Eye Muscle Area Research Articles

Objective grading of eye muscle area, intramuscular fat and marbling in Australian beef and lamb

The objective of this study was to test the performance of a prototype vision system in phenotypically diverse beef and lamb carcasses against visual grading of eye muscle area (EMA), marbling and chemical intramuscular fat (IMF%). Validation in beef demonstrated that the camera prototype in combination with analytical techniques enabled prediction of EMA (r2 = 0.83, RMSEP = 6.4 cm2), MSA marbling (r2 = 0.76, RMSEP = 66.1), AUS-MEAT marbling (r2 = 0.70, RMSEP = 0.74) and chemical IMF% (r2 = 0.78, RMSEP = 1.85%). Accuracy was also maintained on validation with all four traits displaying minimal bias of −3.6, 6.3, 0.07 and − 0.01, for EMA, MSA marbling, AUS-MEAT marbling and IMF% respectively. Preliminary analysis in lamb indicates potential of the system for the prediction of EMA (r2 = 0.41, RMSEP = 1.87) and IMF% (r2 = 0.28, RMSEP = 1.10), however further work to standardise image acquisition and environmental conditions is required.

Application of ensemble learning to genomic selection in chinese simmental beef cattle.

Genomic selection (GS) using the whole-genome molecular makers to predict genomic estimated breeding values (GEBVs) is revolutionizing the livestock and plant breeding. Seeking out novel strategies with higher prediction accuracy for GS has been the ultimate goal of breeders. With the rapid development of artificial intelligence, machine learning algorithms were applied to estimate the GEBVs increasingly. Although some machine learning methods have better performance in phenotype prediction, there is still considerable room for improvement. In this study, we applied an ensemble-learning algorithm, Adaboost.RT, which integrated support vector regression (SVR), kernel ridge regression (KRR) and random forest (RF), to predict genomic breeding values of three economic traits (carcass weight, live weight, and eye muscle area) in Chinese Simmental beef cattle. Predictive accuracy measured as the Pearson correlation between the corrected phenotypes and predicted GEBVs. Moreover, we compared the reliability of SVR, KRR, RF, Adaboost.RT and GBLUP methods. The result showed that machine learning methods outperformed GBLUP, and the average improvement of four machine learning methods over the GBLUP was 12.8%, 14.9%, 5.4% and 14.4%, respectively. Among the four machine learning methods, the reliability of Adaboost.RT was comparable to KRR with higher stability. We therefore believe that the Adaboost.RT algorithm is a reliable and efficient method for GS.

Prediction of dressing percentage, carcass characteristics and meat yield of goats, and implications for live assessment and carcass-grading systems

Abstract Context Dressing percentage (DP) and meat yield (MY) predictions using live assessments and carcass measurements enable objective valuation of animals and their carcasses. We hypothesised that distribution of goat carcass tissues affects predictive value of live body condition scoring (CS) methods and carcass measurements for these traits. Aims The present paper aimed to assess the value of CS methods for prediction of DP and MY and of carcass measurements for prediction of MY. Methods Correlation and regression analyses from a dataset (n = 1014 goats) highly heterogeneous for factors influencing DP and MY were used to assess (1) the value of live-goat assessments and classifications, including five CS methods, age (dentition), liveweight (LW), sex, fleece characteristics and breed or genotype to predict DP and MY, and (2) the value of hot standard carcass weight (HSCW) and carcass GR (soft tissue over the 12th rib) tissue depth, eye-muscle depth and eye-muscle area to predict MY. Key results Among kids, LW accounted for 1% (residual standard deviation of 2.6%) of variation in DP, 22% (2.3%) in MY (% LW) and 34% (2.5%) in MY (% HSCW). LW plus the best CS method accounted for 24% (2.3%) of variation in DP, 58% (1.7%) in MY (% LW) and 61% (2.0%) in MY (% HSCW). Among all goats, LW plus CS accounted for up to 21% (3.2%), 39% (2.1%) and 45% (2.2%) of variation in these traits. Regression models that included age, sex, fleece type, breed or genotype, LW and CS accounted for 67% (2.5%), 72% (1.9%) and 72% (2.1%) of variation in DP, MY (% LW) and MY (% HSCW). Among carcass measurements, HSCW plus eye-muscle depth had best predictive value, accounting for 61% (2.3%) of variation in MY (% HSCW) for kids and 40% (2.9%) for all goats. Conclusions The body condition-score methods that best relate to DP and MY (% LW or % HSCW) assessed the shape of M. longissimus lumborum (eye muscle) in the lumbar region, which relates to muscularity of goats, rather than subcutaneous fat depth such as assessed at the GR-site. Implications The results guide potential targets for future developments in live-goat assessment, carcass classification and grading, and trading languages underpinned by value-based marketing.

