Genomic selection is becoming a standard tool in livestock breeding programs, particularly for traits that are hard to measure. Accuracy of genomic selection can be improved by increasing the quantity and quality of data and potentially by improving analytical methods. Adding genotypes and phenotypes from additional breeds or crosses often improves the accuracy of genomic predictions but requires specific methodology. A model was developed to incorporate breed composition estimated from genotypes into genomic selection models. This method was applied to age at puberty data in female beef cattle (as estimated from age at first observation of a corpus luteum) from a mix of Brahman and Tropical Composite beef cattle. In this dataset, the new model incorporating breed composition did not increase the accuracy of genomic selection. However, the breeding values exhibited slightly less bias (as assessed by deviation of regression of phenotype on genomic breeding values from the expected value of 1). Adding additional Brahman animals to the Tropical Composite analysis increased the accuracy of genomic predictions and did not affect the accuracy of the Brahman predictions.

The hypothesis tested by this study was that sheep with divergent estimated breeding values (EBV) for fleece weight differ in gut metabolism and anatomy" regardless of the level of intake. Adult Merino wethers with contrasting EBVs for fleece weight were fed at two levels of intake in two 7-week periods in a crossover design, where wool growth, gut metabolism and anatomy of the sheep were evaluated. Regardless of the level of intake, wool genotype affected wool growth (P<0.05); however, rumen metabolism and gut anatomy did not differ between wool genotypes (P<0.05). Increases in the level of intake increased the supply of nutrients to the animal and the measured end-products of the process (wool production, live weight, methane) independent of wool genotype. The results obtained in this study indicate that differences in gut fermentation and anatomy are not a major cause of differences in wool production among sheep of different estimated genetic merit for fleece weight when fed restricted intakes.

Context. The texture of beef is highly important for the eating experience, and there is a continued interest in understanding the biochemical basis for the variation in texture between cattle and their meat cuts in order to improve and minimise variation in tenderness due to production and processing factors.

Aims. The present study aimed to investigate the impact of characteristics of meat on Warner-Bratzler shear-force (WBSF) as an indicator of texture of beef as affected by breed type, age/feeding phase, and muscle.

Methods. Seventy-five steers of three breed types (Angus, Hereford and Wagyu x Angus) were slaughtered after weaning 6 months old (n = 15), after backgrounding 17 months old (n = 30) and after feedlotting 25 months old (n = 30). At slaughter three muscles (M. supraspinatus, M. semitendinosus and M. longissimus lumborum) were sampled from each steer, and pH, intramuscular fat and collagen content, sarcomere length, and proteolysis (desmin degradation) were measured and used to explain the variation in WBSF after 7 and 14 days of aging.

Key results. Meat from Hereford and Angus steers had higher WBSF after 7 days of aging compared with Wagyu x Angus steers, but after 14 days of aging there was only a difference between Hereford and Wagyu x Angus in the M. supraspinatus and M. semitendinosus. The WBSF of the young weaned steers and steers slaughtered after backgrounding were dependent on the degree of proteolysis in the muscles, whereas for steers slaughtered after feedlotting the content of collagen was more important for the WBSF. The amount of intramuscular fat had a significant impact on the differences in WBSF within the specific muscle studied. In contrast to the general dogma that WBSF increase with age, WBSF decreased in M. semitendinosus and M. longissimus lumborum from the weaned 6-month-old steers to the 25-month-old steers finished in feed-lot, whereas in M. supraspinatus the older feed-lot finished steers had a higher WBSF.

Conclusion. The factors contributing to the Warner-Bratzler shear force of beef depends on the age/feeding phase of the animal and the muscle and less on the breed type. Implications. Optimisation of texture in beef through breeding and production should address different traits dependent on the age/feeding phase of the slaughter animal.

Implications. Optimisation of texture in beef through breeding and production should address different traits dependent on the age/feeding phase of the slaughter animal.

