Identification of core genes affecting IMF deposition in bovine

Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.

Influence of polymorphisms in candidate genes on carcass and meat quality traits in rabbits

Candidate gene is a powerful approach to study gene-trait association and offers valuable information for genetic improvement using marker-assisted selection. The current work aimed to study the polymorphisms of four single nucleotide polymorphism (SNPs) at located growth hormone (GH), insulin-like growth factor-II (IGF-II), fat mass and obesity-associated (FTO), and insulin receptor substrate-1 (IRS-1) genes, and their association with the carcass, and meat quality traits in rabbits. The SNPs were genotyped using RFLP-PCR in New Zealand White and local Baladi rabbits. The results revealed that the heterozygous genotype was the most frequent in all cases, except for the FTO SNP in LB rabbits. There was a significant effect for GH genotypes on meat lightness after slaughter and hind-part weight. While, IGF-II mutation significantly affected slaughter, hot carcass, commercial carcass, and hind-part weights. The FTO SNP was associated with cooking loss and intramuscular fat weight, and the IRS-1 SNP was significantly associated with drip loss and intramuscular fat. Specific-breed effects were obtained for IGF-II SNP on cooking loss, and for the intramuscular fat. Although the results suggested that these mutations are useful candidate genes for selection, more research for detecting more variants associated with carcass and meat quality traits in rabbits are recommended.

Development of nutrigenomic based precision management model for Hanwoo steers

Focusing high marble deposition, Hanwoo feedlot system uses high-energy diet over the prolonged fattening period. However, due to the individual genetic variation, around 40% of them are graded into inferior quality grades (QG), despite they utilized the same resources. Therefore, focusing on development of a nutrigenomic based precision management model, this study was to evaluated the response to the divergent selection on genetic merit for marbling score (MS), under different dietary total digestible nutrient (TDN) levels. Total of 111 calves were genotyped and initially grouped according to estimated breeding value (high and low) for marbling score (MS-EBV). Subsequently, managed under two levels of feed TDN%, over the calf period, early, middle, and final fattening periods following 2 × 2 factorial arrangement. Carcasses were evaluated for MS, Back fat thickness (BFT) and Korean beef quality grading standard. As the direct response to the selection was significant, the results confirmed the importance of initial genetic grouping of Hanwoo steers for MS-EBV. However, dietary TDN level did not show an effect (p > 0.05) on the MS. Furthermore, no genetic-by-nutrition interaction for MS (p > 0.05) was also observed. The present results showed no correlation response on BFT (p > 0.05), which indicates that the selection based on MS-EBV can be used to enhance the MS without undesirable effect on BFT. Ultimate turnover of the Hanwoo feedlot operation is primarily determined by the QGs. The present model shows that the initial grouping for MS-EBV increased the proportion of carcasses graded for higher QGs (QG1⁺⁺ and QG1⁺) by approximately 20%. Moreover, there appear to be a potential to increase the proportion of QG 1⁺⁺ animals among the high-genetic group by further increasing the dietary energy content. Overall, this precision management strategy suggests the importance of adopting an MS based initial genetic grouping system for Hanwoo steers with a subsequent divergent management based on dietary energy level.

Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.

Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle

Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.

Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days

Simple Summary

When searching for genetic markers for the selection of more tender beef, it is important to maintain minimal environmental variation from pre-slaughter, right through to the ageing process, to ensure the accuracy of the obtained phenotypes. This is because beef quality traits have a large environmental component that can greatly alter the characteristics of the meat, which would not reflect a true genetic effect. We propose that variable ageing times are especially important in determining whether markers are associated with tenderization or not. Our analyses included candidate genes for the protein degrading enzyme system for calpains, because they contribute the most to tenderization. We were able to validate these markers in South African beef cattle, where they could be useful for selection. The timing of the collection of tenderness data was critical, as only a few (6/134) genetic markers sustained their association with tenderization over ageing to 20 days. A larger tenderization effect earlier in ageing, as shown here for the capn1_187 and capn1_4751 markers, would decrease the length of ageing. This would not only increase profits, but also decrease the energy needed during the storage and refrigeration of aged beef, decreasing the carbon footprint of beef production.

Abstract

The most important factor that determines beef tenderness is its proteolytic activity, and the balance between calpain-1 protease activity and calpastatin inhibition is especially important, while contributions can also arise from calpain-2 and, possibly, calpain-3. The meat ageing process itself affects these processes. To determine whether genotypes in the calpain–calpastatin system can enhance tenderness through a 20-day ageing period, South African purebred beef bulls (n = 166) were genotyped using the Illumina BovineHD SNP BeadChip through a gene-based association analysis targeting the cast, capn3, capn2 and capn1 genes. The Warner–Bratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 and d 20 of ageing, with protease enzyme activity in the first 20 h post-mortem. Although several of the 134 SNPs are associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to the ageing-associated increases in tenderness for at least three of the four ageing periods. While most genomic associations were relatively stable over time, some genotypes within the SNP responded differently to ageing, resulting in altered genomic effects over time. The level of ageing at which genomic associations are performed is an important factor that determines whether SNPs affect tenderness phenotypes.

