Carcass Phenotypes Research Articles

Deep Learning-Based Automated Approach for Determination of Pig Carcass Traits.

Pig carcass traits are among the most economically significant characteristics and are crucial for genetic selection in breeding and enhancing the economic efficiency. Standardized and automated carcass phenotyping can greatly enhance the measurement efficiency and accuracy, thereby facilitating the selection and breeding of superior pig carcasses. In this study, we utilized phenotypic images and data from 3912 pigs to propose a deep learning-based approach for the automated determination of pig carcass phenotypic traits. Using the YOLOv8 algorithm, our carcass length determination model achieves an average accuracy of 99% on the test set. Additionally, our backfat segmentation model, YOLOV8n-seg, demonstrates robust segmentation performance, with a Mean IoU of 89.10. An analysis of the data distribution comparing manual and model-derived measurements revealed that differences in the carcass straight length are primarily concentrated between -2 cm and 4 cm, while differences in the carcass diagonal length are concentrated between -3 cm and 2 cm. To validate the method, we compared model measurements with manually obtained data, achieving coefficients of determination (R2) of 0.9164 for the carcass straight length, 0.9325 for the carcass diagonal length, and 0.7137 for the backfat thickness, indicating high reliability. Our findings provide valuable insights into automating carcass phenotype determination and grading in pig production.

Objective grading of rib eye traits using the Q-FOM™ camera in Australian beef carcasses

The objective of this study was to develop calibration models against rib eye traits and independently validate the precision, accuracy, and repeatability of the Frontmatec Q-FOM™ Beef grading camera in Australian carcasses. This study compiled 12 different research datasets acquired from commercial processing facilities and were comprised of a diverse range of carcass phenotypes, graded by industry identified expert Meat Standards Australia (MSA) graders and sampled for chemical intramuscular fat (IMF%). Calibration performance was maintained when the device was independently validated. For continuous traits, the Q-FOM™ demonstrated precise (root mean squared error of prediction, RMSEP) and accurate (coefficient of determination, R2) prediction of eye muscle area (EMA) (R2 = 0.89, RMSEP = 4.3 cm2, slope = 0.96, bias = 0.7), MSA marbling (R2 = 0.95, RMSEP = 47.2, slope = 0.98, bias = −12.8) and chemical IMF% (R2 = 0.94, RMSEP = 1.56%, slope = 0.96, bias = 0.64). For categorical traits, the Q-FOM™ predicted 61%, 64.3% and 60.8% of AUS-MEAT marbling, meat colour and fat colour scores equivalent, and 95% within ±1 classes of expert grader scores. The Q-FOM™ also demonstrated very high repeatability and reproducibility across all traits.

RNA Sequencing of the Pituitary Gland and Association Analyses Reveal PRKG2 as a Candidate Gene for Growth and Carcass Traits in Chinese Ningdu Yellow Chickens.

Growth and carcass traits are of great economic importance to the chicken industry. The candidate genes and mutations associated with growth and carcass traits can be utilized to improve chicken growth. Therefore, the identification of these genes and mutations is greatly importance. In this study, a total of 17 traits related to growth and carcass were measured in 399 Chinese Ningdu yellow chickens. RNA sequencing (RNA-seq) was performed to detect candidate genes using 12 pituitary gland samples (six per group), which exhibited extreme growth and carcass phenotypes: either a high live weight and carcass weight (H group) or a low live weight and carcass weight (L group). A differential expression analysis, utilizing RNA-seq, between the H and L groups identified 428 differentially expressed genes (DEGs), including 110 up-regulated genes and 318 down-regulated genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the identified genes showed a significant enrichment of 158 GO terms and two KEGG pathways, including response to stimulus and neuroactive ligand-receptor interaction, respectively. Furthermore, RNA-seq data, qRT–PCR, and quantitative trait transcript (QTT) analysis results suggest that the PRKG2 gene is an important candidate gene for growth and carcass traits of Chinese Ningdu yellow chickens. More specifically, association analyses of a single nucleotide polymorphism (SNP) in PRKG2 and growth and carcass traits showed that the SNP rs16400745 was significantly associated with 12 growth and carcass traits (P < 0.05), such as carcass weight (P = 9.68E-06), eviscerated weight (P = 3.04E-05), and semi-eviscerated weight (P = 2.14E-04). Collectively, these results provide novel insights into the genetic basis of growth in Chinese Ningdu yellow chickens and the SNP rs16400745 reported here could be incorporated into the selection programs involving this breed.

