019
Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle.
Article in BMC genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 46 citations in OpenAlex.
- Genetic Variation and Haplotype Structure ofLife (Basel, Switzerland) · 2026Article
- Effects of Single-Nucleotide Polymorphisms on the Estimated Breeding Values for Feet in Holstein-Friesian Cows in Hungary.Animals : an open access journal from MDPI · 2026Article
- SNPs with High Linkage Disequilibrium Increase the Explained Genetic Variance and the Reliability of Genomic Predictions.Animals : an open access journal from MDPI · 2026Article
- Genome-Wide Association Study on the Estimated Breeding Values for Udder and Longevity and the Candidate Genes in Holstein-Friesian Cows in Hungary.Animals : an open access journal from MDPI · 2025Article
- Integrative Genomic and Metabolomic Analysis Identifies mQTLs Associated with Genetic Selection for Tenderness in Nellore Cattle.Metabolites · 2025Article
- Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Genomic-based genetic parameters and genome-wide association studies for productive and reproductive traits in Beef-on-Dairy crossbreds.Frontiers in genetics · 2025Article
- 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
- Hepatic Transcriptome Analysis Reveals Genes, Polymorphisms, and Molecules Related to Lamb Tenderness.Animals : an open access journal from MDPI · 2023Article
- Analysis of dog breed diversity using a composite selection index.Scientific reports · 2023Article
- Bibliometric Analysis of Research on the Main Genes Involved in Meat Tenderness.Animals : an open access journal from MDPI · 2022Review
- Association study and expression analysis of olfactomedin like 3 gene related to meat quality, carcass characteristics, retail meat cut, and fatty acid composition in sheep.Animal bioscience · 2022Article
- Article
- Genetic architecture of a composite beef cattle population.Journal of animal science · 2022Article
- Weighted Single-Step Genomic Best Linear Unbiased Prediction Method Application for Assessing Pigs on Meat Productivity and Reproduction Traits.Animals : an open access journal from MDPI · 2022Article
- Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.Plant communications · 2022Article
- Characterization of novelEvolutionary applications · 2022Article
- Transcriptome-metabolome analysis reveals how sires affect meat quality in hybrid sheep populations.Frontiers in nutrition · 2022Article
- Article
- A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs.Frontiers in genetics · 2021Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundTraditional single nucleotide polymorphism (SNP) genome-wide association analysis (GWAA) can be inefficient because single SNPs provide limited genetic information about genomic regions. On the other hand, using haplotypes in the statistical analysis may increase the extent of linkage disequilibrium (LD) between haplotypes and causal variants and may also potentially capture epistastic interactions between variants within a haplotyped locus, providing an increase in the power and robustness of the association studies. We performed GWAA (413,355 SNP markers) using haplotypes based on variable-sized sliding windows and compared the results to a single-SNP GWAA using Warner-Bratzler shear force measured in the longissimus thorasis muscle of 3161 Nelore bulls to ascertain the optimal window size for identifying the genomic regions that influence meat tenderness.
resultsThe GWAA using single SNPs identified eight variants influencing meat tenderness on BTA 3, 4, 9, 10 and 11. However, thirty-three putative meat tenderness QTL were detected on BTA 1, 3, 4, 5, 8, 9, 10, 11, 15, 17, 18, 24, 25, 26 and 29 using variable-sized sliding haplotype windows. Analyses using sliding window haplotypes of 3, 5, 7, 9 and 11 SNPs identified 57, 61, 42, 39, and 21% of all thirty-three putative QTL regions, respectively; however, the analyses using the 3 and 5 SNP haplotypes, cumulatively detected 88% of the putative QTL. The genes associated with variation in meat tenderness participate in myogenesis, neurogenesis, lipid and fatty acid metabolism and skeletal muscle structure or composition processes.
conclusionsGWAA using haplotypes based on variable-sized sliding windows allowed the detection of more QTL than traditional single-SNP GWAA. Analyses using smaller haplotypes (3 and 5 SNPs) detected a higher proportion of the putative QTL.
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