The influence of protected fat in supplements on the performance and carcass characteristics of Nellore beef bulls in tropical pasture

The finishing stages for uncastrated Nellore beef cattle on tropical pasture often produce high yielding carcasses with minimal fat cover. This study aimed to evaluate the performance and carcass characteristics of uncastrated Nellore beef bulls fed a diet containing rumen-protected fat during the rainy period for 210 days. Eighty Nellore beef bulls with 28 months of age, and an initial live weight of 416 kg ± 16 kg, were allocated into eight paddocks (7.0 ha), totaling 56 ha, at 10 animals/paddock, in a continuous-grazing system. The pasture characteristics, performance production, loin-eye area (cm²), subcutaneous fat thickness (mm), and rump fat thickness were evaluated. There was no effect (P > 0.05) on the average total weight gain (203.00 kg) and average daily gain (0.98 kg/day). On the other hand, the subcutaneous fat thickness and rump fat thickness were 42.8% and 49.5% greater, respectively, when the animals were fed a diet containing rumen-protected fat inclusion (P < 0.05). Supplementation with rumen-protected fat provided a thicker fat layer in the carcass of Nellore beef bulls grazing on tropical pasture during the rainy period.

Genetic parameters associated with meat quality of Nellore cattle at different anatomical points of longissimus: Brazilian standards

The present study estimated genetic parameters and evaluated the genetic and phenotypic correlations between meat quality characteristics of Nellore cattle evaluated at different anatomical points of the longissimus. Data from 1329 Nellore young bulls were used to evaluate, in the 5th and 12th ribs, marbling score (MAR), shear force (SF), cooking weight losses (CWL) and intramuscular fat (IMF). In addition, the subcutaneous fat thickness was measured at the 12th rib (SFT₁₂) and between the last lumbar and the first sacral vertebrae (SFT_LR), in the separation of loin and round. Results yielded moderate heritability coefficients for evaluated characteristics, except CWL. High genetic correlations (0.61) were found between measurements of SFT₁₂ and SFT_LR. MAR, IMF and SF were evaluated at the 5th and 12th rib. Meat quality and subcutaneous fat thickness measured at different anatomical points of the longissimus are genetically correlated and can be used in genetic selection programs to improve meat quality characteristics in Nellore cattle.

Measuring quantitative proteomic distance between Spanish beef breeds

Estimates of quantitative proteomic distance between populations have not been reported to date. Here, quantitative proteomic distances between three Spanish bovine breeds (Asturiana de los Valles, AV; Retinta, RE; and Rubia Gallega, RG) were estimated from two-dimensional electrophoresis profiles of meat samples of longissimus thoracis muscle at 2 h post-mortem. Statistically significant distances were detected between AV/RG and the most genetically different RE breed, using the novel QD measure of quantitative proteomic distance. In total, 18 differentially abundant myofibrillar and sarcoplasmic proteins/isoforms contributing to proteomic distances between breeds were confidently identified by tandem mass spectrometry. The fast skeletal myosin regulatory light chain 2 followed by other five interacting proteins exhibited the most pronounced relative change between breeds. In addition, most differentially represented proteins could be associated with variations in meat tenderness. Therefore, they could be candidate biomarkers for molecular breeding programs and authentication of the three Spanish beef breeds.

Genetic analysis of carcass and meat quality traits in Nelore cattle1

The objective of this study was to estimate genetic parameters for carcass and meat quality traits, as well as their genetic correlations using pedigree and genomic information. A total of 3,716; 3,702; 3,439; 3,705; and 3,714 records of 12th-13th rib LM area (LMA), backfat thickness (BF), HCW, marbling score (MARB), and Warner-Bratzler peak shear force (WBSF), respectively, were used. Animals were genotyped with BovineHD BeadChip and GeneSeek Genomic Profiler Indicus HD - GGP75Ki panel. The (co)variance components were estimated by Bayesian inference using a multitrait ssGBLUP analysis. The animal model included fixed effects of contemporary group (defined by the combination of farm and year of birth, and management group at yearling) and age of animal at slaughtering as a covariate (linear). Direct additive genetic and residual effects were fitted as random. The posterior means and SD of heritabilities for LMA, BF, HCW, MARB, and WBSF were 0.28 (0.03), 0.21 (0.04), 0.21 (0.04), 0.12 (0.04), and 0.11 (0.03), respectively. The posterior means for genetic correlations between LMA and meat quality were positive and moderate with MARB (0.38 ± 0.12) and negative with WBSF (-0.47 ± 0.12). Low genetic correlations were estimated between BF and WBSF (-0.03 ± 0.16) and between HCW and MARB (-0.04 ± 0.14), indicating that these traits are not controlled by the same set or linked genes. Carcass traits (LMA, BF, and HCW) presented moderate heritability providing quick response to the selection purpose. The estimates of heritability for meat quality traits (MARB and WBSF) were low and indicate that the rate of genetic improvement for these traits would be slow. Genetic correlations indicated that selection for carcass traits would not be strongly antagonistic for improving meat quality.

