The impact of selection using residual average daily gain and marbling EPDs on growth, performance, and carcass traits in Angus steers1

Predicting feed efficiency of Angus steers using the gastrointestinal microbiome

Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome.

- Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality

Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.

Association analysis of mitochondrial genome polymorphisms with backfat thickness in pigs

Mitochondrial DNA (mtDNA) variations and associated effects on economic traits have been widely reported in farm animals, as these genetic polymorphisms can affect the efficiency of energy production and cell metabolism. In studies related to metabolism, the deposition of fat was highly correlated with mitochondria. However, the effect of mtDNA polymorphisms on porcine backfat thickness (BFT) remained unclear. In this study, 243 pigs were collected to analyse the relationship between BFT and mtDNA polymorphisms. There were considerable differences in BFT, ranging from 5 mm to 18 mm. MtDNA D-loop sequencing discovered 48 polymorphic sites. Association analysis revealed that 30 variations were associated with BFT (P < 0.05). The polymorphism m.794A > G showed the maximum difference in BFT between A and G carriers, which differed at ∼2.5 mm (P < 0.001). The 48 polymorphic sites generated 22 haplotypes (H1-H22), which clustered into 4 haplogroups (HG1-HG4). HG1 had a lower BFT value than other three haplogroups (P < 0.01), whereas H4 in HG1 exhibited the lowest BFT of all haplotypes analyzed (P < 0.01). The results of this study highlight an association between mtDNA polymorphisms and BFT, and suggest the potential application of mtDNA in pig molecular breeding practices.

Importance of Foot and Leg Structure for Beef Cattle in Forage-Based Production Systems

Understanding the relationship of foot angle and claw set to beef cattle structural soundness will be critical to the selection of animals that fit forage-based production systems. In an effort to address concerns about foot and leg structure, the American Angus Association's foot angle and foot claw set expected progeny differences (EPD) were developed in 2019. As a result, these relatively new EPD and associated guidelines have limited phenotypic data submitted thus far. While ample research has evaluated lameness and foot issues in the dairy breeds, less is known about the factors that affect foot structure in beef cattle. This review focuses on beef cattle foot and leg structure, selection factors that may have led to increased problems with feet and legs, and the importance of foot and leg structure in forage-based grazing production systems. Specifically, the importance of locomotion and freedom of movement in extensive rangeland environments is discussed relative to the current literature. In addition, environmental factors that may influence foot and leg structure are addressed as well as heritability of various aspects of foot and leg traits. Where possible, information gaps and research needs are identified to enhance further investigation and the improvement of foot and leg selection tools.

Phenotypic and genetic parameters of circadian rhythms from core body temperature profiles and their relationships with beef steers' production efficiency profiles during successive winter feeding periods

This 2-year study evaluated differences in circadian parameters obtained from measures of core body temperatures using telemetric reticulo-rumen and rectal devices during two winter feeding regimes in western Canada. The study also estimated phenotypic correlations and genetic parameters associated with circadian parameters and other production traits in each feeding regime. Each year, 80 weaned steer calves (initial age: 209 ± 11 days; BW: 264 ± 20 kg) from the same cohort were tested over two successive regimes, Fall-Winter (FW) and Winter-Spring (WS) at Lanigan, Saskatchewan, Canada. The steers received forage-based rations in both regimes where the individual feed intake was measured with automatic feeding units. During the trial, the reticulo-rumen (RTMP) and rectal (RCT) temperatures were simultaneously measured every 5 min using telemetric devices. These were used to calculate the circadian parameters (Midline Estimating Statistic Of Rhythms, amplitude, and acrophase/peak time) for both temperature measures. Growth and efficiency performance traits were also determined for all steers. Each steer was assigned into inefficient, neutral, and efficient classes based on the SD of the residual feed intake (RFI), residual gain (RG), and residual intake and gain (RIG) within each year and feeding regime. Higher (p < 0.0003) RTMP and rectal temperature MESORs were observed in the Fall-Winter compared to the Winter-Spring regime. While the two test regimes were different (p < 0.05) for the majority of the RTMP or RCT temperature parameters, they did not differ (p > 0.10) with the production efficiency profiles. The heritability estimates were higher in FW (0.78 ± 0.18 vs. 0.56 ± 0.26) than WS (0.50 ± 0.18 vs. 0.47 ± 0.22) for the rumen and rectal MESORs, respectively. There were positive genetic correlations between the two regimes for the RTMP (0.69 ± 0.21) and RCT (0.32 ± 0.59). There was a negative correlation (p < 0.001) between body temperature and ambient temperature. The high heritability estimates and genetic correlations for rumen and rectal temperature parameters demonstrate their potential as beef genetic improvement tools of economic traits associated with the parameters. However, there are limited practical implications of using only the core-body temperature as a proxy for production efficiency traits for beef steers during winter.