A parallel survey on the fatty acid composition in backfat and longissimus lumborum and comparison of their associations with growth and carcass traits in pigs

Compositions of fatty acids are critical parameters of meat nutrition and palatability. This study investigated phenotypes of 21 fatty acid composition traits in both backfat (BF) and longissimus lumborum (LL) tissues in 583 F7 mosaic pigs from an eight-breed crossed heterogeneous population, and their associations with 25 detailed measured growth and carcass traits in the same population. We showed that the LL has significantly higher content of saturated and mono-unsaturated fatty acids, and lower poly-unsaturated fatty acids than BF. Most of fatty acid composition traits in both LL and BF show significant correlations with growth and carcass traits. Notably, the correlations with the growth and carcass traits for fatty acid composition traits in BF are much stronger than that in LL, suggesting closer relationship of the growth and carcass traits with metabolism of the fatty acids in fat than in muscle. The polyunsaturated fatty acid traits including C18:2n6, PUFA, C20:2n6, C20:3n6 were among the fatty acid composition traits showing the strongest correlation with growth and carcass traits in both BF and LL, suggesting an interesting link between the metabolism of polyunsaturated fatty acids in muscle and fat tissues with the growth and carcass phenotypes. The results provide helpful insights that are helpful to the breeding program aiming to simultaneously improve the fatty acid composition, growth and carcass traits in pigs.

Effect of feed restriction on the intestinal microbial community structure of growing ducks.

In poultry, feed restriction is common feeding management to limit poultry nutrients intake so that poultry only intake the essential energy, meeting the basic need of growth and development. Our study investigated whether feeding restriction affects the diversity of the intestinal microbiota of growing breeding ducks. In this research, the 60-120-day-old ducks were raised in restricted and free-feeding groups. After slaughtering, the carcass traits and the cecal contents were collected for 16S rRNA sequencing analysis. After feeding restriction, the growth rate of ducks was limited, the weight and rate of abdominal fat decreased, and the rate of chest and leg muscles increased. In addition, feeding restriction can also change the diversity of intestinal microorganisms in breeding ducks, such as the increase of Firmicutes abundance and the decrease of Bacteroidetes abundance. After analyzing of correlation, significant correlations between gut microbiota and carcass phenotypes were found. The results indicated that gut microbiota might be involved in the life activities associated with phenotypic changes. This study proved the effect of feeding methods on the intestinal microbiota of ducks, providing a theoretical basis of the microbial angle for raising ducks in a feeding-restricted period.

Quantifying genetic differences between exported dairy bull calves and those sold for domestic beef production