Effect of Breed Types and Castration on Carcass Characteristics of Boer and Large Frame Indigenous Veld Goats of Southern Africa.

Weaner male Boer Goats (BG; n = 36; 21 bucks and 15 wethers) and large frame Indigenous Veld Goats (IVG; n = 41; 21 bucks and 20 wethers) were raised on hay and natural grass ad libitum and the recommended amount of commercial pelleted diet to a live weight between 30 and 35 kg. Carcass quality characteristics (live weight, carcass weights, dressing %, chilling loss and eye muscle area) were measured. The right sides of the carcasses were divided into wholesale cuts and dissected into subcutaneous fat, meat and bone. Large frame Indigenous Veld Goat (IVG) wethers were slightly lighter than the IVG bucks with no significant difference observed between BG. Wethers compared to bucks had higher dressing %, subcutaneous fat % in all primal cuts, intramuscular fat %, kidney fat % and, overall, slightly less bone %. Some breed-wether interactions were noticed: IVG wethers were slightly lighter than the IVG bucks, but the IVG bucks tended to produce higher % meat compared to other test groups. Judged on the intramuscular fat % characteristics, it seems as if wethers should produce juicier and more flavorsome meat compared to bucks.

Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle.

Simple SummaryHanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. Gene set enrichment analysis indicated that the identified candidate genes were related to biological processes and functional terms that were involved in growth and lipid metabolism. In conclusion, these results suggest that the incorporation of GWAS results and network analysis can help us to better understand the genetic bases underlying growth and carcass traits.In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle.

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.

Genetic parameters and correlations of related feed efficiency, growth, and carcass traits in Hanwoo beef cattle.

ObjectiveThis study aimed to estimate the genetic parameters and genetic correlations for related feed efficiency, growth, and carcass traits in Hanwoo cattle.MethodsPhenotypic data from 15,279 animals born between 1989 and 2015 were considered. The related feed efficiency traits considered were Kleiber ratio (KR) and relative growth rate (RGR). Carcass traits analyzed were backfat thickness (BT), carcass weight, eye muscle area, and marbling score. Growth traits were assessed by the average daily gain (ADG), metabolic body weight (MBW) at mid-test age from 6 to 24 months, and yearling weight (YW). Variance and covariance components were estimated using restricted maximum likelihood using nine multi-trait animal models.ResultsThe heritability estimates for related feed efficiency (0.28±0.04 for KR and RGR) and growth traits (0.26±0.02 to 0.33±0.04) were moderate, but the carcass traits tended to be higher (0.38±0.04 to 0.61±0.06). The related feed efficiency traits were positively genetically correlated with all the carcass traits (0.37±0.09 to 0.47±0.07 for KR, and 0.14±0.09 to 0.37±0.09 for RGR), except for BT, which showed null to weak correlation. Conversely, the genetic correlations of RGR with MBW (−0.36±0.08) and YW (−0.30±0.08) were negative, and those of KR with MBW and YW were close to zero, whereas the genetic correlations of ADG with RGR (0.40±0.08) and KR (0.70±0.05) were positive and relatively moderate to high. The genetic (0.92±0.02) correlations between KR and RGR were very high.ConclusionSufficient genetic variability and heritability were observed for traits of interest. Moreover, the inclusion of KR and/or RGR in Hanwoo cattle breeding programs could improve the feed efficiency without producing any unfavorable effects on the carcass traits.