Dressing percentage and the differential between live weight and carcass weight in cattle are influenced by both genetic and non-genetic factors1

The objective of the present study was to quantify the genetic and non-genetic contributors to variability in both carcass dressing percentage and dressing difference (i.e., the difference between carcass weight and live weight immediately prior to slaughter) in young animals and cows. The datasets contained 18,479 young animals from 653 herds, and 2,887 cows from 665 herds. Live weight records within 7 d of slaughter and associated carcass weight were available for all animals. Association analyses were undertaken using linear mixed models with fixed effects for the model of young animals consisting of animal breed, days between the date of last recorded live weight and slaughter date, heterosis and recombination loss coefficients, dam parity, a 3-way interaction between whether the animal originated in a dairy or beef herd, animal sex, and age at slaughter, as well as a 2-way interaction between calendar year of slaughter and month of slaughter; contemporary group was included as a random effect. Fixed effects in the cow model were cow breed, the number of days between the date of last recorded live weight and slaughter date, heterosis and recombination loss coefficients, the number of days postcalving, parity of the cow, and a 2-way interaction between calendar year of slaughter and month of slaughter; contemporary group was included as a random effect. The mean dressing percentage (phenotypic standard deviation in parentheses) and dressing difference in young animals were 55.86% (3.21%) and 280.03 kg (41.44 kg), respectively. Steers had the heaviest dressing difference at 34.18 and 60.44 kg heavier than a 16-mo old bull and 22-mo old heifer, respectively. Dressing difference for 30-mo old Simmental steers (breed with heaviest dressing difference) was 41.66 kg heavier than 30-mo old Belgian Blue steers (breed with lightest dressing difference). The heritability of dressing percentage (0.48) and dressing difference (0.35) in young animals was relatively similar to each other, in contrast to dressing percentage (0.08) in cows which was considerably lower than dressing difference (0.28). Considerable genetic variability existed in dressing difference amongst young animals (genetic standard deviation of 15.03 kg), despite the near unity genetic correlation (0.93) between carcass weight and live weight. This therefore indicates that genetic selection for increased saleable product can be achieved by selecting for increased carcass weight while concurrently selecting for lighter animals although the opportunity is limited by the strong part-whole relationships that exists between carcass weight, live weight, and dressing difference.

Towards a new phenotype for tick resistance in beef and dairy cattle: a review

About 80% of the world’s cattle are affected by ticks and tick-borne diseases, both of which cause significant production losses. Cattle host resistance to ticks is the most important factor affecting the economics of tick control, but it is largely neglected in tick-control programs due to technical difficulties and costs associated with identifying individual-animal variation in resistance. The present paper reviews the scientific literature to identify factors affecting resistance of cattle to ticks and the biological mechanisms of host tick resistance, to develop alternative phenotype(s) for tick resistance. If new cost-effective phenotype(s) can be developed and validated, then tick resistance of cattle could be genetically improved using genomic selection, and incorporated into breeding objectives to simultaneously improve cattle productive attributes and tick resistance. The phenotype(s) could also be used to improve tick control by using cattle management. On the basis of the present review, it is recommended that three possible phenotypes (haemolytic analysis; measures of skin hypersensitivity reactions; simplified artificial tick infestations) be further developed to determine their practical feasibility for consistently, cost-effectively and reliably measuring cattle tick resistance in thousands of individual animals in commercial and smallholder farmer herds in tropical and subtropical areas globally. During evaluation of these potential new phenotypes, additional measurements should be included to determine the possibility of developing a volatile-based resistance phenotype, to simultaneously improve cattle resistance to both ticks and biting flies. Because the current measurements of volatile chemistry do not satisfy the requirements of a simple, cost-effective phenotype for use in commercial cattle herds, consideration should also be given to inclusion of potentially simpler measures to enable indirect genetic selection for volatile-based resistance to ticks.

Genomic regions and enrichment analyses associated with carcass composition indicator traits in Nellore cattle

The aim of this study was to estimate genetic parameters and identify genomic regions associated with carcass traits obtained by ultrasound and visual scores in Nellore cattle. Data from ~66,000 animals from the National Association of Breeders and Researchers (ANCP) were used. The variance components for backfat thickness, rump fat thickness and Longissimus muscle area (LMA) were estimated considering a linear model whereas a threshold model for body structure (BS), finishing precocity (FP) and musculature (MS) traits. The SNP solutions were estimated using the ssGBLUP approach by considering windows of 10 consecutive SNPs. Regions that accounted for more than 1.0% of the additive genetic variance were used. Genes identified within the significant windows, such as FOXA3, AP2S1, FKRP, NPASI and ATP6V1G1, were found to be related with MS, while OMA1 and FFGY with BS and FP traits. The PLTP, TNNC2 and GPAT2 genes were found in the regions associated with LMA, as well as TKT, FNDC5 and CHRND can strongly be related with fat deposition. Gene enrichment analysis revealed processes that might be directly influenced the organism growth and development. These results should help to better understand the genetic and physiological mechanisms regulating growth and body composition, muscle tissue development and subcutaneous fat expression, and this information might be useful for future genomic studies in Nellore cattle.