Background:

Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants and genes that underpin economically important traits. Merino wool is globally sought after for luxury fabrics, but some key wool quality attributes are unfavourably correlated with the characteristic skin wrinkle of Merinos. In turn, skin wrinkle is strongly linked to susceptibility to "fly strike" (Cutaneous myiasis), which is a major welfare issue. Here, we use whole-genome sequence data in a multi-trait GWAS to identify pleiotropic putative causal variants and genes associated with changes in key wool traits and skin wrinkle.

Results:

A stepwise conditional multi-trait GWAS (CM-GWAS) identified putative causal variants and related genes from 178 independent quantitative trait loci (QTL) of 16 wool and skin wrinkle traits, measured on up to 7218 Merino sheep with 31 million imputed whole-genome sequence (WGS) genotypes. Novel candidate gene findings included the MAT1A gene that encodes an enzyme involved in the sulphur metabolism pathway critical to production of wool proteins, and the ESRP1 gene. We also discovered a significant wrinkle variant upstream of the HAS2 gene, which in dogs is associated with the exaggerated skin folds in the Shar-Pei breed.

Conclusions:

The wool and skin wrinkle traits studied here appear to be highly polygenic with many putative candidate variants showing considerable pleiotropy. Our CM-GWAS identified many highly plausible candidate genes for wool traits as well as breech wrinkle and breech area wool cover.

Milk electrical conductivity and milk flow rate are potential indicators in selection targeting mastitis resistance. This study aimed to estimate the genetic parameters for clinical mastitis, average daily milk electrical conductivity (EC), milk flow rate (FR), and milk yield (MY) for the first lactation of imported Jersey and Jersey-Friesian dairy cows in Sri Lanka. Genetic parameters for mastitis traits, the prevalence of clinical mastitis in each cow, the duration of clinical mastitis treatment, and the number of episodes of mastitis were estimated using univariate sire models with permanent environmental effect of the cow added to models for prevalence of clinical mastitis in each day of milk over the whole lactation, or within the first 100-days of milk. The genetic parameters for the traits EC, FR, and MY over the whole lactation and for these traits defined for 30-day intervals were estimated using univariate animal models. For all mastitis traits, a zero heritability was estimated under both normal and logit scales. Heritabilities of EC and FR ranged from 0.02 to 0.11 and from 0.02 to 0.14, respectively. Genetic correlations between MY and EC and between MY and FR around peak milk yield were 0.25 ± 0.46 and 0.46 ± 0.29, respectively. Based on the heritability estimates for mastitis, dairy cows in this study cannot be directly selected for mastitis resistance, but indirect selection via EC and FR is feasible. Recording all cases of both sub-clinical and clinical mastitis in subsequent lactations is recommended to aid selection of dairy cows for mastitis resistance.

Growth, feed intake, feed efficiency, and carcass and meat quality characteristics of 136 Angus steers differing in genetic merit for post-weaning residual feed intake (RFIp) were measured over 251 days in a large commercial feedlot. The steers were evaluated in two groups, low (Low-RFI) and high (High-RFI) genetic RFIp, measured by estimated breeding values for RFIp (RFIp-EBV). The difference in RFIp-EBV between the Low- and High-RFI groups was 1.05 kg/day (–0.44 vs 0.61 kg/day; P < 0.05). The Low- and High-RFI steers were similar (P > 0.05) in age (445 vs 444 days) and weight (435 vs 429 kg) at induction, and at the end of the feeding period (705 vs 691 kg). Average daily gain (ADG) over 251 days had a small negative association with variation in RFIp-EBV (P < 0.05), reflecting a 3.6% greater ADG accompanying a difference of 1 kg/day in RFIp-EBV. Pen feed intake and feed conversion by the Low-RFI group were 10.4 kg/day and 9.3 kg/kg, and for the High-RFI group were 11.1 kg/day and 10.4 kg/kg, but without availability of individual animal feedintake data it was not possible to test for significant differences. Carcass weight and dressing-percentage was similar for the Low- and High-RFI steers. High-RFI steers had a significantly (P < 0.05) greater depth of subcutaneous rib fat at induction and finished with 5 mm more (P < 0.05) fat at the 10/11th ribs on the carcass than the Low-RFI steers. Crosssectional area of the eye-muscle and three measures of intramuscular or marbling fat did not differ (P > 0.05) between the Low- and High-RFI steers. Shear force was higher (P < 0.05) in meat samples aged for 1 day from the Low-RFI steers, but there was no difference (P > 0.05) from the High-RFI steers after 7 days of ageing. Compression values for meat samples aged for 1 day did not differ between the RFI groups but were higher in meat samples aged for 7 days from the Low-RFI steers. For these Angus steers, genetic superiority in RFI was associated phenotypically with superior weight gain, decreased rib fat depth, slightly less tender meat, and no compromise in marbling fat or other carcass and meat quality traits.