The study on estimated breeding value and accuracy for economic traits in Gyoungnam Hanwoo cow (Korean cattle).

This study was conducted to construct basic data for the selection of elite cows by analyzing the estimated breeding value (EBV) and accuracy using the pedigree of Hanwoo cows in Gyeongnam. The phenotype trait used in the analysis are the carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT) and marbling score (MS). The pedigree of the test group and reference group was collected to build a pedigree structure and a numeric relationship matrix (NRM). The EBV, genetic parameters and accuracy were estimated by applying NRM to the best linear unbiased prediction (BLUP) multiple-trait animal model of the BLUPF90 program. Looking at the pedigree structure of the test group, there were a total of 2,371 cows born between 2003 to 2009, of these 603 cows had basic registration (25%), 562 cows had pedigree registration (24%) and 1,206 cows had advanced registration (51%). The proportion of pedigree registered cows was relatively low but it gradually increased and reached a point of 20,847 cows (68%) between 2010 to 2017. Looking at the change in the EBV, the CWT improved from 4.992 kg to 9.885 kg, the EMA from 0.970 cm2 to 2.466 cm2, the BFT from −0.186 mm to −0.357 mm, and the MS from 0.328 to 0.559 points. As a result of genetic parameter estimation, the heritability of CWT, EMA, BFT, and MS were 0.587, 0.416, 0.476, and 0.571, respectively, and the accuracy of those were estimated to be 0.559, 0.551, 0.554, and 0.558, respectively. Selection of superior genetic breed and efficient improvement could be possible if cow ability verification is implemented by using the accurate pedigree of each individual in the farms.

Comparison of two muscle fibre staining techniques and their relation to pork quality traits

This study compared two histochemical staining methods of muscle fibres and evaluated their relationship with the meat quality traits of two high-value porcine muscles. Immunohistochemical (IHC) and adenosine triphosphatase (ATPase) staining was used to assess the cross-sectional area and proportion of fibre-types I, IIa, IIx and IIb in the samples of longissimus lumborum (LL) and psoas major (PM) muscles collected one-hour post-mortem from 25 crossbred pigs [Large White<sub>Sire</sub> × (Landrace × Large White<sub>Dam</sub>)] at an average age of 152 days. Muscles differed in all fibre parameters, except the proportion and relative area of type IIx fibres. The LL muscle exhibited greater fibre cross-sectional areas of all fibre types, higher proportions of type IIb/IIB, and lower proportions of I and IIa fibres than the PM muscle in both staining techniques. These two muscles also differed marginally in moisture, crude protein and intramuscular fat content. The PM muscle showed a low correlation between fibre types and chemical composition, but the LL muscle showed moderate correlations between fibre CSA and area composition for moisture and ash content. After IHC staining, an increase in LL eye muscle area and drip loss were correlated with lower proportions of type I fibres, while a greater proportion of type IIx fibres resulted in increased LL eye muscle area and moisture content. Furthermore, a higher CSA of all fibre types in the LL decreased redness (a*) and moisture content of the muscle. Results showed that IHC is more appropriate than ATPase staining for the assessment of relationships between muscle fibre parameters and meat quality traits in pigs.

Analysis of the Bovine DLK1 Gene Polymorphism and Its Relation to Lipid Metabolism in Chinese Simmental.

