Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

Autor: M. Vinsky, Robert Mukiibi, Feng Zhang, Graham Plastow, Paul Stothard, Changxi Li, Liuhong Chen, John A. Basarab, Yining Wang
Rok vydání: 2020
Předmět:
lcsh:QH426-470
lcsh:Biotechnology
Quantitative Trait Loci
Population
Inheritance Patterns
Imputed whole genome sequence variants
Carcass merit traits
Genome-wide association study
Biology
Quantitative trait locus
Polymorphism
Single Nucleotide
03 medical and health sciences
Quantitative Trait
Heritable
lcsh:TP248.13-248.65
Genetic variation
Genetic architecture
Genetics
Animals
Gene Regulatory Networks
Allele
education
Gene
Genetic Association Studies
030304 developmental biology
2. Zero hunger
Whole genome sequencing
0303 health sciences
education.field_of_study
Whole Genome Sequencing
Gene Expression Profiling
0402 animal and dairy science
Genetic Variation
Beef cattle
Genome wide association studies
04 agricultural and veterinary sciences
040201 dairy & animal science
Red Meat
lcsh:Genetics
Phenotype
Cattle
Research Article
Genome-Wide Association Study
Biotechnology
Zdroj: BMC Genomics, Vol 21, Iss 1, Pp 1-22 (2020)
Wang, Y, Zhang, F, Mukiibi, R, Chen, L, Vinsky, M, Plastow, G, Basarab, J, Stothard, P & Li, C 2020, ' Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants : II: carcass merit traits ', BMC Genomics, vol. 21, no. 1, 38 . https://doi.org/10.1186/s12864-019-6273-1
BMC Genomics
ISSN: 1471-2164
DOI: 10.1186/s12864-019-6273-1
Popis: BackgroundGenome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated.ResultsThe distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold ofP-value –5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3’UTR variants, 5’UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3’UTR variants, 5’UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits.ConclusionsThe GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.
Databáze: OpenAIRE
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