Phenotypic and genetic correlations of fatty acid composition in subcutaneous adipose tissue with carcass merit and meat tenderness traits in Canadian beef cattle

Bivariate animal models were used to estimate phenotypic and genetic correlations between 9 carcass merit and meat tenderness traits with 25 individual and grouped fatty acids in the subcutaneous adipose tissue of a population of 1,366 Canadian beef cattle finishing heifers and steers. In general, phenotypic correlations were low (<0.25 in magnitude) except for moderate phenotypic correlations of 9-17:1 (-0.29 ± 0.16), 18:0 (0.26 ± 0.14), 11-18:1 (-0.33 ± 0.15), 11-18:1 (0.35 ± 0.14) with Warner-Bratzler shear force measured 3 d postmortem and between 14:0 (-0.36 ± 0.1), 9-14:1 (-0.34 ± 0.08), 9-16:1 (-0.36 ± 0.08), 9-18:1 (0.26 ± 0.07), and sum of branched-chain fatty acids (BCFA; -0.27 ± 0.06) and back fat thickness (BFAT). Genetic correlations were also low for most of the traits. However, moderate to moderately high genetic correlations (0.25 to 0.50 in magnitude) were detected for some traits, including 17:0 (0.4 ± 0.11), 18:0 (0.44 ± 0.12), 9-14:1 (-0.47 ± 0.11), 9-16:1 (-0.43 ± 0.11), and the -6:-3 PUFA ratio (-0.5 ± 0.15) with HCW; 9-14:1 (-0.41 ± 0.13) and 9-16:1 (-0.42 ± 0.13) with BFAT; 17:0 (0.43 ± 0.19) and BCFA (0.45 ± 0.19) with lean meat yield; 13-18:1 (0.40 ± 0.15) with carcass marbling score; sum of CLA (0.45 ± 0.22), 18:2-6 (0.47 ± 0.17), and sum of PUFA (0.48 ± 0.17) with overall tenderness measured 3 d postmortem; the -6:-3 PUFA ratio (0.41 ± 0.22) and sum of CLA (0.42 ± 0.25) with overall tenderness measured 29 d postmortem; and BCFA (0.41 ± 0.27) with Warner-Bratzler shear force measured 29 d postmortem. The genetic correlations observed in this study suggest that contents of some fatty acids in beef tissue and carcass merit and meat tenderness traits are likely influenced by a subset of the same genes in beef cattle. Due to some antagonistic genetic correlations, multiple-trait economic indexes are recommended when fatty acid composition, carcass merit, and meat tenderness traits are included in the breeding objective.

Individual and combined effects of <i>CAPN1</i>, <i>CAST</i>, <i>LEP</i> and <i>GHR</i> gene polymorphisms on carcass characteristics and meat quality in Holstein bulls

Abstract. The objective of this study was to determine the association of single nucleotide polymorphisms (SNPs) with carcass characteristics and meat quality traits in selected candidate genes in Holstein bulls. Five SNPs in four genes, i.e. calpain 1 (CAPN1), calpastatin (CAST), leptin (LEP) and growth hormone receptor (GHR), were genotyped in 400 purebred bulls using PCR-RFLP. Statistically significant associations were as follows: CAPN1 G316A with live weight, carcass weight, back fat thickness, m. longissimus thoracis et lumborum area and carcass measurements; CAPN1 V530I with pH and L∗; CAST S20T with live weight, inner chest depth and b∗ value; and GHR with ph, a∗ and h∗. In addition, significant genotypic interactions were observed for dressing percentage (LEP A80V  ×  CAST S20T), pH (CAPN1 V530I  ×  GHR S555G and LEP A80V  ×  GHR S555G) and rump width (CAPN1 V530I  ×  CAST S20T). There was no association between the LEP A80V marker and any of the traits evaluated, nor was there any association of the tested SNPs with chest width, C∗ and marbling score. The present results could therefore be indicative for future studies on meat yield and quality.

Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Background

Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits.

Results

By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis.

Conclusion

In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3897-x) contains supplementary material, which is available to authorized users.

Genetic correlation estimates between beef fatty acid profile with meat and carcass traits in Nellore cattle finished in feedlot

The objective of this study was to estimate the genetic-quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24 months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fat thickness (BF), shear force (SF) and total intramuscular fat (IMF). The fatty acid (FA) profile of the Longissimus thoracis samples was determined. Twenty-five FAs (18 individuals and seven groups of FAs) were selected due to their importance for human health. The animals were genotyped with the BovineHD BeadChip and, after quality control for single nucleotide polymorphisms (SNPs), only 470,007 SNPs from 1556 samples remained. The model included the random genetic additive direct effect, the fixed effect of the contemporary group and the animal's slaughter age as a covariable. The (co)variances and genetic parameters were estimated using the REML method, considering an animal model (single-step GBLUP). A total of 25 multi-trait analyses, with four traits, were performed considering SF, BF and IMF plus each individual FA. The heritability estimates for individual saturated fatty acids (SFA) varied from 0.06 to 0.65, for monounsaturated fatty acids (MUFA) it varied from 0.02 to 0.14 and for polyunsaturated fatty acids (PUFA) it ranged from 0.05 to 0.68. The heritability estimates for Omega 3, Omega 6, SFA, MUFA and PUFA sum were low to moderate, varying from 0.09 to 0.20. The carcass and meat traits, SF (0.06) and IMF (0.07), had low heritability estimates, while BF (0.17) was moderate. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with BF were 0.04, 0.64 and -0.41, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with SF were 0.29, -0.06 and -0.04, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with IMF were 0.24, 0.90 and -0.67, respectively. The selection to improve meat tenderness in Nellore cattle should not change the fatty acid composition in beef, so it is possible to improve this attribute without affecting the nutritional beef quality in zebu breeds. However, selection for increased deposition of subcutaneous fat thickness and especially the percentage of intramuscular fat should lead to changes in the fat composition, highlighting a genetic antagonism between meat nutritional value and acceptability by the consumer.