Simple SummaryDelta-like non-canonical Notch ligand 1 (DLK1) is a candidate gene associated with lipid metabolism. In order to verify the function of the DLK1 gene on lipid metabolism in Chinese Simmental cattle, we identified the effect of DLK1 on lipid metabolism in bovine fetal fibroblast cells (BFFs). At the same time, we also detected the relationship between single-nucleotide polymorphism sites (SNPs) of bovine DLK1 with the economic traits and fatty acids composition in Chinese Simmental cattle, such as the carcass fat coverage rate, loin eye muscle area, and fat color score, etc. In the present study, we precisely constructed and transfected the overexpression and interference vectors of the DLK1 gene in BFFs. the results showed that the overexpression of the DLK1 gene could decrease the contents of intracellular triglycerides (TGs) while interference of the DLK1 gene could increase the TGs contents. Gas chromatography analysis of the fatty acid composition showed that the contents of octanoate acid and γ-linolenate acid were regulated as the expression of DLK1 was altered. We found two SNPs and genes associated with these traits in Chinese Simmental by the restriction fragment length polymorphism (RPLF-PCR) detection method. In summary, we verified the effects of bovine DLK1 on fatty acid metabolism from the cellular level to population genetic polymorphism, which also paved the way for further studying of the effects of the DLK1 gene on lipid metabolism in vivo.In this study, we precisely constructed and transfected the overexpression and interference vectors in BFFs to evaluate the role of DLK1 gene on lipid metabolism in vitro. The expression of of DLK1 in the mRNA and protein level tended to reduce, and TGs were significantly increased in the pGPU6-shDLK1 group compared to the control group (p < 0.05). The expression of DLK1 in the mRNA and protein level were increased in the pBI-CMV3-DLK1 group compared to the control group, and the TGs content showed a significant decrease in the pBI-CMV3-DLK1 group (p < 0.05). Meanwhile, we used the restriction fragment length polymorphism (RFLP-PCR) detection method to screen SNPs further to explore and analyze the relationship between the gene and the economic traits of 28-month-old Chinese Simmental and the fatty acids composition of cattle longissimus muscle. The result showed that two SNPs, IVS3 + 478 C > T and IVS3 + 609 T > G, were identified as being significantly associated with carcass and meat quality traits in Chinese Simmental, such as the carcass fat coverage rate, loin eye muscle area, and fat color score. In summary, our results indicated that DLK1 can affect lipid metabolism in bovine and these two SNPs might be applied as genetic markers of meat quality traits for beef cattle breeding.

Supplementation of rangeland primiparous Bos indicus x Bos taurus beef heifers during lactation. 1. Effects on dam milk production and liveweight, bull calf growth, live carcass characteristics and metabolic hormone concentrations

The practice of feeding replacement-breeding bulls on high energy diets after weaning to meet liveweight (LW) and carcass expectations between 18 and 24 months of age negatively affects reproductive potential. This experiment reports upon the effects of an alternative management strategy aimed at improving calfhood nutrition in rangeland-reared bulls to enhance LW and live carcass characteristics at 2 years. Following artificial insemination (AI cohort; n = 26), or natural mating, subsequent to the addition of bulls at 39 d post-AI (NM cohort; n = 36), primiparous Santa Gertrudis heifers grazing rangeland pastures with bull calf progeny were allocated at parturition to receive either nil supplement (control; CON) or provided with unrestricted access to a pelleted vegetable protein meal-based supplement containing 35% CP (SUPP) until weaning at 199 ± (SD) 26 d. The mean estimated pellet consumption by SUPP heifers during lactation was 2.6 ± (SEM) 0.5 kg DM daily. Grazing diet quality measurements indicated nutritional restriction of CON heifers until at least 115 d of lactation. This was confirmed by lower blood urea nitrogen concentrations at 88 d (P < 0.001) and greater mean NEFA (P < 0.001) concentrations. Rainfall during mid-lactation subsequently improved grazing diet quality; thus the CON heifers experienced moderate nutritional restriction across lactation, but sufficient to reduce milk yield by 1.6 kg/d (P < 0.001) and maternal LW at weaning by 18.4 kg (P < 0.001). Bulls reared by SUPP heifers were 17.5 kg heavier at weaning (P = 0.001) and had elevated IGF-I and leptin concentrations between 4 and 4.5 months of age (P < 0.05). Effects on metabolic hormones during calfhood were cohort specific, with greater concentrations of IGF-I confined to AISUPP bulls and NMSUPP bulls demonstrating greater concentrations of leptin. Bulls were amalgamated at weaning and grazed common pastures without supplementation until the experiment concluded at 675 d. Pre-weaning plane of nutrition did not affect the LW, carcass fat depth, IGF-I or leptin concentrations of bulls after weaning. Mean eye muscle area (EMA) was greater in SUPP compared to CON bulls (68.5 ± 0.9 cm2vs 65.2 ± 0.9 cm2; P < 0.05) and AISUPP bulls tended to have greater EMA (P = 0.06) than AICON bulls from 495 d of age. Thus when primiparous heifers experience moderate nutritional restriction during lactation, supplementation may have persistent effects upon increasing carcass muscle characteristics of bull progeny.