Factors important for bull purchasing decisions and management in extensive rangeland production systems of New Mexico: a producer survey

There were 463,000 head of beef cows in New Mexico as of January 1, 2021 (NASS, 2020), down roughly 4% from 2020 (NASS, 2019). Frequent drought often results in herd reduction and loss of valuable genetic progress. Bull selection is critical due to their influence on herd development. A survey was conducted to identify traits important to bull selection in New Mexico. Surveys were collected digitally (n = 83) and via the mail (n = 74). Responses were largely by cow/calf producers averaging 57 ± 1 years old with 24 ± 1 years' experience. Survey respondents represented 4,384,296 acres of private owned, private leased, and leased public rangeland and irrigated pasture meadow in New Mexico and surrounding states. Average cow/calf operation size was 294 ± 39 head and average bull herd size was 21 ± 3 head. Average price paid for a bull in the past 2 years was $3,981 ± 213. Physical characteristics, individual bull performance information, and genetic information are all important traits to New Mexico bull buyers; however, most producers (56%) indicated that structural soundness was the most important factor influencing their selection decisions. Amongst expected progeny differences (EPDs), New Mexico producers consider the calving ease direct (CED) and birth weight (BW) EPDS to be most important (40% and 35%, respectively). Producers also indicated that multitrait selection indexes used by the American Angus Association were important to their selection decisions, with the beef value ($B) and weaned calf value ($W) indexes being cited most often (35% and 31%, respectively). Elements important to bull purchase include the bull's sale preview (87%), body condition score (86%), feed efficiency/average daily gain information (85%), and actual scrotal circumference (82%). Following purchase of a new bull, most (60%) keep the bull separate from the cow herd until the following breeding season, while the remaining 40% of producers turn newly purchased bulls out within 30 days of purchase. Sixty eight percent of producers evaluate semen quality annually or prior to the start of the breeding season. Interestingly, 39% of producers indicated they used reproductive technologies like artificial insemination and synchronization of estrus while most (80%) test for trichomoniasis. The primary factor influencing culling decisions is age, followed by soundness and fertility.

Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase

The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle.

Longitudinal Changes of the Ruminal Microbiota in Angus Beef Steers

The ruminal microbiota of Angus cows and steers were characterized using 16s rRNA gene sequencing, and the expression of their metabolic pathways was predicted. Samples were collected on weaning day from the steers and the cows, and subsequently on three other occasions from the steers. Results showed that microbial richness, evenness, and diversity decreased (p < 0.001) in the rumen of the steers as they were weaned and transitioned to a high-concentrate feedlot diet. However, on the day of weaning, microbial evenness was similar to that observed in the rumen of cows (p = 0.12). The abundance of archaea was similar (p = 0.59) between the cows and steers at weaning, but it decreased (p = 0.04) in the rumen of steers after weaning, and remained stable (p ≥ 0.44) for the remainder of their lives. Likewise, no difference (p = 0.51) in the abundance of Bacteroidetes was detected between the cows and the calves on the day they were weaned, but the abundance of this phylum increased (p = 0.001) and remained stable after that. These results suggest that cows may have a strong influence on the composition, and help modulate the ruminal microbiota of young calves; however, following weaning, their ruminal microbiotas tend to differentiate from that state observed at earlier ages.

Main regulatory factors of marbling level in beef cattle

The content of intramuscular fat (IMF), that determines marbling levels is considered as one of the vital factors influencing beef sensory quality including tenderness, juiciness, flavour and colour. The IMF formation in cattle commences around six months after conception, and continuously grows throughout the life of the animal. The accumulation of marbling is remarkably affected by genetic, sexual, nutritional and management factors. In this review, the adipogenesis and lipogenesis process regulated by various factors and genes during fetal and growing stages is briefly presented. We also discuss the findings of recent studies on the effects of breed, gene, heritability and gender on the marbling accumulation. Various research reported that feeding during pregnancy, concentrate to roughage ratios and the supplementation or restriction of vitamin A, C, and D are crucial nutritional factors affecting the formation and development of IMF. Castration and early weaning combined with high energy feeding are effective management strategies for improving the accumulation of IMF. Furthermore, age and weight at slaughter are also reviewed because they have significant effects on marbling levels. The combination of several factors could positively affect the improvement of the IMF deposition. Therefore, advanced strategies that simultaneously apply genetic, sexual, nutritional and management factors to achieve desired IMF content without detrimental impacts on feed efficiency in high-marbling beef production are essential.

Evaluation of the Fecal Bacterial Communities of Angus Steers With Divergent Feed Efficiencies Across the Lifespan From Weaning to Slaughter