Growth performance, and carcass and meat quality traits in progeny of Poll Nellore, Angus and Brahman sires under tropical conditions

This study aimed to characterise progeny of sires representing major families in the Poll Nellore breed. Fourteen Poll Nellore sires, two Angus sires and one Brahman sire were mated by AI to ~400 multiparous Poll Nellore dams. Calves were raised and stocked on pasture in central Brazil until reaching ~18 months of age, then fed a sugarcane bagasse-based diet on an ad libitum basis until reaching market weight and finish (average 23 months). There were 236 Poll Nellore (N), 38 Angus × Poll Nellore (AN) and 31 Brahman × Poll Nellore (BN) calves born in total. The weaning and 423-day weight weights, and growth rates and pre- and post-weaning were greater (P < 0.05) in males than in female calves, and were influenced by breed and by sire within the N animals. The weaning weights were higher (P < 0.05) in AN and BN than in N calves. The 423-day weight weights were greater (P < 0.05) in AN calves, followed by BN, with straightbred N being lightest. Feedlot average daily gain was unaffected (P > 0.05) by sex or by sire within N, but was lowest (P < 0.05) in N cattle, and highest in AN and BN animals, which did not differ (P > 0.05). Heifers reached the end of the study with lower bodyweight (BW) and dressing percentage than steers, resulting in lower carcass weights, smaller longissimus muscle areas (LMA), but greater 12th to 13th rib backfat (BF) and similar marbling score and mean shear force. However, the proportion of carcasses grading Choice or Prime was numerically greater in heifers than in steers (23.6% vs 9.8%). AN cattle reached greater harvest weights than BN, and those were heavier than N cattle (P < 0.001). However, dressing percentages were lowest in AN animals, so that there was no significant difference in carcass weight between AN and BN cattle. AN carcasses also had greater LMA, BF and marbling scores than the N carcasses. The proportion of carcasses grading Choice or Prime was numerically greater in AN cattle than in the BN and N groups (25.9%, 11.8% and 15.9%, respectively). Steaks from AN calves were more tender than N steaks, with the BN steaks being intermediate. There was significant variation among N sires for final BW, dressing percentage, carcass weight, LMA and marbling score, but not for BF or mean shear force. The percentages of carcasses of N cattle grading Choice or Prime ranged from 0% to 61.5%. Three N sires produced progeny with greater than 40% of carcasses grading Choice or above (Berílio OB, Furador OB, and Litoral OB). Likewise, three N sires (Blitz OB, Furador OB and Sossego OB) had progeny with 67%, 62% and 75%, respectively, of steaks classified as tender. This study confirmed that Zebu cattle have inferior carcass and meat quality relative to AN crossbreds under tropical conditions, however there is substantial variation within the N breed for these traits, and several sires have a proportion of their progeny comparable in terms of meat tenderness to those of Angus sires.

Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds

Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.

Regulation of post-mortem glycolysis in ruminant muscle

As a tissue, muscle has the unique ability to switch its metabolic source of ATP, the energy currency underpinning muscle function. During oxygen debt, such as that occurring immediately following the death of animals, anaerobic metabolism is initiated in an attempt to restore homeostasis within the muscle. The cascade of biochemical events that are initiated is paramount in the context of meat quality. This review revisits this reasonably well-known subject but takes a new perspective by drawing on the understanding outside the traditional discipline of meat science. Our understanding of the intrinsic regulators of glycolytic flux has improved but knowledge gaps remain. Further efforts to understand how the glycolytic enzyme kinetics are influenced by both pre- and post-slaughter factors will be beneficial in the ongoing quest to maximise fresh meat quality.

Heritability of beef tenderness at different aging times and across breed comparisons

Zwambag, A., Kelly, M., Schenkel, F., Mandell, I., Wilton, J. and Miller, S. 2013. Heritability of beef tenderness at different aging times and across breed comparisons. Can. J. Anim. Sci. 93: 307–312. The heritability of shear force at 7, 14 and 21 d was estimated from a crossbred population of beef cattle. The population consisted of approximately 1400 crossbred cattle that were predominantly the offspring of Angus, Simmental, Gelbvieh and Piedmontese sires bred to predominantly Angus and Simmental females. Significant breed effects on tenderness were found within each aging time and no effect of heterosis was detected. The heritability of shear force declined from 0.194 to 0.048 as aging time increased from 7 to 21 d, highlighting the effectiveness of aging as a tool to improve tenderness. The repeatability of shear force was also found to be moderate (0.53). However, as energy prices increase it may be attractive to reduce aging times, thus breeding animals that are more tender at shorter aging times would be beneficial. The heritability of tenderness found at shorter aging times would indicate that improvement in this trait would be possible within a population where phenotypes are available.