Naringin supplementation affects performance, carcass traits, meat quality and oxidative stability of finishing pigs

Naringin is a major flavanone derivate that has many important biological functions in animals. However, its effect on pigs is unknown. The aim of this study was to investigate the effect of naringin supplementation on performance, carcass traits, meat quality and oxidative stability in finishing pigs. Ninety-six pigs, with an average initial body weight of 66.2 ± 0.63 kg, were randomly divided into four groups. One group was fed a basal diet without supplementation (control), and the three others were fed diets supplemented with 0.5, 1.0 or 1.5 g naringin /kg DM of feed for 50 days. Each treatment was replicated six times with four pigs per replicate. Feed and water were available ad libitum. The 0.5 g/kg naringin treatment group had an improved loin eye muscle area, reduced serum triglycerides and were leaner compared with the other groups. Pigs in the 1.5 g/kg naringin treatment had higher pH45min values and inosine monophosphate concentrations, and lower MyHC IIb mRNA expression in muscle than the other groups. MyHC IIa mRNA expression was significantly up-regulated in all naringin-supplemented diet groups. Naringin significantly increased superoxide dismutase (SOD) activity and total anti-oxidative capacity in meat, as well as SOD and glutathione peroxidase activity in the liver. These results indicate that the dietary addition of naringin at 0.5 g/kg improved carcass characteristics, while 1.5 g/kg improved the oxidative stability and pork quality in finishing pigs.&#x0D; Keywords: antioxidant capacity; carcass characteristics; naringin-supplemented diets; pork quality

Prediction of the Hind-Leg Muscles Weight of Yearling Dairy-Beef Steers Using Carcass Weight, Wither Height and Ultrasound Carcass Measurements

Simple SummaryCarcass classification and grading systems are typically inadequate for young cattle processed for beef production. Conformation of the hindquarter region of cattle has been used to classify and grade the whole carcass from older beef cattle. This study was initiated with the objective of providing a carcass classification and grading system based on hind-leg muscles weight. Prediction equations for the indirect prediction of saleable meat yield using hind-leg muscles weight from young dairy-origin steers were developed, and could be used for their carcass classification and grading. These equations avoid the need to isolate and track boneless subprimal cuts to establish the saleable meat yield of individual animals.Prediction equations have been widely utilized for carcass classification and grading systems in older beef cattle. However, the equations are mostly relevant for common beef breeds and 18 to 24 month old animals; there are no equations suitable for yearling, dairy-origin cattle. Therefore, this study developed prediction models using 60 dairy-origin, 8 to 12 month old steers to indicate saleable meat yield from hind-legs, which would assist with carcass classification and grading. Fat depth over the rump, rib fat depth, and eye muscle area between the 12th and 13th ribs were measured using ultrasound, and wither height was recorded one week prior to slaughter. The muscles from the hind-leg were retrieved 24 h after slaughter. Prediction equations were modeled for the hind-leg muscles weight using carcass weight, wither height, eye muscle area, rump, and rib fat depths as predictors. Carcass weight explained 61.5% of the variation in hind-leg muscles weight, and eye muscle area explained 39.9% (p < 0.05). Their combination in multivariate analysis explained 63.5% of the variation in hind-leg muscles weight. The R2 of the prediction in univariate and multivariate analyses was improved when data were analyzed per age group. Additional explanatory traits for yearling steers, including body length, hearth girth, and muscle depth and dimensions measured using video image analysis scanning (VIAscan), could improve the prediction ability of saleable meat yield from yearling dairy beef steers across the slaughter age groups.

