Dataset Information

Linear classification scores in beef cattle as predictors of genetic merit for individual carcass primal cut yields1.

ABSTRACT: Having access to early predictions of both the genetic merit and expected phenotypic performance of an individual or its progeny can contribute to more informed decision-making. The objective here was to evaluate the usefulness of routinely available subjectively scored linear conformation information on live animals to predict genetic merit for primal carcass cut yields of their relatives. Data on 6 muscular and 6 skeletal traits on 43,078 live animals were used; the weights of up to 14 primal cuts plus 3 groups of primal cuts of 31,827 cattle were also used. Genetic correlations between the linear scores and the primal cut weights were estimated using sire linear mixed models; correlations were estimated with or without phenotypic adjustment of the primal cut weights to a constant carcass weight. The genetic correlations between each of the muscular and skeletal linear type traits with each of the primal cut weights (not adjusted for carcass weight) were all positive with the exception of the correlations between both chest width and pelvic length with cuberoll. On average, the muscular type traits were more strongly correlated (on average 0.42) with the primal cut weights than the skeletal traits (on average 0.35). Moreover, the average of the genetic correlations between each of the 6 muscular traits with all 8 hindquarter traits was, on average, 10% to 18% stronger than the average of the genetic correlations between the same muscular traits with all 5 forequarter primal cuts. When adjusted for differences in carcass weight, the correlations between all linear scores and the carcass traits regressed to zero or became negative. The skeletal traits were, in general, weakly genetically correlated with the primal cuts adjusted to a common carcass weight. The average of the genetic correlation between the muscular type traits and the primal cuts adjusted for differences in carcass weight was only 0.09 with only 13 of the 84 pairwise correlations being stronger than 0.30; the genetic correlation between silverside with the muscular traits was all stronger than 0.30, whereas the majority of the muscular traits had a correlation stronger than 0.30 with the topside primal cut. In fact, the average of the genetic correlations between the topside and silverside cuts with all the muscular traits was 0.50 and 0.42, respectively, with none of the correlations being negative.

SUBMITTER: Berry DP

PROVIDER: S-EPMC6541829 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Linear classification scores in beef cattle as predictors of genetic merit for individual carcass primal cut yields1.

Berry Donagh P DP Pabiou Thierry T Fanning Rory R Evans Ross D RD Judge Michelle M MM

Journal of animal science 20190501 6

Having access to early predictions of both the genetic merit and expected phenotypic performance of an individual or its progeny can contribute to more informed decision-making. The objective here was to evaluate the usefulness of routinely available subjectively scored linear conformation information on live animals to predict genetic merit for primal carcass cut yields of their relatives. Data on 6 muscular and 6 skeletal traits on 43,078 live animals were used; the weights of up to 14 primal ...[more]

PMID: 31100112

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Project description:The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38-39 Mb, 11 at 21-22 Mb, 14 at 6-7 Mb and 26-27 Mb, and 19 at 26-27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM-receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.

Project description:Improvement of carcass merit traits is a priority for the beef industry. Discovering DNA variants and genes associated with variation in these traits and understanding biological functions/processes underlying their associations are of paramount importance for more effective genetic improvement of carcass merit traits in beef cattle. This study integrates 10,488,742 imputed whole genome DNA variants, 31 plasma metabolites, and animal phenotypes to identify genes and biological functions/processes that are associated with carcass merit traits including hot carcass weight (HCW), rib eye area (REA), average backfat thickness (AFAT), lean meat yield (LMY), and carcass marbling score (CMAR) in a population of 493 crossbred beef cattle. Regression analyses were performed to identify plasma metabolites associated with the carcass merit traits, and the results showed that 4 (3-hydroxybutyric acid, acetic acid, citric acid, and choline), 6 (creatinine, L-glutamine, succinic acid, pyruvic acid, L-lactic acid, and 3-hydroxybutyric acid), 4 (fumaric acid, methanol, D-glucose, and glycerol), 2 (L-lactic acid and creatinine), and 5 (succinic acid, fumaric acid, lysine, glycine, and choline) plasma metabolites were significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using the 10,488,742 imputed SNPs, 103, 160, 83, 43, and 109 candidate genes were identified as significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 1 × 10-5), respectively. By applying functional enrichment analyses for candidate genes of each trait, 26, 24, 26, 24, and 28 significant cellular and molecular functions were predicted for HCW, REA, AFAT, LMY, and CMAR, respectively. Among the five topmost significantly enriched biological functions for carcass merit traits, molecular transport and small molecule biochemistry were two top biological functions associated with all carcass merit traits. Lipid metabolism was the most significant biological function for LMY and CMAR and it was also the second and fourth highest biological function for REA and HCW, respectively. Candidate genes and enriched biological functions identified by the integrative analyses of metabolites with phenotypic traits and DNA variants could help interpret the results of previous genome-wide association studies for carcass merit traits. Our integrative study also revealed additional potential novel genes associated with these economically important traits. Therefore, our study improves understanding of the molecular and biological functions/processes that influence carcass merit traits, which could help develop strategies to enhance genomic prediction of carcass merit traits with incorporation of metabolomic data. Similarly, this information could guide management practices, such as nutritional interventions, with the purpose of boosting specific carcass merit traits.