Genetic effects on carcass quantity, quality, and palatability traits in straightbred and crossbred Romosinuano steers

The objectives of this work were to estimate heterosis and breed genetic effects for carcass quantity, quality, and palatability traits of steers (Bos spp.) produced from matings of Romosinuano, Brahman, and Angus cattle. Steers (n = 464) were weaned at 7 mo of age and transported to the Southern Great Plains where they grazed winter wheat for 6 mo and were then fed a finishing diet until serial slaughter after different days on feed (average 130 d). Carcass quality and quantity traits were measured; steaks (aged 7 d) were obtained for palatability evaluation. Heterosis was detected for BW, HCW, dressing percentage, LM area, and yield grade for all pairs of breeds. Generally, Romosinuano-Angus heterosis estimates were smallest, Romosinuano-Brahman estimates were intermediate, and Brahman-Angus heterosis estimates were largest. The direct Romosinuano effect was to decrease (P < 0.05) BW (-67 ± 16 kg), HCW (-48 ± 10 kg), dressing percentage (-1.4 ± 0.5 units), 12th rib fat thickness (-5.2 ± 0.8 mm), and yield grade (-0.9 ± 0.1), and to increase LM area per 100 kg HCW (3.6 ± 0.3 cm(2)/100 kg). Significant Brahman direct effects were detected for BW (34 ± 17 kg), HCW (29 ± 10 kg), dressing percentage (1.6 ± 0.6 %), LM area per 100 kg HCW (-3.3 ± 0.4 cm(2)/100 kg), and yield grade (0.6 ± 0.1). Significant Angus direct effects were to increase 12th rib fat thickness (3.8 ± 1 mm). Among sire breed means, Romosinuano had reduced (P = 0.002) marbling score (393 ± 9) than Angus, but greater mean sensory tenderness scores (5.8 ± 0.1), and reduced percentage Standard carcasses (10 ± 2%) than Brahman (P < 0.002). Angus sire breed means for marbling score (475 ± 10), overall tenderness (5.8 ± 0.1), and percentage Choice carcasses (75 ± 5%) were greater (P < 0.05) than Brahman sire breed means (360 ± 11, 5.4 ± 0.1, 31 ± 5%). From consideration only of characteristics of the end product of beef production, Romosinuano did not provide a clearly superior alternative to Brahman for U.S. producers, as they had some quality and palatability advantages relative to Brahman, but at lighter HCW.

Managing meat tenderness

This paper discusses the management of meat tenderness using a carcass grading scheme which utilizes the concept of total quality management of those factors which impact on beef palatability. The scheme called Meat Standards Australia (MSA) has identified the Critical Control Points (CCPs) from the production, pre-slaughter, processing and value adding sectors of the beef supply chain and quantified their relative importance using large-scale consumer testing. These CCPs have been used to manage beef palatability in two ways. Firstly, CCPs from the pre-slaughter and processing sectors have been used as mandatory criteria for carcasses to be graded. Secondly, other CCPs from the production and processing sectors have been incorporated into a model to predict palatability for individual muscles. The evidence for the importance of CCPs from the production (breed, growth path and HGP implants), pre-slaughter and processing (pH/temperature window, alternative carcass suspension, marbling and ageing) sectors are reviewed and the accuracy of the model to predict palatability for specific muscle×cooking techniques is presented.

Genetic and environmental effects on meat quality

In order for livestock industries to consistently produce high quality meat, there must be an understanding of the factors that cause quality to vary, as well as the contribution of genetics. A brief overview of meat tenderness is presented to understand how genotype and environment may interact to influence this trait. Essentially, meat tenderness is determined from the contribution of connective tissue, sarcomere length determined pre-rigor and rate of proteolysis during ageing, as well as contributions from intramuscular fat and post-mortem energy metabolism. The influence of mutations in myostatin, the callipyge gene, the Carwell or rib eye muscle gene as well as the calpain system on meat tenderness is presented. Specific examples of interactions between the production or processing environment and genetics are presented for both sheep and cattle. The day-to-day variation in tenderness is evident across experiments and this variation needs to be controlled in order to consistently produce tender meat.

Effect of postweaning growth and bulls selected for extremes in retail beef yield and intramuscular fat on progeny liveweight and carcass traits

The present study is a component of a multi-site experiment, using Bos taurus cattle generated at four locations across southern Australia, designed to examine postweaning growth pathways for progeny whose sires were extreme in retail beef yield and intramuscular fat. Treatment and interaction effects on beef production and meat quality were examined within and across sites. The present paper describes the effect of postweaning growth and sire carcass type on liveweight and carcass traits at the Hamilton site. Angus sires selected on estimated breeding values for extremes in retail beef yield (RBY%), intramuscular fat (IMF%) (estimated breeding values for IMF% are derived by using live-animal ultrasound scanning) or both and sire breed types considered to be more extreme in those traits (Limousin, and Belgian Blue for yield, and Wagyu for intramuscular fat) were joined to crossbred and straight-bred cows. After weaning, the resultant 645 steer and heifer progeny were grown on a fast and slow growth path to ~550 kg and slaughtered, averaging 0.68 kg/day and 22.2 months, and 0.49 kg/day and 27.8 months for growth rate and age at slaughter, respectively. Growth path, sire carcass type and sex affected carcass traits; however, there were no sire carcass type by growth treatment interactions. The fast growth-path cattle were fatter, had more intramuscular fat (measured chemically), a higher Meat Standards of Australia (MSA) USA and AUS marble score, and a higher predicted MSA eating-quality score. Progeny of Wagyu sires were lighter at weaning and slaughter and had a lower hot standard carcass weight than the other sire carcass types. The Belgian Blue and Limousin progeny had a higher dressing percentage, a higher RBY% and a lower P8 and rib-fat depth and lower IMF% than the other sire breed types. Progeny of the high RBY% Angus had a lower rib-fat depth, a lower IMF% and higher RBY% than those selected for high IMF%. There was no difference in IMF% between the Wagyu or the high IMF% Angus. Progeny from the Belgian Blue, Limousin and Wagyu had a larger eye muscle area than the other sire breeds. The results indicate that simultaneous selection for supposedly antagonistic traits of IMF% and RBY% would result in carcass having high values of both measurements. Females were lighter than steers at slaughter, had a lower hot standard carcass weight, were fatter at the P8 and rib, and had a higher marble score and IMF%, a lower yield and a lower MSA-predicted eating-quality score than did steers. There was no interaction between postweaning growth and sire carcass type. These results indicate that with the use of appropriate sire carcass types and BREEDPLAN, and post-weaning nutrition, beef producers can confidently change carcass parameters to suit market specifications.