Selection bias is introduced when selection among individuals exists but the information used to inform that selection decision is not considered in downstream genetic evaluations. Genetic evaluations are undertaken in several countries for carcass-related metrics in prime cattle; no consideration is generally taken for animals that are harvested at a younger age for veal production and thus do not express the prime carcass phenotype. Although no veal industry exists in Ireland, dairy calves are routinely exported to continental Europe for veal production. The objective of the present study, based on a cross-sectional analysis of calf export data, was to determine quantitatively if genetic variability exists in whether purchased dairy-bred bull calves are immediately exported or retained within the country for domestic production. Also of interest was whether such a genetic difference was associated with differences in carcass weight, conformation score, and fat score in prime cattle relatives. Editing criteria were imposed to consider only Holstein-Friesian bull calves. Post-editing, the fate of 43,890 Holstein-Friesian bull calves (<100 d of age) was available; variance components for the binary phenotype (sold for export or not) were estimated using both linear and threshold animal models, and genetic correlations with carcass traits from 56,366 prime cattle were estimated. The heritability (standard error) of whether or not a calf was exported was 0.04 (0.01) on the linear scale and 0.07 (0.02) on the threshold scale. Although no explicit maternal genetic effect was detected, the proportion of the phenotypic variance due to maternal effects was 0.03 to 0.07. The genetic correlation (standard error) between the export phenotype with carcass weight, conformation score [scale 1 (poor) to 15 (excellent)], and fat score [scale 1 (thin) to 15 (fat)] in prime cattle was 0.002 (0.12), −0.25 (0.12), and −0.32 (0.11), respectively. The low heritability of the calf export phenotype and lack of a strong genetic correlation with carcass metrics suggest that other calf features might be greater determinants of the eventual fate of the calf. Accounting for the export phenotype in genetic evaluations of carcass traits in prime cattle had a negligible effect on the estimated breeding values for carcass merit.

Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle

BackgroundIn this study, we assessed the accuracy of genomic prediction for carcass weight (CWT), marbling score (MS), eye muscle area (EMA) and back fat thickness (BFT) in Hanwoo cattle when using genomic best linear unbiased prediction (GBLUP), weighted GBLUP (wGBLUP), and a BayesR model. For these models, we investigated the potential gain from using pre-selected single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) on imputed sequence data and from gene expression information. We used data on 13,717 animals with carcass phenotypes and imputed sequence genotypes that were split in an independent GWAS discovery set of varying size and a remaining set for validation of prediction. Expression data were used from a Hanwoo gene expression experiment based on 45 animals.ResultsUsing a larger number of animals in the reference set increased the accuracy of genomic prediction whereas a larger independent GWAS discovery dataset improved identification of predictive SNPs. Using pre-selected SNPs from GWAS in GBLUP improved accuracy of prediction by 0.02 for EMA and up to 0.05 for BFT, CWT, and MS, compared to a 50 k standard SNP array that gave accuracies of 0.50, 0.47, 0.58, and 0.47, respectively. Accuracy of prediction of BFT and CWT increased when BayesR was applied with the 50 k SNP array (0.02 and 0.03, respectively) and was further improved by combining the 50 k array with the top-SNPs (0.06 and 0.04, respectively). By contrast, using BayesR resulted in limited improvement for EMA and MS. wGBLUP did not improve accuracy but increased prediction bias. Based on the RNA-seq experiment, we identified informative expression quantitative trait loci, which, when used in GBLUP, improved the accuracy of prediction slightly, i.e. between 0.01 and 0.02. SNPs that were located in genes, the expression of which was associated with differences in trait phenotype, did not contribute to a higher prediction accuracy.ConclusionsOur results show that, in Hanwoo beef cattle, when SNPs are pre-selected from GWAS on imputed sequence data, the accuracy of prediction improves only slightly whereas the contribution of SNPs that are selected based on gene expression is not significant. The benefit of statistical models to prioritize selected SNPs for estimating genomic breeding values is trait-specific and depends on the genetic architecture of each trait.

Cattle production practices and the incidence of dark cutting beef

The effects of cattle sex, production system, growth promotant use, slaughter season, carcass phenotype, and pre-slaughter cattle management on the incidence of beef carcasses grading Canada B4 (dark cutting) were investigated using two data sets (A, n = 2009, and B, n = 86,408) containing data from cattle that produced Canada Prime, AAA, AA, A, and B4 carcasses. The probability of producing a Canada B4 carcass was greater (P < .0001) for heifers than steers in both data sets, with the likelihood of dark cutting decreasing with increased carcass weight in heifers in data set B. The incidence of dark cutting was increased (P < .0001) in Winter-born calf-fed (WC) and Fall-born calf-fed (FC) heifers. Production system and phenotype appear to interact to influence the incidence of dark cutting.

Predicted carcass meat yield and primal cut yields in cattle divergent in genetic merit for a terminal index.

