Feed Efficiency In Cattle Research Articles

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

Estimating breeding values for feed efficiency in dairy cattle by regression on expected feed intake.

The efficiency with which a dairy cow utilises feed for the various physiological and metabolic processes can be evaluated by metrics that contrast realised feed intake with expected feed intake. In this study, we presented a new metric - regression on expected feed intake (ReFI). This metric is based on the idea of regressing DM intake (DMI) on expected DMI using a random regression model, where energy requirement formulations are applied for the calculation of expected DMI covariables. We compared this new metric with the metrics residual feed intake (RFI) and genetic residual feed intake (gRFI), by applying them on 18581 feed efficiency records from 654 primiparous Nordic Red dairy cows. We estimated variance components for the three metrics and their respective genetic correlations with intake and production traits. In addition, we examined the phenotypes of superior cows. With ReFI, we estimated for feed efficiency a higher genetic variation (4.7%) and heritability (0.23) compared to applying RFI or gRFI. The ReFI metric was genetically uncorrelated with DMI and negatively correlated within energy-corrected milk (ECM), whereas the RFI metric was genetically positively correlated with DMI and metabolic BW. The gRFI metric was genetically positively correlated with DMI and uncorrelated with energy sink traits. Overall, the estimated SE were large. The ReFI metric resulted in a different ranking of cows compared to those based on RFI or gRFI and was superior in selecting the most efficient animals. When the selection was based on ReFI breeding values, then the 10% most efficient cows produced 12.3% more ECM per unit metabolisable energy intake, whereas the corresponding values were only 4.3 or 5.9% when using RFI or gRFI breeding values, respectively. Based on ReFI, superior cows had also higher milk production, whereas based on RFI or gRFI milk production either decreased or was unaffected, respectively. The superiority of the ReFI metric in selecting efficient cows was due to a better modelling of the expected feed intake. The ReFI metric simplified modelling of feed utilisation efficiency in dairy cattle and resulted in breeding values that are equal to percentages of feed saved.

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production.

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

Determination of climatologically suitable places in Türkiye for feedlot cattle production using the Comprehensive Climate Index model.

The purpose of this study was to determine climatologically suitable places to raise feedlot cattle in Türkiye. The Comprehensive Climate Index (CCI), a model that enables one to quantify beef cattle performance based on environmental conditions (temperature, relative humidity, wind speed, solar radiation) at any time in the year, was used to predict dry matter intake (DMI), average daily gain (ADG), and feed efficiency (FE) of feedlot cattle. Thirty years of daily average temperature, relative humidity, and wind speed values were obtained for 15 cities, namely, Antalya, Balikesir, Çorum, Diyarbakir, Edirne, Elazig, Erzincan, Erzurum, Eskisehir, Isparta, Izmir, Kayseri, Konya, Sivas, and Van. Measured daily solar radiation values were not available and values were calculated based on a formula that takes hemisphere, latitude, and day of the year into account. Since mostly dairy breed calves are placed into a feedlot in Türkiye, the Holstein option in the CCI model was chosen to calculate the maintenance energy requirement. Based on previous feedlot feeding studies conducted in Türkiye, it was assumed that calves would be placed on feed at 250 kg and be marketed at 520 kg, that the diet would have 2600 kcal/kg metabolic energy, and that DMI would be 2.31% of the body weight. Results indicate that cattle raised in Antalya (the hottest place) and Erzurum (the coldest place) had the lowest and highest DMI, respectively (P<0.05). Summer months depressed the DMI of cattle in hotter cities and winter months increased the DMI of cattle in colder cities (P<0.05). Feedlot cattle raised in hotter and colder regions of Türkiye had lower ADG than other places having a more temperate climate (P<0.05). In general, cattle raised in a hotter climate had better FE than those raised in a cold climate (P<0.05).

Effect of IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms on growth performance and feed efficiency in young Kazakh white-headed cattle.