Extensive analysis of long-chain polyunsaturated fatty acids, CLA, trans-18:1 isomers, and plasmalogenic lipids in different retail beef types

The objective of this investigation was to provide a comprehensive analysis of the total lipid composition of present-day retail beef meat available at the consumer level and to evaluate the total lipid composition with special emphasis on the nutritional value. For this purpose, 40 beef cuts were obtained from four cattle farms based on either a natural grazing system (NGS) or an intensive production system (IPS). The total lipid composition was analyzed using complementary chemical and chromatographic procedures. The content of n-3 LC-PUFA, CLA, total trans-18:1, and branched-chain fatty acids was significantly higher in NGS beef than in IPS beef. The trans-18:1 and CLA profiles were affected by the different production systems, whereby they can be utilized empirically to differentiate between feeding regimen and production management. Fatty acid ratios that have health implications ( n-6/ n-3, LA/alphaLNA, and AA/EPA) were remarkably beneficial for NGS beef compared with IPS beef. In conclusion, from the human health perspective, beef raised on NGS is clearly superior with regard to a more favorable fatty acid profile in comparison to IPS beef.

Evolution of the Meat Standards Australia (MSA) beef grading system

The Australian Beef Industry identified variable eating quality as a major contributor to declining beef consumption in the early 1990s and committed research funding to address the problem. The major issue was the ability to predict the eating quality of cooked beef before consumption. The Meat Standards Australia (MSA) program developed a consumer testing protocol, which led to MSA grading standards being defined by consumer score outcomes. Traditional carcass grading parameters proved to be of little value in predicting consumer outcomes. Instead a broader combination of factors forms the basis of an interactive prediction model that performs well. The grading model has evolved from a fixed parameter ‘Pathway’ approach, to a computer model that predicts consumer scores for 135 ‘cut by cooking method’ combinations for each graded carcass. The body of research work conducted in evaluating critical control points and in developing the model predictions and interactions has involved several Australian research groups with strong support and involvement from the industry.

Effects of genotype, sex and stocking rate on postweaning efficiency and value-adding potential at turnoff of weaners grazing improved pasture in the Douglas Daly region of the Northern Territory

An experiment was undertaken to establish the effects of genotype, sex and stocking rate on postweaning growth and value-adding potential at turnoff of weaners grazing improved pasture in the Douglas Daly region of the Northern Territory, Australia. The growth of 27 steer and 27 heifer weaners of four genotypes was studied each year for 4 years (i.e. n = 216 animals per year). Animals from each group were run at one of three stocking rates. The cattle were weighed monthly and fat depth was measured ultrasonically at the end of the postweaning year. Genotype had no significant effect on weight gain but one-quarter Charolais × three-quarters Brahman and Droughtmaster animals were significantly (P < 0.0001) leaner than Brahman (purebred and commercial) cattle at the end of the postweaning year. Steers grew more (12%; P < 0.0001) and were leaner (2.6 mm less P8 fat depth; P < 0.0001) than heifers. Animals that grazed at lower stocking rates gained more weight (P < 0.0001) but were not significantly fatter than those at higher stocking rates. The way these factors can be used to produce leaner animals with more value-adding potential for South-East Asian feedlots is discussed.

Regrouping unfamiliar animals in the weeks prior to slaughter has few effects on physiology and meat quality in Bos taurus feedlot steers

The response of cattle to alterations in social groupings can lead to physiological changes that affect meat quality. Feedlot practices frequently lead to a proportion of cattle in a pen being drafted for slaughter with the balance retained for a further period until they meet market specifications. An ability to regroup such retained cattle for short periods without consequences for meat quality would facilitate efficient use of feedlot pen space. The current experiment examined the impact on physiological variables and meat quality of regrouped British breed steers 4, 2 or 1 week before dispatch for slaughter. There was little effect of regrouping cattle on physiological variables associated with stress responses. Physical assessment of meat quality indicated that regrouping steers 1 week before slaughter led to higher compression and a tendency for higher peak force values in animals from one genotype than in their respective controls (1.89 v. 1.71 ± 0.05 kg, P = 0.017); however, these assessments were not matched by changes in sensory perception of meat quality. Average daily gain during feedlot finishing was negatively related to the temperament measure and flight time. It was also associated with breed, white cell count, plasma cortisol and haemoglobin at the midpoint of the 70-day finishing period. The results confirm the impact of flight time on growth rate during feedlot finishing and that regrouping cattle less than 2 weeks before slaughter may reduce meat quality.