Effects of Different Selenium Sources on Meat Quality and Shelf Life of Fattening Pigs.

Simple SummaryThis study was conducted to assess the effects of different Se sources on the growth performance, carcass performance, meat quality and shelf life of fattening pigs. A control diet was supplemented with SS, and experimental diets were supplemented SY, Se-Met, and SS + Se-Met, respectively. The data showed that using organic Se in fattening pig’s diet could improve meat quality and prolong the shelf life of pork. Thus, replacing inorganic Se in diet with organic Se improved meat quality and pork shelf life of fattening pigs significantly under the conditions of the current study.The aim of this study was to evaluate the effects of different Se sources on the meat quality and shelf life of fattening pigs. The control diet was supplemented with 0.3 mg/kg of Se from sodium selenite (SS), and experimental diets included 0.3, 0.3 and 0.15 + 0.15 mg/kg of Se from Se-enriched yeast (SY), selenomethionine (Se-Met) and SS + Se-Met, respectively. The results showed that using organic Se or Se + Se-Met in fattening pigs’ diet could increase average daily gain (ADG) (p < 0.05), decrease F/G (p < 0.05), reduce (p < 0.01) moisture, drip loss and cooking loss of longissimus thoracis, as well as increase (p < 0.05) protein and fat contents of longissimus thoracis. Diet supplementation with SY or Se + Se-Met could increase (p < 0.01) back fat thickness and skin thickness, and SY could increase (p < 0.01) belly fat rat. Adding SY or Se + Se-Met could reduce (p < 0.01) L value (45 min, 24 h). Adding Se-Met could decrease (p < 0.01) b value (45 min, 24 h), adding Se + Se-Met could reduce b value (45 min), and adding SY could reduce the b value (24 h). However, there were no (p < 0.05) significant effects on dressing percentage, carcass sloping length, eye muscle area, pH, a value (45 min) and a value (24 h) of longissimus thoracis. Moreover, the TVB-N contents of longissimus thoracis on the first and fifth days, the numbers of Lactobacillus on the third to seventh days and the numbers of E. coli in in the fifth to seventh days of longissimus thoracis were reduced (p < 0.01) by diet supplementation with organic Se. In conclusion, all the results indicate that replacing inorganic Se in diet with organic Se could improve meat quality of fattening pigs. In addition, organic Se could reduce the total volatile basic nitrogen (TVB-N) contents of longissimus thoracis and reduce the numbers of E. coli and Lactobacillus in longissimus thoracis, prolonging the shelf life of pork. These results demonstrated that organic Se supplementation was more effective than SS supplementation for meat quality and the shelf life of fattening pigs.

A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle.

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10−7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein–protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.

Genomic Prediction Accuracy Using Haplotypes Defined by Size and Hierarchical Clustering Based on Linkage Disequilibrium.