Several studies have clearly demonstrated the favorable impact of genetic selection on increasing beef cattle performance within the farm gate. Few studies, however, have attempted to quantify the value of genetic selection to downstream sectors of the beef industry, such as the meat processing sector. The objective of the current study was to characterize detailed carcass attributes of animals divergent in genetic merit for a terminal index as well as individual measures of genetic merit for carcass weight, conformation, and fat. The data used consisted of 53,674 young bulls and steers slaughtered between the years 2010 and 2013 in multiple Irish processing plants. All animals had a genetic evaluation as well as phenotypic measures of carcass characteristics. A terminal index, based on pedigree index for calving performance, feed intake, and carcass traits, calculated from the Irish national genetic evaluations, was obtained for each animal. Animals were categorized into four terminal index groups based on genetic merit estimates derived prior to the expression of the carcass phenotype by the animal. The association between genetic merit for terminal index with predicted phenotypic carcass red meat yield, carcass fat, carcass bone, and carcass composition, as well as between genetic merit for carcass weight, conformation, and fat with predicted phenotypic carcass red meat yield and composition were all quantified using linear mixed models. A greater terminal index value was associated with, on average, heavier phenotypic weights of each wholesale cut category. A greater terminal index value was also associated with a greater weight of meat and bone, but reduced carcass fat. Relative to animals in the lowest 25% genetic merit group, animals in the highest 25% genetic merit group had, on average, a greater predicted yield of very high value cuts (4.52 kg), high value cuts (13.13 kg), medium value cuts (6.06 kg), low value cuts (13.25 kg) as well as more total meat yield (37 kg). The results from the present study clearly signify a benefit to meat processers from breeding programs for terminal characteristics; coupled with the previously documented benefits to the producer, the benefits of breeding programs across the entire food production chain are obvious.

Genetic correlations between endo-parasite phenotypes and economically important traits in dairy and beef cattle.

Parasitic diseases have economic consequences in cattle production systems. Although breeding for parasite resistance can complement current control practices to reduce the prevalence globally, there is little knowledge of the implications of such a strategy on other performance traits. Records on individual animal antibody responses to Fasciola hepatica, Ostertagia ostertagi, and Neospora caninum were available from cows in 68 dairy herds (study herds); national abattoir data on F. hepatica-damaged livers were also available from dairy and beef cattle. After data edits, 9,271 dairy cows remained in the study herd dataset, whereas 19,542 dairy cows and 68,048 young dairy and beef animals had a record for the presence or absence of F. hepatica-damaged liver in the national dataset. Milk, reproductive, and carcass phenotypes were also available for a proportion of these animals as well as their contemporaries. Linear mixed models were used to estimate variance components of antibody responses to the three parasites; covariance components were estimated between the parasite phenotypes and economically important traits. Heritability of antibody responses to the different parasites, when treated as a continuous trait, ranged from 0.07 (O. ostertagi) to 0.13 (F. hepatica), whereas the coefficient of genetic variation ranged from 4% (O. ostertagi) to 20% (F. hepatica). The antibody response to N. caninum was genetically correlated with the antibody response to both F. hepatica (-0.29) and O. ostertagi (-0.67); a moderately positive genetic correlation existed between the antibody response to F. hepatica and O. ostertagi (0.66). Genetic correlations between the parasite phenotypes and the milk production traits were all close to zero (-0.14 to 0.10), as were the genetic correlations between F. hepatica-damaged livers and the carcass traits of carcass weight, conformation, and fat score evaluated in cows and young animals (0.00 to 0.16). The genetic correlation between F. hepatica-damaged livers in cows and milk somatic cell score was 0.32 (SE = 0.20). Antibody responses to F. hepatica and O. ostertagi had favorable genetic correlations with fertility traits, but conversely, antibody response to N. caninum and F. hepatica-damaged livers were unfavorably genetically correlated with fertility. This study provides the necessary information to undertake national multitrait genetic evaluations for parasite phenotypes.

