Three interrelated genes postulated to affect economically important traits related to growth and/or carcass quality of beef cattle were chosen to characterize and perform association analyses for this study. Melanocortin 1 receptor (MC1R), melanocortin 4 receptor (MC4R) and agouti related protein (AGRP) play an integral role in the appetite pathway and in fat deposition.<p> We genotyped 328 crossbred steers of various coat colours that were purchased at weaning and fed until slaughter for the previously published alleles ED, E+ and e. The E+ allele was present at five percent in this population and therefore was not included in further analysis. Black cattle of ED/ED or ED/e genotype had increased backfat (P<0.05) and required significantly fewer days (15-25) (P<0.01) on feed to reach a target fat level for slaughter compared to the red cattle. Red cattle of e/e genotype were found to have significantly larger longissimus dorsi (l. dorsi) area, shipping weight and hot carcass weight. Subsequent analysis revealed that the differences were comparable whether black versus red coat colour or MC1R genotype was used as the criteria for the group of cattle.<p> MC4R sequence was obtained from 20 random crossbred steers. In addition to several previously published polymorphisms, a novel Ser330Asn polymorphism was detected. A population of 382 crossbred Canadian steers and 985 crossbred American steers was genotyped for this Ser330Asn polymorphism. A minor allele frequency of 0.01 was observed in the Canadian and 0.02 in the American steer populations. No homozygous g.989AA cattle were detected. In the Canadian population, heterozygous steers had increased grade fat (P=0.036) and decreased lean meat yield (P=0.032). Similarly in the American population, steers of the g.989GA genotype had increased backfat (P=0.031) and less desirable yield grades (P=0.022,) but also lower ribeye area measurements (P=0.031). These results suggest that genotyping for the Ser330Asn polymorphism may lead to increased quality of carcasses either through lean meat production or backfat measurements, depending on the goal of the beef operation.<p> Sequence data obtained from 38 Bos taurus beef cattle, 4 Holsteins and 4 Bos indicus cattle revealed six polymorphisms in the AGRP gene. No polymorphisms that altered amino acids were detected in Bos taurus cattle. Genotyping of 382 crossbred beef steers was performed for two polymorphisms, an intronic deletion (g.439_440delTC) and a base pair substitution in exon 4 that did not alter an amino acid (g.715G>A). An ANOVA analysis, using PROC Mixed, was performed for both polymorphisms on several growth and carcass traits. No significant differences were observed.<p> Polymorphisms in MC1R and MC4R could be used as genetic tests which may be beneficial for beef producers in North America. The significant differences observed in this study in relation to cattle growth and fat deposition would represent savings for producers when used for sorting feedlot cattle or in selection of breeding cattle.

Three interrelated genes postulated to affect economically important traits related to growth and/or carcass quality of beef cattle were chosen to characterize and perform association analyses for this study. Melanocortin 1 receptor (MC1R), melanocortin 4 receptor (MC4R) and agouti related protein (AGRP) play an integral role in the appetite pathway and in fat deposition.<p> We genotyped 328 crossbred steers of various coat colours that were purchased at weaning and fed until slaughter for the previously published alleles ED, E+ and e. The E+ allele was present at five percent in this population and therefore was not included in further analysis. Black cattle of ED/ED or ED/e genotype had increased backfat (P<0.05) and required significantly fewer days (15-25) (P<0.01) on feed to reach a target fat level for slaughter compared to the red cattle. Red cattle of e/e genotype were found to have significantly larger longissimus dorsi (l. dorsi) area, shipping weight and hot carcass weight. Subsequent analysis revealed that the differences were comparable whether black versus red coat colour or MC1R genotype was used as the criteria for the group of cattle.<p> MC4R sequence was obtained from 20 random crossbred steers. In addition to several previously published polymorphisms, a novel Ser330Asn polymorphism was detected. A population of 382 crossbred Canadian steers and 985 crossbred American steers was genotyped for this Ser330Asn polymorphism. A minor allele frequency of 0.01 was observed in the Canadian and 0.02 in the American steer populations. No homozygous g.989AA cattle were detected. In the Canadian population, heterozygous steers had increased grade fat (P=0.036) and decreased lean meat yield (P=0.032). Similarly in the American population, steers of the g.989GA genotype had increased backfat (P=0.031) and less desirable yield grades (P=0.022,) but also lower ribeye area measurements (P=0.031). These results suggest that genotyping for the Ser330Asn polymorphism may lead to increased quality of carcasses either through lean meat production or backfat measurements, depending on the goal of the beef operation.<p> Sequence data obtained from 38 Bos taurus beef cattle, 4 Holsteins and 4 Bos indicus cattle revealed six polymorphisms in the AGRP gene. No polymorphisms that altered amino acids were detected in Bos taurus cattle. Genotyping of 382 crossbred beef steers was performed for two polymorphisms, an intronic deletion (g.439_440delTC) and a base pair substitution in exon 4 that did not alter an amino acid (g.715G>A). An ANOVA analysis, using PROC Mixed, was performed for both polymorphisms on several growth and carcass traits. No significant differences were observed.<p> Polymorphisms in MC1R and MC4R could be used as genetic tests which may be beneficial for beef producers in North America. The significant differences observed in this study in relation to cattle growth and fat deposition would represent savings for producers when used for sorting feedlot cattle or in selection of breeding cattle.