Genomic prediction is an effective way to estimate the genomic breeding values from genetic information based on statistical methods such as best linear unbiased prediction (BLUP). The used of haplotype, clusters of linked single nucleotide polymorphism (SNP) as markers instead of individual SNPs can improve the accuracy of genomic prediction. Since the probability of a quantitative trait loci to be in strong linkage disequilibrium (LD) with a cluster of markers is higher compared to an individual marker. To make haplotypes efficient in genomic prediction, finding optimal ways to define haplotypes is essential. In this study, 770K or 50K SNP chip data was collected from Hanwoo (Korean cattle) population consisted of 3,498 cattle. Using SNP chip data, haplotype was defined in three different ways based on 1) the number of SNPs included, 2) length of haplotypes (bp), and 3) agglomerative hierarchical clustering based on LD. To compare the methods in parallel, haplotypes defined by all methods were set to have comparable sizes; 5, 10, 20 or 50 SNPs on average per haplotype. A linear mixed model using haplotype to calculated the covariance matrix was applied for testing the prediction accuracy of each haplotype size. Also, conventional SNP-based linear mixed model was tested to evaluate the performance of the haplotype sets on genomic prediction. Carcass weight (CWT), eye muscle area (EMA) and backfat thickness (BFT) were used as the phenotypes. This study reveals that using haplotypes generally showed increased accuracy compared to conventional SNP-based model for CWT and EMA, but found to be small or no increase in accuracy for BFT. LD clustering-based haplotypes specifically the five SNPs size showed the highest prediction accuracy for CWT and EMA. Meanwhile, the highest accuracy was obtained when length-based haplotypes with five SNPs were used for BFT. The maximum gain in accuracy was 1.3% from cross-validation and 4.6% from forward validation for EMA, suggesting that genomic prediction accuracy can be increased by using haplotypes. However, the improvement from using haplotypes may depend on the trait of interest. In addition, when the number of alleles generated by each haplotype defining methods was compared, clustering by LD generated the least number of alleles, thereby reducing computational costs. Therefore, finding optimal ways to define haplotypes and using the haplotype alleles as markers can improve the accuracy of genomic prediction.

Effects of rumen-protected betaine supplementation on meat quality and the composition of fatty and amino acids in growing lambs

Rumen-protected betaine (RPB) can enhance betaine absorption in the small intestine of ruminants, while betaine can alter fat distribution and has the potential to affect the meat quality of livestock. Hence, we hypothesized that RPB might also affect the meat quality of lambs. Sixty male Hu sheep of similar weight (30.47 ± 2.04 kg) were selected and randomly subjected to five different treatments. The sheep were fed a control diet (control treatment, CTL); 1.1 g/day unprotected-betaine supplemented diet (UPB); or doses of 1.1 g/day (low RPB treatment; L-PB), 2.2 g/day (middle RPB treatment; M-PB) or 3.3 g/day (high RPB treatment; H-PB) RPB-supplemented diet for 70 days. Slaughter performance, meat quality, fatty acid and amino acid content in the longissimus dorsi (LD) muscle, shoulder muscle (SM) and gluteus muscle (GM) were measured. Compared with CTL, betaine (including UPB and RPB) supplementation increased the average daily weight gain (ADG) (P < 0.05) and average daily feed intake (P < 0.01) of lambs. Rumen-protected betaine increased ADG (P < 0.05) compared with UPB. With increasing RPB doses, the eye muscle area of the lambs linearly increased (P < 0.05). Compared with CTL, betaine supplementation decreased water loss (P < 0.05) in SM and increased pH24 in the SM (P < 0.05) and GM (P < 0.05). Compared with UPB, RPB decreased water loss in the GM (P < 0.01), decreased shear force (P < 0.05) in the LD and SM and increased the pH of the meat 24 h after slaughter (pH24). With increasing RPB doses, the shear force and b* value in the LD linearly decreased (P < 0.05), and the pH24 of the meat quadratically increased (P < 0.05). Compared with CTL, betaine supplementation increased the polyunsaturated fatty acid in the GM (P < 0.05). Compared with UPB, RPB supplementation decreased the saturated fatty acid (SFA) content in the LD (P < 0.05) and increased the unsaturated fatty acids (UFA), mono-unsaturated fatty acids and UFA/SFA ratio in the LD (P < 0.05). Compared with CTL, the content of histidine in the LD increased with betaine supplementation. Compared with UPB, RPB supplementation increased the content of total free amino acids and flavor amino acids in the LD of lambs (P < 0.05). With increasing RPB, the isoleucine and phenylalanine contents in the LD linearly increased (P < 0.05). Overall, the data collected indicated that the meat quality of lambs (especially in the LD) improved as a result of betaine supplementation, and RPB showed better effects than those of UPB.