Understanding the Quality of Atypical Dark Cutting Beef from Heifers and Steers

ObjectivesStudies have indicated that dark cutting beef with pH > 6.0 has glucidic potential lower than normal beef but can be as or more tender. Dark cutting beef with pH 5.9, TB4, n = 20) and after aging, muscles were assessed for color (L*, a*, b*; Commission Internationale de L’Eclairage), drip loss, cooking loss, Warner-Bratzler shear force (WBSF), and crude fat and protein. Statistical analyses were performed using the Statistical Analysis System (SAS Inst. Inc., Cary, NC) Version 9.3. The glucidic, sarcomere and carcass data were analyzed using the MIXED procedure where animal gender, grade and their interaction served as fixed effects while batch was random. Ante-mortem lairage time, post-mortem sampling time, hot carcass weight, rib-eye area and fat depth were individually tested as covariates for glucidic analysis. Beef quality data were analyzed as a split-plot, where gender and grade were tested in the main plot and aging in the sub-plot. ResultsResults indicated that reduced lactate and glucidic potential were accompanied by increased pH and reduced L*, a*, and b* values. Mean LT glucidic potential was lowest (P < 0.0001) for TB4, but the mean values for AB4 were theoretically sufficient to attain normal beef pH. Grades and gender interaction approached significance (P = 0.056) for mean residual glycogen concentration, which was lowest for TB4 LT from both genders while heifer AB4 had mean values similar to AA. In contrast to AA and TB4, the pH for AB4 continued falling during aging, implying a slow glycolysis in AB4. Gender had no effect on WBSF (P = 0.18); however, mean WBSF of AB4, unlike that of TB4, remained higher than that of AA muscles even after 21 d aging. Sarcomere length was not different (P = 0.37) between the grades, and was unrelated (r = –0.20, P = 0.102) to WBSF. Mean LT crude fat was greatest (P = 0.003) for AB4 while treatments were not different for mean carcass rib-eye area (P = 0.35) or fat depth (P = 0.93). ConclusionResults confirmed AB4 as the toughest LT within the Canada B4 dark cutting grade irrespective of carcass gender and phenotype, substantiating the significant financial penalty applied to dark cutting carcasses.

Genetic differences based on a beef terminal index are reflected in future phenotypic performance differences in commercial beef cattle

The increased demand for animal-derived protein and energy for human consumption will have to be achieved through a combination of improved animal genetic merit and better management strategies. The objective of the present study was to quantify whether differences in genetic merit among animals materialised into phenotypic differences in commercial herds. Carcass phenotypes on 156 864 animals from 7301 finishing herds were used, which included carcass weight (kg), carcass conformation score (scale 1 to 15), carcass fat score (scale 1 to 15) at slaughter as well as carcass price. The price per kilogram and the total carcass value that the producer received for the animal at slaughter was also used. A terminal index, calculated in the national genetic evaluations, was obtained for each animal. The index was based on pedigree index for calving performance, feed intake and carcass traits from the national genetic evaluations. Animals were categorised into four terminal index groups on the basis of genetic merit estimates that were derived before the expression of the phenotypic information by the validation animals. The association between terminal index and phenotypic performance at slaughter was undertaken using mixed models; whether the association differed by gender (i.e. young bulls, steers and heifers) or by early life experiences (animals born in a dairy herd or beef herd) was also investigated. The regression coefficient of phenotypic carcass weight, carcass conformation and carcass fat on their respective estimated breeding values (EBVs) was 0.92 kg, 1.08 units and 0.79 units, respectively, which is close to the expectation of one. Relative to animals in the lowest genetic merit group, animals in the highest genetic merit group had, on average, a 38.7 kg heavier carcass, with 2.21 units greater carcass conformation, and 0.82 units less fat. The superior genetic merit animals were, on average, slaughtered 6 days younger than their inferior genetic merit contemporaries. The superior carcass characteristics of the genetically elite animals materialised in carcasses worth €187 more than those of the lowest genetic merit animals. Although the phenotypic difference in carcass traits of animals divergent in terminal index differed statistically by animal gender and early life experience, the detected interactions were generally biologically small. This study clearly indicates that selection on an appropriate terminal index will produce higher performing animals and this was consistent across all production systems investigated.