Numerous studies have examined the link between the presence of specific gastrointestinal bacteria and the feed efficiency of cattle. However, cattle undergo dietary changes during their productive life which can cause fluctuations in their microbial consortium. The objective of the present study was to assess changes in the fecal microbiome of beef steers genetically selected to be divergent in feedlot feed efficiency, to determine whether differences in their fecal microbiomes could be detected as early as weaning, and continued throughout the rearing process regardless of dietary changes. Fecal samples were collected at weaning, yearling age, and slaughter for a group of 63 steers. Based on their feedlot-finishing performance, the steers were selected and divided into two groups according to their residual feed intake (RFI): efficient steers (low-RFI; n = 7) and inefficient steers (high-RFI; n = 8). To ascertain the fecal microbial consortium and volatile fatty acid (VFA) content, 16S rRNA gene sequencing and VFA analysis were performed. Overall, bacterial evenness and diversity were greater at weaning compared to yearling and slaughter for both efficiency groups (P < 0.001). Feedlot RFI linearly decreased as both Shannon diversity and Ruminococcaceae abundance increased (R² = 65.6 and 60.7%, respectively). Abundances of Ruminococcaceae, Rikenellaceae, and Christensenellaceae were higher at weaning vs. yearling age and slaughter (P < 0.001); moreover, these families were consistently more abundant in the feces of the low-RFI steers (for most of the timepoints evaluated; P ≤ 0.05), compared to the high-RFI steers. Conversely, abundances of Bifidobacteriaceae were numerically higher in the feces of the high-RFI steers throughout their lifespan. Total VFA concentrations increased at slaughter compared to weaning and yearling for both efficiency groups (P < 0.001). The acetate:propionate ratio decreased linearly (P < 0.001) throughout the life of the steers regardless of their efficiency, reflective of dietary changes. Our results indicate that despite fluctuations due to animal age and dietary changes, specific bacterial families may be correlated with feed efficiency of steers. Furthermore, such differences may be identifiable at earlier stages of the production cycle, potentially as early as weaning.

The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot

Feed is the greatest cost of animal production, so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the bacterial taxonomic profile of the rumen, cecum, and feces of feedlot steers at slaughter in order to link feed efficiency and the GIT bacterial populations from these three locations. Twenty commercial Angus steers were selected and divided into two groups according to their residual feed intake (RFI) classification determined during the feedlot-finishing period: high-RFI (n = 10) and low-RFI (n = 10). After the ruminal, cecal, and fecal samples were collected at slaughter, DNA extraction and 16S rRNA gene sequencing were performed on them to determine their bacterial composition. One-way ANOVA was performed on the animal performance data, alpha diversities, and bacterial abundances using RFI classification as the fixed effect. Overall, the ruminal bacterial population was the most different in terms of taxonomic profile compared with the cecal and fecal populations as revealed by beta diversity analysis (P < 0.001). Moreover, bacterial richness (Chao1) was greatest (P = 0.01) in the rumen of the high-RFI group compared with the low-RFI group. In contrast, bacterial richness and diversity in the intestinal environment showed that Chao1 was greater (P = 0.01) in the cecum, and the Shannon diversity index was greater in both the cecum and feces of low-RFI compared with high-RFI steers (P = 0.01 and P < 0.001, respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P = 0.01); fecal Bifidobacteriaceae was more abundant in high-RFI steers (P = 0.03). No correlations (P ≥ 0.13) between any ruminal bacterial family and RFI were detected; however, Ruminococcaceae, Mogibacteriaceae, Christensenellaceae, and BS11 were negatively correlated with RFI (P < 0.05) in the cecum and feces. Succinivibrionaceae in the cecum was positively correlated with RFI (P = 0.05), and fecal Bifidobacteriaceae was positively correlated with RFI (P = 0.03). Results collectively indicate that in addition to the ruminal bacteria, the lower gut bacterial population has a significant impact on feed efficiency and nutrient utilization in feedlot steers; therefore, the intestinal bacteria should also be considered when examining the basis of ruminant feed efficiency.

The relationship between the rumen microbiome and carcass merit in Angus steers

The objective of this study was to explore the relationships between ruminal microbial populations from Angus steers that were divergent in carcass traits related to adipose accumulation. Twenty-four feedlot-finished Angus steers (age: 538 ± 21 d; body weight following lairage: 593.9 ± 43.7 kg) were slaughtered, and ruminal contents and carcass data were collected. Ruminal microbial deoxyribonucleic acid (DNA) extraction and 16S ribosomal ribonucleic acid (rRNA) gene sequencing were performed to determine microbial relative abundances, to estimate microbial diversity, and to predict microbial metabolic pathways. A variety of correlation analyses and one-way ANOVA were performed to investigate the relationships between the rumen microbiome and carcass traits. Marbling score (P = 0.001) and longissimus lipid content (P = 0.009) were positively correlated to Chao1 Richness Index, suggesting that increased intramuscular fat was associated with increased numbers of ruminal microbial species. The phyla Tenericutes and TM7 were negatively correlated (P ≤ 0.05) to marbling score and longissimus lipid content, indicating that lower abundances of these phyla may be associated with improvements in intramuscular fat content. Greater abundance of the bacterial family S24-7 was positively correlated (P = 0.002) to marbling score. Analysis by marbling classification revealed further linkages to microbial richness (P ≤ 0.063), diversity (P = 0.044), and S24-7 (P < 0.001) populations. Computational prediction of the microbial metabolic pathways revealed no differences (P ≥ 0.05) in metabolic pathway expression in rumen microbes between steers in the high- and low-marbling classes. Several phyla, families, and genera were positively correlated (P ≤ 0.05) to both rib fat thickness and yield grade. Collectively, our results suggest that microbial composition is associated to differing performance in carcass adipose traits. Overall, most of the bacterial taxa correlated to the intramuscular and subcutaneous fat depots did not overlap, suggesting the microbial population end products likely impacted adipose accumulation largely via separate adipogenic pathways of the host animal.