<p>Humans are more carnivorous than other hominoids. It has been hypothesized that, during the evolution of this increased carnivory, hominins transitioned through a scavenging niche made viable by certain carnivoran taxa (especially sabertooths) that may have lacked the morphology necessary to fully utilize all parts of carcasses (e.g., marrow), therefore leaving an open niche in the form of high-quality scavengable remains available for hominins. In this dissertation, I examine the postcanine dentition of modern carnivorans, using quantifications of occlusal radii of curvature and intercuspid notches, and study the correlation of this morphology with carcass-processing behavior. I use these correlations to deduce the carcass-processing capabilities of the Plio-Pleistocene carnivores of South Africa (a guild for which we have a good appreciation of taxonomic diversity, and that existed at an important time during the evolution of our lineage - possibly the time that we transitioned into that guild), and compare these results with those of previous studies that relied on more conventional morphological measures.</p><p>Both radius of curvature and intercuspid notch data do a good job of separating taxa by dietary category, revealing subtle patterns including possible differences in the carcass-processing abilities of fossil and modern members of some extant species. Other strong trends confirm that the "hunting-hyena," Chasmaporthetes, was probably a hypercarnivore, and not a durophage like its modern confamilial taxa. Somewhat surprisingly, results do not support the hypothesis that sabertooth felids were more hypercarnivorous than modern felids. Furthermore, though the sympatric hypercarnivorous taxa were more numerous, so to were the durophageous taxa, with one taxon, Pachycrocuta, probably exceeding the durophageous capabilities of modern durophages.</p><p>As such, this dissertation shows no evidence that members of the paleo-carnivore guild were capable of producing higher quality scavengable carcasses than are modern carnivorans, and thus, based on these analyses of fossil carnivorans, it does not appear that high-quality scavengable remains were more available in the Plio-Pleistocene than there are today. Therefore, though there is clear evidence from other sources that hominins did scavenge at least occasionally, this dissertation does not support the hypothesis that there was an open niche consisting of high-quality scavengable remains.</p> / Dissertation

Beef carcasses from F2 Nellore × Angus (n = 181) and half-blood Bos indicus × Bos taurus (n = 57) were used to evaluate the responsiveness of sire and family groups nested within sires to post-mortem electrical stimulation (ES). In the F2 population, biological response to ES was identified for myofibrillar fragmentation index, and 6 h post-mortem pH. The genetic contributions of sire and families nested within sires were found for the average Warner-Bratzler shear force (WBS), location of shear core extraction, post-mortem carcass temperatures, and carcass pH. ES sides had lower WBS values, higher carcass temperatures, and lower carcass pH. In the half-blood population, biological response to ES was found for WBS core location. Sire and families nested within sires significantly affected WBS core location and carcass temperature. The ES sides had lower WBS values, higher carcass temperatures, and lower carcass pH in the half-blood population. From a carcass temperature and pH standpoint, carcass weight and fat thickness were used as covariates in the analysis of variance. This covariate analysis still showed a genetic component to carcass temperature and pH. There are genetic factors that impact how carcasses respond to electrical stimulation, which is the first work to demonstrate this relationship between genetics and a post-mortem tenderization treatment.

Two similarly managed trials were conducted to investigate serial ultrasound measures of body composition (longissimus muscle area (ULMA), 12th - rib fat thickness (UFAT), and percentage of intramuscular fat (UIMF)) early in the lives of feeder calves as they compared to carcass traits. Group 1 cattle were Charolais-sired by Brahman-British crossbred dams whereas Group 2 cattle were purebred Beefmaster. Both groups were fed at the same commercial feedlot (Graham Land and Cattle Co.) in Gonzales, Texas. In both data sets classifications were developed for ribeye area of Lower (less than 70.95 cm2, Middle (between 70.95 cm2 and 90.3 cm2) and Upper (over 90.3 cm2) based on a range that fit within the ribeye specifications of such branded beef programs as Certified Angus Beef and Nolan Ryan?s Tender Aged Beef. Differences among ribeye area and quality grade (Choice vs. Select) categories were evaluated for ultrasound and carcass traits. As reported previously, correlations between ultrasound measures and carcass traits became larger at times closer to harvest. In both sets of cattle, there were no differences in fat thickness or intramuscular fat at the ultrasound scan sessions or in these carcass traits due to ribeye area category. The same trend for quality grade classification was not seen across both groups of cattle however. In Group 1, there were no differences in early measures of body composition between carcass quality grade classes except for ultrasound fat thickness at weaning. However, in Group 2 cattle there were differences in ultrasound fat at times 1 and 2, IMF at time 1, and ribeye area at time 2 between cattle that graded choice verses those that graded select. Correlations between ultrasound measures of REA (r of .26 to .50) and ultrasound REA and carcass REA (r of .16 to .81) appeared to be lower in Group 1 vs. Group 2 (r of .55, and .64 to 81 respectively). Results from this project imply that changes in ribeye area will not automatically result in changes of marbling and vice versa. Furthermore, these results also show that ultrasound is useful to help predict beef carcass traits, but that early measures of body composition used alone do not explain a large portion of the variation in the carcass measures and specific methods should be developed by different biological cattle types.