Genomic selection using beef commercial carcass phenotypes

In this study, an industry terminal breeding goal was used in a deterministic simulation, using selection index methodology, to predict genetic gain in a beef population modelled on the UK pedigree Limousin, when using genomic selection (GS) and incorporating phenotype information from novel commercial carcass traits. The effect of genotype–environment interaction was investigated by including the model variations of the genetic correlation between purebred and commercial cross-bred performance (ρX). Three genomic scenarios were considered: (1) genomic breeding values (GBV)+estimated breeding values (EBV) for existing selection traits; (2) GBV for three novel commercial carcass traits+EBV in existing traits; and (3) GBV for novel and existing traits plus EBV for existing traits. Each of the three scenarios was simulated for a range of training population (TP) sizes and with three values of ρX. Scenarios 2 and 3 predicted substantially higher percentage increases over current selection than Scenario 1. A TP of 2000 sires, each with 20 commercial progeny with carcass phenotypes, and assuming a ρX of 0.7, is predicted to increase gain by 40% over current selection in Scenario 3. The percentage increase in gain over current selection increased with decreasing ρX; however, the effect of varying ρX was reduced at high TP sizes for Scenarios 2 and 3. A further non-genomic scenario (4) was considered simulating a conventional population-wide progeny test using EBV only. With 20 commercial cross-bred progenies per sire, similar gain was predicted to Scenario 3 with TP=5000 and ρX=1.0. The range of increases in genetic gain predicted for terminal traits when using GS are of similar magnitude to those observed after the implementation of BLUP technology in the United Kingdom. It is concluded that implementation of GS in a terminal sire breeding goal, using purebred phenotypes alone, will be sub-optimal compared with the inclusion of novel commercial carcass phenotypes in genomic evaluations.

The effects of heat stress and plane of nutrition on metabolism in growing pigs1

Heat stress (HS) jeopardizes pig health, reduces performance variables, and results in a fatter carcass. Whether HS directly or indirectly (via reduced feed intake) is responsible for the suboptimal production is not known. Crossbred gilts (n = 48; 35 ± 4 kg BW) were housed in constantly climate-controlled rooms in individual pens and exposed to 1) thermal-neutral (TN) conditions (20°C; 35% to 50% humidity) with ad libitum intake (n = 18), 2) HS conditions (35°C; 20% to 35% humidity) with ad libitum intake (n = 24), or 3) pair-fed [PF in TN conditions (PFTN), n = 6, to eliminate confounding effects of dissimilar feed intake (FI)]. Pigs in the TN and HS conditions were sacrificed at 1, 3, or 7 d of environmental exposure, whereas the PFTN pigs were sacrificed after 7 d of experimental conditions. Individual rectal temperature (Tr), skin temperature (Ts), respiration rates (RR), and FI were determined daily. Pigs exposed to HS had an increase (P < 0.01) in Tr (39.3°C vs. 40.8°C) and a doubling in RR (54 vs. 107 breaths per minute). Heat-stressed pigs had an immediate (d 1) decrease (47%; P < 0.05) in FI, and this magnitude of reduction continued through d 7; by design the nutrient intake pattern for the PFTN controls mirrored the HS group. By d 7, the TN and HS pigs gained 7.76 and 1.65 kg BW, respectively, whereas the PFTN pigs lost 2.47 kg BW. Plasma insulin was increased (49%; P < 0.05) in d 7 HS pigs compared with PFTN controls. Compared with TN and HS pigs, on d 7 PFTN pigs had increased plasma NEFA concentrations (110%; P < 0.05). Compared with TN and PFTN controls, on d 7 circulating N(τ)-methylhistidine concentrations were increased (31%; P < 0.05) in HS pigs. In summary, despite similar nutrient intake, HS pigs gained more BW and had distinctly different postabsorptive bioenergetic variables compared with PFTN controls. Consequently, these heat-induced metabolic changes may in part explain the altered carcass phenotype observed in heat-stressed pigs.