Genetic and environmental effects on the muscle structure response post-mortem

This paper reviewed the mechanisms by which glycolytic rate and pre-rigor stretching of muscle impact on meat quality. If muscle is free to shorten during the rigor process extremes in glycolytic rate can impact negatively on meat quality by inducing either cold or rigor shortening. Factors that contribute to variation in glycolytic rate include the glycogen concentration at slaughter and fibre type of the muscle. Glycolysis is highly sensitive to temperature, which is an important factor in heavy grain fed carcasses. An alternative solution to controlling glycolysis is to stretch the muscle pre-rigor so that it cannot shorten, thus providing an insurance against extremes in processing conditions. Results are presented which show a large reduction in variance (both additive and phenotypic) in tenderness caused by pre-rigor stretching. Whilst this did not impact on the heritability of shear force, it did reduce genotype differences. The implications of these results on the magnitude of genotype effects on tenderness is discussed.

Impact of animal health and welfare research within the CRC for Cattle and Beef Quality on Australian beef production

Research within the health and welfare program of the Cooperative Research Centre for Cattle and Beef Quality has delivered important improvements to the Australian cattle industry. Vaccines to assist with the control of bovine respiratory disease were developed and commercialised from Australian isolates of Mannheimia haemolytica and pestivirus (mucosal disease). Our understanding of the benefits of weaning cattle by confinement and hand feeding in yards (yard weaning) has been consolidated, and yard weaning has been adopted as ‘best practice’ for cattle production in the temperate zones of Australia. The importance of good temperament for improved growth rates and reduced morbidity during feedlot finishing, and for adaptation to stressors such as road transport, has been demonstrated. In response to this knowledge, industry is increasingly measuring flight time for use in breeding programs and feedlot management. The risk to meat quality of stressors such as mixing unfamiliar cattle in the weeks preceding slaughter or acute stress in the last 15 min before slaughter has been described. Adoption of these findings through Quality Assurance schemes will assist in assurance for the community and for export markets of the welfare standards of the Australian cattle and beef industry. This review provides details of the experiments that led to these achievements and to some improved understandings of temperament and behaviour of beef cattle.

The impact of innovation on beef production in far northern Australia

In this paper we examine the forces that have shaped Australia’s far northern (north of 20° south) beef industry over the past 35 years. This is done for the purpose of tracing its transformation from a state of relative isolation to an integral part of the national beef industry. We note that integration is being accompanied by a greater focus, particularly by corporate producers, on specialised breeding in the far north and this is being assisted by innovations that increase herd fertility and raise the meat quality of the progeny, while retaining adaptation of the breeding herd to the local environment. Among a range of technologies, genetic improvement has significant potential to bring about rapid improvement in the meat quality of tropically adapted cattle. With respect to gene-based technology, however, independent producers will have to be convinced about the rigour of the technology and the prospects of economic gains before they make significant management changes. To this end, innovative marketing systems are needed that will reveal the link between expected meat returns and the offer prices applying to groups of growing cattle in any location. Accordingly, there is an urgent need to develop and introduce a descriptive and informative trading language for growing cattle that incorporates inherent qualities including those that influence meat quality. Innovations that will complement those applying to enhancement of meat quality are more general but will significantly raise herd productivity. We also compare the operating systems of both corporate and independent producers in the region.

The efficacy of a vitamin D(3) metabolite for improving the myofibrillar tenderness of meat from Bos indicus cattle

The influence of a once only administration of a metabolite of vitamin D(3) (HY·D(®)-25-hydroxy vitamin D(3)) on myofibrillar meat tenderness in Australian Brahman cattle was studied. Ninety-six Brahman steers of three phenotypes (Indo-Brazil, US and US/European) and with two previous hormonal growth promotant (HGP) histories (implanted or not implanted with Compudose(®)) were fed a standard feedlot ration for 70d. Treatment groups of 24 steers were offered daily 10g/head HY·D(®) (125mg 25-hydroxyvitamin D(3)) for 6, 4, or 2d before slaughter. One other group of 24 steers was given the basal diet without HY·D(®). Feed lot performance, blood and muscle samples and carcass quality data were collected at slaughter. Calcium, magnesium, potassium, sodium, iron and Vitamin D(3) metabolites were measured in plasma and longissimus dorsi muscle. Warner-Bratzler (WB) shear force (peak force, initial yield) and other objective meat quality measurements were made on the longissimus dorsi muscle of each steer after ageing for 1, 7 and 14d post-mortem at 0-2°C. There were no significant effects of HY·D(®) supplements on average daily gain (ADG, 1.28-1.45kg/d) over the experimental period. HY·D(®) supplements given 6d prior to slaughter resulted in significantly higher (P<0.05) initial yield values compared to supplements given 2d prior to slaughter. Supplementation had no significant effect on meat colour, ultimate pH, sarcomere length, cooking loss, instron compression or peak force. There was a significant treatment (HY·D(®)) by phenotype/HGP interaction for peak force (P=0.028), in which Indo-Brazil steers without previous HGP treatment responded positively (increased tenderness) to HY·D(®) supplements at 2d when compared with Indo-Brazil steers previously given HGP. There were no significant effects of treatment on other phenotypes. HY·D(®) supplements did not affect muscle or plasma concentrations of calcium, potassium or sodium, but did significantly decrease plasma magnesium and iron concentrations when given 2d before slaughter. There were no detectable amounts of 25-hydroxyvitamin D(3) in the blood or muscle of any cattle at slaughter.