Project description:The ability to alter the morphology of cattle towards greater yields of higher value primal cuts has the potential to increase the value of animals at slaughter. Using weight records of 14 primal cuts from 31,827 cattle, the objective of the present study was to quantify the extent of genetic variability in these primal cuts; also of interest was the degree of genetic variability in the primal cuts adjusted to a common carcass weight. Variance components were estimated for each primal cut using animal linear mixed models. The coefficient of genetic variation in the different primal cuts ranged from 0.05 (bavette) to 0.10 (eye of round) with a mean coefficient of genetic variation of 0.07. When phenotypically adjusted to a common carcass weight, the coefficient of genetic variation of the primal cuts was lesser ranging from 0.02 to 0.07 with a mean of 0.04. The heritability of the 14 primal cuts ranged from 0.14 (bavette) to 0.75 (topside) with a mean heritability across all cuts of 0.48; the heritability estimates reduced, and ranged from 0.12 (bavette) to 0.56 (topside), when differences in carcass weight were accounted for in the statistical model. Genetic correlations between each primal cut and carcass weight were all ?0.77; genetic correlations between each primal cut and carcass conformation score were, on average, 0.59 but when adjusted to a common carcass weight, the correlations weakened to, on average, 0.27. The genetic correlations among all 14 primal cut weights was, on average, strong (mean correlation of 0.72 with all correlations being ?0.37); when adjusted to a common carcass weight, the mean of the genetic correlations among all primal cuts was 0.10. The ability of estimated breeding values for a selection of primal cuts to stratify animals phenotypically on the respective cut weight was demonstrated; the weight of the rump, striploin, and fillet of animals estimated to be in the top 25% genetically for the respective cut, were 10 to 24%, 12 to 24%, and 7 to 17% heavier than the weight of cuts from animals predicted to be in the worst 25% genetically for that cut. Significant exploitable genetic variability in primal carcass cuts was clearly evident even when adjusted to a common carcass weight. The high heritability of many of the primal cuts infers that large datasets are not actually required to achieve high accuracy of selection once the structure of the data and the number of progeny per sire is adequate.

Project description:BACKGROUND:Genome 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. RESULTS:The 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 of P-value <?10-5, 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. CONCLUSIONS:The 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.

Project description:BACKGROUND: Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. This paper presents a genome-wide association approach utilizing single nucleotide polymorphisms (SNP) in the Illumina BovineSNP50 BeadChip to seek genomic regions that potentially harbor genes or QTN underlying variation in carcass quality of beef cattle.This study used 747 genotyped animals, mainly crossbred, with phenotypes on twelve carcass quality traits, including hot carcass weight (HCW), back fat thickness (BF), Longissimus dorsi muscle area or ribeye area (REA), marbling scores (MRB), lean yield grade by Beef Improvement Federation formulae (BIFYLD), steak tenderness by Warner-Bratzler shear force 7-day post-mortem (LM7D) as well as body composition as determined by partial rib (IMPS 103) dissection presented as a percentage of total rib weight including body cavity fat (BDFR), lean (LNR), bone (BNR), intermuscular fat (INFR), subcutaneous fat (SQFR), and total fat (TLFR). RESULTS: At the genome wide level false discovery rate (FDR?<?10%), eight SNP were found significantly associated with HCW. Seven of these SNP were located on Bos taurus autosome (BTA) 6. At a less stringent significance level (P?<?0.001), 520 SNP were found significantly associated with mostly individual traits (473 SNP), and multiple traits (47 SNP). Of these significant SNP, 48 were located on BTA6, and 22 of them were in association with hot carcass weight. There were 53 SNP associated with percentage of rib bone, and 12 of them were on BTA20. The rest of the significant SNP were scattered over other chromosomes. They accounted for 1.90 - 5.89% of the phenotypic variance of the traits. A region of approximately 4 Mbp long on BTA6 was found to be a potential area to harbor candidate genes influencing growth. One marker on BTA25 accounting for 2.67% of the variation in LM7D may be worth further investigation for the improvement of beef tenderness. CONCLUSION: This study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting carcass quality traits in beef cattle. It also revealed many SNP that acted pleiotropically to affect carcass quality. This knowledge is important in selecting subsets of SNP to improve the performance of beef cattle.

Dataset Information

Linear classification scores in beef cattle as predictors of genetic merit for individual carcass primal cut yields1.

Publications

Linear classification scores in beef cattle as predictors of genetic merit for individual carcass primal cut yields1.

Similar Datasets

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