Genomic selection for the improvement of meat quality in beef

Selection index theory was used to compare different selection strategies aiming at the improvement of meat quality in beef cattle. Alternative strategies were compared with a reference scenario with three basic traits in the selection index: BW at 200 d (W200) and 400 d (W400) and muscling score (MUSC). These traits resemble the combination currently used in the German national beef genetic evaluation system. Traits in the breeding goal were defined as the 3 basic traits plus marbling score (MARB), to depict a situation where an established breeding program currently selecting for growth and carcass yield intends to incorporate meat quality in its selection program. Economic weights were either the same for all 4 traits, or doubled or tripled for MARB. Two additional selection criteria for improving MARB were considered: Live animal intramuscular fat content measured by ultrasound (UIMF) as an indicator trait and a genomic breeding value (GEBV) for the target trait directly (gMARB). Results were used to estimate the required number of genotyped animals in an own calibration set for implementing genomic selection focusing on meat quality. Adding UIMF to the basic index increased the overall genetic gain per generation by 15% when the economic weight on MARB was doubled and by 44% when it was tripled. When a genomic breeding value for marbling could be estimated with an accuracy of 0.5, adding gMARB to the index provided larger genetic gain than adding UIMF. Greatest genetic gain per generation was obtained with the scenario containing GEBV for 4 traits (gW200, gW400, gMUSC, and gMARB) when the accuracies of these GEBV were ≥0.7. Adding UIMF to the index substantially improved response to selection for MARB, which switched from negative to positive when the economic weight on MARB was doubled or tripled. For all scenarios that contained gMARB in the selection index, the response to selection in MARB was positive for all relative economic weights on MARB, when the accuracy of GEBV was >0.7. Results indicated that setting up a calibration set of ∼500 genotyped animals with carcass phenotypes for MARB could suffice to obtain a larger response to selection than measuring UIMF. If the size of the calibration set is ∼2,500, adding the ultrasound trait to an index containing already the GEBV would bring little benefit, unless the relative economic weight for marbling is much larger than for the other traits.

Evaluation of Bovine chemerin (RARRES2) Gene Variation on Beef Cattle Production Traits.

A previous study in cattle based on >48,000 markers identified markers on chromosome 4 near the chemerin gene associated with average daily feed intake (ADFI) in steers (P < 0.008). Chemerin is an adipokine associated with obesity and metabolic syndrome in humans, representing a strong candidate gene potentially underlying the observed association. To evaluate whether the bovine chemerin gene is involved in feed intake, 16 markers within and around the gene were tested for association in the same resource population. Eleven were nominally significant for ADFI (P < 0.05) and two were significant after Bonferroni correction. Two and five SNP in this region were nominally significant for the related traits of average daily gain (ADG) and residual feed intake (RFI), respectively. All markers were evaluated for effects on meat quality and carcass phenotypes. Many of the markers associated with ADFI were associated with hot carcass weight (HCW), adjusted fat thickness (AFT), and marbling (P < 0.05). Marker alleles that were associated with lower ADFI were also associated with lower HCW, AFT, and marbling. Markers associated with ADFI were genotyped in a validation population of steers representing 14 breeds to determine predictive merit across populations. No consistent relationships for ADFI were detected. To determine whether cattle feed intake or growth phenotypes might be related to chemerin transcript abundance, the expression of chemerin was evaluated in adipose of 114 heifers that were siblings of the steers in the discovery population. Relative chemerin transcript abundance was not correlated with ADFI, ADG, or RFI, but associations with body condition score and yearling weight were observed. We conclude that variation in the chemerin gene may underlie observed association in the resource population, but that additional research is required to determine if this variation is widespread among breeds and to develop robust markers with predictive merit across breeds.