Improving the feed efficiency of beef cattle is necessary to increase the profitability of meat production. Implementing marker-assisted selection breeding systems can improve the genetic potential of beef cattle for increased productivity. This research aimed to study the effects of insulin-like growth factor (IGF)-1 C472T, growth hormone (GH) C2141G, and GH receptor (GHR) T914A polymorphisms on growth performance and feed efficiency in young Kazakh white-headed cattle. Young Kazakh white-headed cattle (n = 50) were grouped after weaning according to sex (28 bulls and 22 heifers) and they were genotyped according to the IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms. The test period was conducted from 8 to 15 months of age. The experimental animals were evaluated for live weight (LW) at the beginning and end of the test period. They were also assessed for average daily gain, hip height, metabolic mid-weight (MMWT), actual dry matter intake (DMI), and residual feed intake (RFI). Significant differences in MMWT were found between the bulls with the IGF-1TT and IGF-1CT genotypes, which was a 2.2 kg increase in heterozygous cattle (p < 0.05). Heterozygous IGF-1CT bulls differed with a higher DMI of 0.087 kg/day (p < 0.05) compared to IGF-1TT homozygotes. Carriers of the IGF-1TT genotype had the greatest feed efficiency at 0.068 kg/day (p < 0.05). Heifers with the GHCC genotype differed in their maximum DMI with an increase of 1.17%-1.57% (p < 0.05) relative to the other genotypes. The G allele in the GH C2141G polymorphism was associated with better (p < 0.05) feed efficiency in the Kazakh white-headed breed. The minimum DMI and RFI in GHR T914A heterozygous heifers were significantly inferior (p < 0.05) to the other genotypes. Association studies of the IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms indicate a relationship between growth, development, and feed efficiency with the genetic characteristics of young Kazakh white-headed cattle. A significant (p < 0.05) dominant effect was found in the IGF-1 gene in bulls and in the GHR gene in heifers, which should be considered when breeding with heterogeneous parental pairs. The negative effect of the allele substitution in the IGF-1 C472T polymorphism was observed in the LW of heifers (-3.25 kg) at the age of 8 months and bulls (-6.05 kg) at 15 months. The substitution in the GH C2141G polymorphism was associated with a significant reduction in DMI by 0.036 kg (p < 0.05) and an increase in feed efficiency by 0.023 kg (p < 0.05) during the rearing of heifers. These results can improve the production efficiency of mature herds of Kazakh white-headed cattle.

Feasibility of feeding cadmium accumulator maize (Zea mays L.) to beef cattle: Discovering a strategy for eliminating phytoremediation residues

Eco-friendly and efficient strategies for eliminating cadmium (Cd) phytoremediation plant residues are needed. The present study investigated the feasibility of feeding Cd accumulator maize to beef cattle. In total, 20 cattle at 6 months of age were selected and randomly allocated into two groups fed with 85.82% (fresh basis) Cd accumulator maize (CAM) or normal maize (control [Con]) silage diets for 107 d. Feeding CAM did not affect the body weight (P = 0.24), while it decreased feed intake and increased feed efficiency of beef cattle (P < 0.01). Feeding CAM increased serum concentrations of immunoglobulin A and G, complement 3 and 4, blood urea nitrogen, and low-density lipoprotein cholesterol, decreased serum concentrations of interleukin-6 and lipopolysaccharide (P < 0.05), and caused wider lumens in the renal tubules. The Cd residue in meat was 7 μg/kg beyond the restriction for human food. In the muscle, the unsaturated fatty acids (t11C18:1 and C20:4), Lys, Arg, Pro, and Cys were decreased, while the saturated fatty acids (C10:0, C12:0, and C17:0) and Leu were increased (P < 0.05). Therefore, at the current feeding level, phytoremediation maize increased the feed efficiency of beef cattle, but did present risks to cattle health and production safety, and decreased the meat nutrition and flavor. Further research must be performed to determine whether a lower proper dose of phytoremediation maize and an appropriate feeding period may be possible to ensure no risk to cattle health and the supply of safe meat for humans.

Cricket (Gryllus bimaculatus) meal pellets as a protein supplement to improve feed efficiency, ruminal fermentation and microbial protein synthesis in Thai native beef cattle.

Replacing soybean meal (SBM) with cricket (Gryllus bimaculatus) meal pellets (CMP) in concentrate diets was investigated for feed efficiency, ruminal fermentation and microbial protein synthesis in Thai native beef cattle. Four male beef cattle were randomly assigned to treatments using a 4×4 Latin square design with four levels of SBM replaced by CMP at 0%, 33%, 67%, and 100% in concentrate diets. Results revealed that replacement of SBM with CMP did not affect dry matter (DM) consumption, while digestibilities of crude protein, acid detergent fiber and neutral detergent fiber were significantly enhanced (p<0.05) but did not alter digestibility of DM and organic matter. Increasing levels of CMP up to 100% in concentrate diets increased ruminal ammoniacal nitrogen (NH3-N) concentrations, blood urea nitrogen, total volatile fatty acids and propionate concentration (p<0.05), whereas production of methane and protozoal populations decreased (p<0.05). Efficiency of microbial nitrogen protein synthesis increased when SBM was replaced with CMP. Substitution of SBM with CMP in the feed concentrate mixture at up to 100% resulted in enhanced nutrient digestibility and rumen fermentation efficiency, with increased volatile fatty acids production, especially propionate and microbial protein synthesis, while decreasing protozoal populations and mitigating rumen methane production in Thai native beef cattle fed a rice straw-based diet.

Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake

Improving cattle feed efficiency through selection of residual feed intake (RFI) is a widely accepted approach to sustainable beef production. A greater understanding of the molecular control of RFI in various breeds offered contrasting diets is necessary for the accurate identification of feed efficient animals and will underpin accelerated genetic improvement of the trait. The aim of this study was to determine genes and biological processes contributing to RFI across varying breed type and dietary sources in skeletal muscle tissue. Residual feed intake was calculated in Charolais and Holstein–Friesian steers across multiple dietary phases (phase-1: high concentrate (growing-phase); phase-2: zero-grazed grass (growing-phase); phase-3: high concentrate (finishing-phase). Steers divergent for RFI within each breed and dietary phase were selected for muscle biopsy collection, and muscle samples subsequently subjected to RNAseq analysis. No gene was consistently differentially expressed across the breed and diet types examined. However, pathway analysis revealed commonality across breeds and diets for biological processes including fatty acid metabolism, immune function, energy production and muscle growth. Overall, the lack of commonality of individual genes towards variation in RFI both within the current study and compared to the published literature, suggests other genomic features warrant further evaluation in relation to RFI.

Heritability and genetic association of social organization traits with feeding behavior, feed efficiency and growth in Bos indicus

Dominance relationships are important to maintain a stable social organization in group living animals and reduces conflicts between individuals. However, there is a lack of knowledge on the genetic components of social organization. The aim of this study was to estimate the heritability of social organization traits obtained using electronic feed bunk data and their genetic and phenotypic correlations with feeding behavior, feed efficiency and growth in Nellore cattle. Data were obtained from 970 young bulls evaluated in 12 feed efficiency tests. The method used to evaluate social organization was based on feeding event data to detect displacements at the feed bunks. Social organization was evaluated using two traits: dominance value (DV) and social hierarchy (SH). The (co)variance components were estimated by the restricted maximum likelihood method using an animal model in single- and two-traits analyses. The heritability estimates for DV and SH were 0.23 ± 0.07 and 0.25 ± 0.08, respectively. The genetic correlations of the social organization traits with dry matter intake per visit (DV: −0.37 ± 0.17; SH: −0.29 ± 0.17) and time spent at the feed bunk per visit (DV: −0.47 ± 0.16; SH: −0.46 ± 0.15) were negative and ranged from moderate to high, while the genetic correlations with the frequency of feed bunk visits were moderate and positive (DV: 0.34 ± 0.18; SH: 0.22 ± 0.19). On the other hand, the genetic correlations between social organization and growth traits were close to zero. The results indicate that the visits of dominant animals to the feed bunk are shorter but more frequent throughout the day; and these animals tend to consume less feed per visit than subordinate animals. Furthermore, the genetic correlations of DV and SH with growth traits close to zero suggest that selection for higher growth does not affect the social position that the animal occupies within the group. The social organization traits are inheritable and are genetically associated with feeding behavior traits. There is evidence that DV and SH are not genetically correlated with growth traits.

The Potential Used of Humic Substance As Natural Organic Additives For Ruminants: A Review

Humate substances (HSs) are raw materials very easy to obtain and are naturally occurring organic molecules found in soil due to the humification of dead organic components. Traditionally used as conventional medicine in China and India and as soil fertilizer in agriculture. Humic acids are widely utilized as feed additives and could enhance ruminant performance. The effect of humic acid on feed intake depends on the level of supplementation, a humic acid source, experimental animals used and the region experimented. Humic acid also increases the average daily gain, and sometimes increases feed digestibility and feed efficiency in goats, cows and cattle. Enhancement of milk yield, total solids, fat-corrected milk (FCM), and energy but does not influence milk composition. That supplementation also lowers blood cholesterol, excluding eosinophil and neutrophil, without affecting the haematological value. HSs also have anti-bacterial properties and HSs affect gut microbiota and rumen, such as increasing fungi counts and pH alteration, but the effect on bacteria and the protozoal population is non-consistent. In other trials, HSs have also been shown to reduce the process of methanogenesis.