Dual energy X-ray absorptiometry precisely and accurately predicts lamb carcass composition at abattoir chain speed across a range of phenotypic and genotypic variables

Dual energy X-ray absorptiometry (DEXA) is an imaging modality that has been used to predict the computed tomography (CT)-determined carcass composition of multiple species, including sheep and pigs, with minimal inaccuracies, using medical grade DEXA scanners. An online DEXA scanner in an Australian abattoir has shown that a high level of precision can be achieved when predicting lamb carcass composition in real time. This study investigated the accuracy of that same online DEXA when predicting fat and lean percentages as determined by CT over a wide range of phenotypic and genotypic variables across 454 lambs over 6 kill groups and contrasted these results against the current Australian industry standard of grade-rule (GR) measurements to grade carcasses. Lamb carcasses were DEXA scanned and then CT scanned to determine CT Fat % and CT Lean %. All phenotypic traits and genotypic information, including Australian Sheep Breeding Values, were recorded for each carcass. Residuals of the DEXA predicted CT Fat % and Lean %, and the actual CT Fat % and Lean % were calculated and tested against all phenotypic and genotypic variables. Excellent overall precision was recorded when predicting CT Fat % (R2 = 0.91, RMSE = 1.19%). Small biases present for sire breed, sire type, dam breed, hot carcass weight and c-site eye muscle area could be explained by a regression paradox; however, biases among kill group (−0.73% to 1.01% for CT Fat %, −1.48% to 0.76% for CT Lean %) and the Merino sire type (0.36% for CT Fat %, −0.73% for CT Lean %) could not be explained by this effect. Over the large range of phenotypic and genotypic variation, there was excellent precision when predicting CT Fat % and CT Lean % by an online DEXA, with only minor biases, showing superiority to the existing Australian standard of GR measurements.

Improvement of Kolbroek Boar Growth Performance and Carcass Quality through Dietary Crude Protein Supplementation

Kolbroek pigs have numerous advantages as an indigenous breed including its contributions to food security. However, there are numerous concerns over the current feed regime that compromises its growth performance and carcass quality. Therefore, this study was conducted to evaluate the growth performance traits, attainment of puberty, backfat thickness (BFT), and carcass traits when boar fed diets supplemented with 10% (standard diet), 13% and 16% crude protein. Fifteen pigs per protein diets were individually housed and fed ad-libitum for eight weeks in a complete randomised design. Average daily gain (ADG), average daily feed intake (ADFI) and feed conversion ratio (FCR) were measured on a weekly basis. At the end of the trial, all boars were slaughtered and carcass quality parameters measured. Pearson’s correlation coefficients were calculated between growth performance parameters. Our data revealed that there was an increase in final body weight, ADG, ADFI accompanied by decreases in BFT and the age of attainment of puberty. There was also a positive correlation between ADFI and ADG (r = 0.78) accompanied by a low positive correlation between ADG and BFT (r = 0.12) with a high negative correlation between FCR and ADG (r = -0.94). The water holding capacity (WHC), dressing percentage and marbling mass appeared to decrease while the eye muscle area increased with protein supplementation of the diet. There were also increases in the lungs, liver, small plus large intestines and stomach with no changes in the pancreas and heart tissues. Accompanying these was observations that the meat colour lightness improved accompanied by a decline in meat redness and yellowness. In conclusion, supplementation of boar diet with increasing crude protein improved the carcass quality and growth performance of Kolbroek boars.

Carcass characteristics and meat quality of commercial lambs reared in different forage systems

Carcass attributes and meat quality characteristics of the Longissimus thoracis muscle were evaluated from 135 lambs from 9 commercial forage production systems (n = 15) on 3 farms. Wethers had greater eye muscle area and loin intramuscular fat percentage than cryptorchid lambs (P < 0.05). Chicory-fed lambs had a heavier carcass weight and greater loin intramuscular fat percentage compared to pasture-fed lambs (P < 0.05), but similar eye muscle area and fat depth over the loin (P > 0.05). Lambs that were processed at weaning had heavier carcasses and greater loin intramuscular fat percentage and shear force values than lambs slaughtered after further finishing on pasture or chicory (P < 0.05). The effects of the sex of the lamb, its castration status, forage diet and age at slaughter on meat quality were subtle.