Association of bovine carcass phenotypes with genes in an adaptive thermogenesis pathway

Associations of carcass phenotypes with genes regulating fat and energy metabolism involved in adaptive thermogenesis were examined in beef cattle. Carcass weight (CW) was found to be associated with MAP2K6 and UCP2 genes; back fat thickness (BFT) was found to be associated with PPARGC1A, MAP2K6, and UCP2 genes; marbling score (MS) was found to be associated with PPARGC1A and MAP2K6 genes; and eye-muscle area (EMA) was found to be associated only with UCP2 gene (P < 0.05). Further analyses found significant associations of interactions between PPARGC1A and MAP2K6 genes with CW and MS. Especially, interactive genetic associations were identified between c.424 and 222 G>A in PPARGC1A and c.17-10118 T>G in MAP2K6 and between c.228+28619 A>G in PPARGC1A and c.17-10118 T>G in MAP2K6, and they were both detected for CW and MS at a significant level (P < 0.05). The current study suggested that the individual and interactive associations of PPARGC1A, MAP2K6, and UCP2 genes with carcass phenotypes might be resulted from the pathway with fat and energy metabolism through the adaptive thermogenesis.

Genome‐wide association study reveals five nucleotide sequence variants for carcass traits in beef cattle

Genetic associations of nucleotide sequence variants with carcass traits in beef cattle were investigated using a genome-wide single nucleotide polymorphism (SNP) assay. Three hundred and thirteen Korean cattle were genotyped with the Illumina BovineSNP50 BeadChip, and 39,129 SNPs from 311 animals were analysed for each carcass phenotype after filtering by quality assurance. Five sequence markers were associated with one of the meat quantity or quality traits; rs109593638 on chromosome 3 with marbling score, rs109821175 on chromosome 11 and rs110862496 on chromosome 13 with backfat thickness (BFT), and rs110228023 on chromosome 6 and rs110201414 on chromosome 16 with eye muscle area (EMA) (P < 1.27 × 10(-6) , Bonferonni P < 0.05). The ss96319521 SNP, located within a gene with functions of muscle development, dishevelled homolog 1 (DVL1), would be a desirable candidate marker. Individuals with genotype CC at this gene appeared to have increased both EMA and carcass weight. Fine-mapping would be required to refine each of the five association signals shown in the current study for future application in marker-assisted selection for genetic improvement of beef quality and quantity.

A genome scan for quantitative trait loci influencing carcass, post‐natal growth and reproductive traits in commercial Angus cattle

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.

Evaluation of Simmental carcass EPD estimated using live and carcass data1

This study was conducted to compare carcass EPD predicted using yearling live animal data and/or progeny carcass data, and to quantify the association between the carcass phenotype of progeny and the sire EPD. The live data model (L) included scan weight, ultrasound fat thickness, longissimus muscle area, and percentage of intramuscular fat from yearling (369 d of age) Simmental bulls and heifers. The carcass data model (C) included hot carcass weight, fat thickness, longissimus muscle area, and marbling score from Simmental-sired steers and cull heifers (453 d of age). The combined data model (F) included live animal and carcass data as separate but correlated traits. All data and pedigree information on 39,566 animals were obtained from the American Simmental Association, and all EPD were predicted using animal model procedures. The genetic model included fixed effects of contemporary group and a linear covariate for age at measurement, and a random animal genetic effect. The EPD from L had smaller variance and range than those from either C or F. Further, EPD from F had highest average accuracy. Correlations indicated that evaluations from C and F were most similar, and L would significantly (P < 0.05) re-rank sires compared with models including carcass data. Progeny (n = 824) with carcass data collected subsequent to evaluation were used to quantify the association between progeny phenotype and sire EPD using a model including contemporary group, and linear regressions for age at slaughter and the appropriate sire EPD. The regression coefficient was generally improved for sire EPD from L when genetic regression was used to scale EPD to the appropriate carcass trait basis. The EPD from C and F had similar linear associations with progeny phenotype, although EPD from F may be considered optimal because of increased accuracy. These data suggest that carcass EPD based on a combination of live and carcass data predict differences in progeny phenotype at or near theoretical expectation.