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The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle

ABSTRACT: The relative contributions of both copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) to the additive genetic variance of carcass traits in cattle is not well understood. A detailed understanding of the relative importance of CNVs in cattle may have implications for study design of both genomic predictions and genome-wide association studies. The first objective of the present study was to quantify the relative contributions of CNV data and SNP genotype data to the additive genetic variance of carcass weight, fat, and conformation for 945 Charolais, 923 Holstein-Friesian, and 974 Limousin sires. The second objective was to jointly consider SNP and CNV data in a least absolute selection and shrinkage operator (LASSO) regression model to identify genomic regions associated with carcass weight, fat, and conformation within each of the three breeds separately. A genomic relationship matrix (GRM) based on just CNV data did not capture any variance in the three carcass traits when jointly evaluated with a SNP-derived GRM. In the LASSO regression analysis, a total of 987 SNPs and 18 CNVs were associated with at least one of the three carcass traits in at least one of the three breeds. The quantitative trait loci (QTLs) corresponding to the associated SNPs and CNVs overlapped with several candidate genes including previously reported candidate genes such as MSTN and RSAD2, and several potential novel candidate genes such as ACTN2 and THOC1. The results of the LASSO regression analysis demonstrated that CNVs can be used to detect associations with carcass traits which were not detected using the set of SNPs available in the present study. Therefore, the CNVs and SNPs available in the present study were not redundant forms of genomic data.

SUBMITTER: Rafter P

PROVIDER: S-EPMC8593468 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process.ResultsA total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit.ConclusionsThe present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.

Project description:Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits.By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis.In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.

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The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle

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