Extensive farming systems require beef cows to cope with varying environmental conditions while repeatedly producing calves. Cows use body energy reserves as a buffer in times of feed shortage and replenish reserves under a feed surplus. The aims of the research were to (1) quantify live weight (LW) and body condition score (BCS) fluctuations among farms, years and over the production cycle (mating, weaning and calving) and to (2) quantify the relationship between LW and BCS at mating, weaning and calving, for cows of different hip heights. A total of 7,649 individual cow records from nine commercial New Zealand farms with information on LW and BCS (1–10 scale, 1 = emaciated and 10 = obese) were analysed. Analyses revealed significant (P < 0.001) within-year variation in mean LW (32.4–77.2 kg) and BCS (0.4–1.8 scores) profiles among farms, but profiles were not consistent from year to year. There was a quadratic relationship (P < 0.001) between LW and BCS, such that one unit change in BCS corresponded to 15.1 kg LW increase at BCS 4–5 compared to 41.1 kg LW increase at BCS 8–9 at mating. This relationship was similar, irrespective of hip height.

Some mutations (or 'major genes') have a desirable effect in heterozygous carriers but an undesirable effect in homozygous carriers. When these mutations affect a trait of significant economic importance, their eradication, depending on their effect and frequency, may be counterproductive. This is especially the case of major genes affecting the ovulation rate and thus the prolificacy in meat sheep populations. To manage such situations, a mating design based on the major genotypes of reproducers has to be optimized. Both the effect of the major gene and the cost of genotyping candidates at this locus influence the expected genetic progress and profitability of the breeding plan. The aim of this study was to determine the optimal combination of matings that maximizes profitability at the level of the whole population (nucleus + commercial flocks). A deterministic model was developed and, using sequential quadratic programming methodology, the optimal strategy (optimal combination of matings) that maximized the economic gain achieved by the population across a range of genotype effects and genotyping costs was determined. The optimal strategy was compared with simpler and more practical strategies based on a limited number of parental genotype mating types. Depending on the genotype effect and genotyping costs, the optimal strategy varied, such that either the heterozygous frequency and/or polygenic gain was maximized with a large number of animals genotyped, or when genotyping costs were higher, the optimization led to lower heterozygous frequency and/or polygenic gain with fewer animals genotyped. Comparisons showed that some simpler strategies were close to the optimal strategy. An overlapping model was then derived as an application of the real case of the French Lacaune meat sheep OVI-TEST breeding program. Results showed that a practical strategy based on mating non-carriers to heterozygous carriers was only slightly less effective than the optimal strategy, with a reduction in efficiency from 3% to 8%, depending on the genotyping costs. Based on only two different parental genotype mating types, this strategy would be easy to implement.