Context and rationale – This work originates from policy priorities established within Defra to manage exotic animal diseases (EAD); specifically to understand the causes of low probability events, and to establish contingencies to manage outbreak incidents. Outbreaks of exotic animal diseases, e.g. FMD, CSF and HPAI, can cause economic and social impacts of catastrophic proportions. The UK’s government develops and implements policies and controls to prevent EAD and thus minimise these impacts. Control policies to achieve this are designed to address the vulnerabilities within the control systems. However, data are limited for both the introduction of an EAD as well as its resurgence following the disposal of infected carcasses, i.e. the pre-outbreak and post-outbreak phases of an EAD event. These lack of data compromises the development of policy interventions to improve protection. To overcome these data limitations, predictive models are used to predict system vulnerabilities. Cont/d.

A study was conducted to evaluate the quality characteristics in a comparative manner of grass-fed and grain-fed beef. Thirty two commercially bred beef steers were used. These steers were assigned to one of four treatments; grain-fed, grass/grain-fed, grass-fed and irrigated. These treatments were each reflective of the ration that would be provided to the animal. Individual animal weights were recorded every 28 days throughout the portion of the study. The grain-fed animals realized the highest (P<0.05) average daily gain with the grass-fed and irrigated having the lowest. The steers were harvested when they reached the pre-determined criteria, which was 0.4 inch back fat as measured at the 12th rib via ultrasonography, for the grain-fed or 800 pounds for the grass-fed animals. All animals, once harvested, were graded based upon USDA quality grades with results mirroring those previously mentioned. Carcasses were involved in an aging study in which all left sides of the carcasses were fabricated into primal cuts, vacuumed packaged and aged for 14 days while the right sides were dry aged during the same period. Shear force data were collected to provide for a measure of tenderness. All samples were significantly (P<0.05) more tender following aging with no difference being realized between aging techniques. Percent cutout was also calculated for the two techniques to quantify what difference, if any, existed. No significant difference (P>0.05) was shown between wet and dry aging with regard to percent cutout. Sensory evaluation was also conducted based upon the attributes of juiciness, tenderness and flavor intensity. For all three attributes grain-fed beef was favored (P<0.05). The panelists detected no difference in aging technique for any of the treatments (P>0.05).Carcass soft tissue chemical composition (lipid, protein and moisture) was also evaluated for the treatments. Grain-fed beef was shown to be highest (P<0.05) for overall percent lipid and lowest for percent moisture and protein. The grass-fed carcasses were the opposite, being highest for overall moisture and protein and lowest for lipid (P<0.05).

The cost of feed remains an important factor affecting the profitability of beef production, and the difficulty of recording feed intake is a major limitation in an industry-wide selection program. Novel genomics approaches offer opportunities to select for efficient cattle. Therefore, the main objective of this work was to identify genetic markers responsible for genetic variation in feed efficiency traits as well as to understand the molecular basis of feed efficiency traits. The candidate gene approach revealed new single nucleotide polymorphisms (SNPs) in the Cholecystokinin B receptor (CCKBR) and pancreatic anionic trypsinogen (TRYP8) genes that showed strong evidence of association with feed efficiency traits. An in silico approach was proposed as a cost-effective method for SNP discovery. SNPs within genes Pyruvate carboxylase, ATPaseH+, UBQEI, UCP2, and PTI showed evidence of association with carcass traits without negatively affecting feed efficiency traits. The polymorphisms within genes CCKBR and TRYP8 were associated with pancreas mass and pancreatic exocrine secretion. A fine-mapping study on 1,879 SNPs revealed 807 SNPs with significant associations corresponding to 1,012 genes. These 807 SNPs represented a genomic heritability of 0.32 and 89% of the genetic variance of residual feed intake (RFI). Genomic breeding values estimated from the SNP set (807) were highly correlated (0.96) to the breeding values estimated from a mixed animal model. The 10 most influential SNPs were located in chromosomes 16, 17, 9, 11, 12, 20, 15, and 19. Enrichment analysis for the identified genes (1,012) suggested 110 biological processes and 141 pathways contributed to variation in RFI. The 339 newly identified SNPs corresponding to 180 genes identified by fine-mapping were tested for association with feed efficiency, growth, and carcass traits. Strong evidence of associations for RFI was located on chromosomes 8, 15, 16, 18, 19, 21, and 28. Combing validated SNPs from fine-mapping and the candidate gene approach may help develop a DNA test panel for commercial use and increase our understanding of the biological basis of feed efficiency in beef cattle. / The Ministry of Higher Education of Egypt

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