Physiological maturity, measured as carcass ossification [10 unit increments (100, 110, 120, …)], is used by the United States Department of Agriculture and the Meat Standards Australia carcass grading systems to reflect age-associated differences in beef tenderness and determine producer payments. In most commercial cattle herds, the exact age of animals is unknown; thus, prediction of ossification in association with phenotypic prediction systems has the capacity to assist producer decision making to improve carcass and eating quality. This study developed and evaluated prediction equations that use either live animal or carcass traits to predict ossification for use in phenotypic prediction systems to predict meat quality. The average ossification in the model development dataset was 138 with a SD of 21 and a range between 100 and 200. Model development involved regressing various combinations of live animal traits: age at recording, sex, live weight (BW), average daily gain, ultrasound scanned eye muscle area, 12/13th rib and subcutaneous P8 rump fat thickness; or carcass traits: age at slaughter, sex, hot standard carcass weight (HSCW), carcass eye muscle area, marble score, rib, and P8 rump fat (CP8) thickness, against ossification. The models were challenged with data from 3 independent datasets: 1) Angus steers produced by divergent selection for visual muscle score; 2) temperate (Angus, Hereford, Shorthorn and Murray Grey) steers and heifers; and 3) tropically adapted (Brahman and Santa Gertrudis) steers and heifers. Five models with adjusted R² _adj above 0.55 were evaluated. When challenged with dataset 1, the absolute mean bias (MB) and root mean square error of prediction (RMSEP) ranged from 0.1 to 4.2, and 9.8 to 10.7, which are within the bounds of the 10 point increment on the ossification scale. When subsequently challenged with dataset 2, MB and RMSEP ranged from 2.8 to 13.4, and 19.6 to 23.7, respectively; and with dataset 3, MB and RMSEP ranged from 14.4 to 17.5, and 23.3 to 31.9, respectively. Generally, when compared in relation to the ossification scale, all evaluated models had similar accuracy. For predicting meat quality, the model containing live animal traits considered most useful was [85.35 + 0.16 × BW + 10.94 × sex – 0.09 × sex × BW (adjusted R2 = 0.59; SE = 13.51)] and the most useful model containing carcass traits was [107.15 + 11.53 × sex + 1.10 × CP8 + 0.16 × HSCW – 0.15 × sex × HSCW (adjusted R2 = 0.60; SE = 13.39)].

Context. Selection using visual muscle score (MS) has been proposed to increase carcass leanness (i.e. meat yield), without compromising eating quality.

Aims. The aim of the present study was to examine the impact that selection for divergent MS has on live animal, commercial carcass and carcass tissue weights by using computed tomography (CT) including Meat Standards Australia (MSA) index-predicted eating quality.

Methods. Data from 67 steers originating from three muscling lines, namely, low, high and heterozygous high (High^Het – heterozygous for the 821 del11 myostatin mutation), were used. Visual MS was assessed on all steers. All steers were slaughtered and the left-hand side of each carcass was processed with fat trimming limited to only that required for hygiene purposes and kidney fat was not removed. All carcasses were MSA graded and then boned-out into untrimmed boneless primals (e.g. rump, cube roll). A CT scan of each beef primal was processed with image analysis software to estimate lean and fat tissue weights. The following traits were analysed: MS, weaning and slaughter weights" commercial carcass traits, including cold carcass weight, rump fat, MSA rib fat, MSA eye-muscle area, MSA marble score and MSA index" and CT-scanned compositional carcass traits, including lean, fat and bone tissues (%) and lean : bone ratio. All data were analysed with a linear mixed-effects model using REML. Least-squares means for the three muscling lines are reported. Linear trends between MS and seven carcass traits, with and without the myostatin mutation, are presented graphically.

Key results. Muscling line effects (P < 0.05) were found for visual MS and carcass traits. Linear trends between MS and carcass traits with and without the myostatin mutation demonstrate that increases in MS (P = 0.24) did not compromise predictions of MSA index even though MSA marble score decreased (P = 0.026), but myostatin decreased MSA marble score and tended to decrease MSA index (P = 0.097). Increases in the MSA eye-muscle area were associated with increases in MS (P < 0.01), with little effect of myostatin. Increases in MS and the myostatin mutation were both associated with increases (P < 0.01) in lean tissue (%) and the lean : bone ratio, and decreases (P = 0.02) in fat tissue (%).

Conclusions. The results indicate selection for high MS can be used to increase carcass yield, without negatively affecting MSA index predictions of eating quality.

Implications. Producers can use MS to identify animals with higher yields to increase carcass leanness and decrease carcass waste fat, without compromising MSA index predictions of eating quality, but should do so while considering all traits that affect profitability, in particular marble score and its association with eating quality.