Application of the multivariate and univariate analyses to estimate the feed efficiency in beef cattle

This study aimed to compare the univariate analyses (relationship between dry matter intake (DMI) and average daily gain (ADG), Kleiber ratio, and residual feed intake) and multivariate analysis (bionutritional index [BNI]) to determine feed efficiency. Were used a total of 160 cattle (individual data) and the analyzed variables were dry matter intake, weight gain, and body weight of the animals. We used five methods to evaluate feed efficiency, the BNI, FE, corrected feeding efficiency (corFE), Kleiber ratio (KR), and residual feed intake (RFI). Study 1 demonstrated that only the FE (p=0.0472) was significant, although the FE after the transformation of Box-Cox (corFE) (p=0.0642) showed a statistical trend. In studies 2, 3, and 5, we observed that BNI was the best biological efficiency indicator. In the study 4, we observed that the best indicators were FE (0.110; p=0.0281), corFE (0.380; p=0.0429), and RFI (0.465; p=0.0340) for the genders. However, corFE decreased the coefficient of variation in all studies. In conclusion, the use of the Box-Cox transformation is as efficient as the multivariate analysis in discriminating experimental groups (genetic groups, different levels of concentrate in the diet, and genders) concerning the other univariate analyzes.

Genetic association between feed efficiency, growth, scrotal circumference, and carcass traits in Guzerat cattle.

The objective of this study was to estimate the genetic parameters for feed efficiency-related traits and their genetic correlations with growth, male fertility, and carcass traits using multi-trait analysis in Guzerat cattle. Further, it aimed to predict the direct and correlated responses for feed efficiency traits when selection was applied for growth, male fertility, and carcass traits. The evaluated traits were adjusted weight at 120 (W120), 210 (W210), 365 (W365), and 450days of age (W450), adjusted scrotal circumference at 365days of age (SC365) and at 450days of age (SC450), scrotal circumference, ribeye area (REA), backfat thickness (BFT), rump fat thickness (RFT), residual feed intake (RFI), and dry matter intake (DMI). The genetic parameters were obtained by the restricted maximum likelihood method (REML), using an animal model in multi-trait analyses. The heritability estimates for W120, W210, W365, W450, SC365, and SC450 varied from low to high (0.17 to 0.39). The carcass traits, REA, BFT, and RFT, displayed low to moderate heritability estimates, 0.27, 0.10, and 0.31, respectively. The heritability estimates for RFI (0.15) and DMI (0.23) were low and moderate, respectively. The RFI showed low genetic correlations with growth traits, ranging from - 0.07 to 0.22, from 0.03 to 0.05 for scrotal circumference, and from - 0.35 to 0.16 for carcass, except for DMI, which ranged from 0.42 to 0.46. The RFI and DMI presented enough additive genetic variability to be used as selection criteria in Guzerat breed genetic improvement program. Additionally, the response to selection for RFI would be higher when selection is performed directly for this trait. The selection for residual feed intake would not promote unfavorable correlated responses for scrotal circumference, carcass (yield and finish), and growth traits. Therefore, the selection for more efficient animals would not compromise the productive, reproductive, and carcass performance, contributing to reduce the production costs, increasing the profitability and sustainability of beef cattle production in tropical areas.

Genetic correlation between feed efficiency and carcass traits in Nellore cattle in Brazil

The aim was to estimate the genetic correlations between residual feed intake (RFI) and dry matter intake (DMI) with carcass finish (CF), rib eye area (REA), and marbling (MAR) of Nellore cattle. Data from 7,808 animals were considered. In addition, data from 2,261 females included in the complete database were also considered. Estimates of variance and covariance components, as well as heritabilities and genetic correlations were obtained by means of two-character analysis under animal model. Heritability estimates were found to be moderate for the RFI (0.22) and DMI (0.29) traits. It was observed that genetic correlation was close to zero for all traits, except between RFI and REA (-0.11). However, considering the female population, there was an increase in the estimated genetic correlation between RFI and DMI, although still a favorable genetic association of low magnitude (-0.30). There was also an increase in the genetic association of REA with RFI (-0.21). It can be concluded that the direct selection for RFI and DMI will not influence the CF, MAR, or REA of Nellore cattle. However, this selection may generate some favorable responses in MAR and REA in Nellore females.

In utero choline exposure alters growth, metabolism, feed efficiency, and carcass characteristics of Holstein x Angus cattle from weaning to slaughter.

Feeding rumen protected choline (RPC) to late gestation dairy cows has potential to affect growth in offspring. The objective of this study was to evaluate the effects of in utero choline exposure on the growth, feed efficiency (FE), metabolism, and carcass quality of Angus x Holstein cattle. Multiparous Holstein cows pregnant with male (n=17) or female (n=30) Angus-sired calves were enrolled 21 d prepartum and randomly assigned to one of four dietary treatments varying in quantity and formulation of rumen-protected choline (RPC). The treatments included a control with 0g/d supplemental RPC (CTL), supplemental RPC fed at the recommended dose (RD) of 15g/d from either an established RPC product (RPC1RD; ReaShure; Balchem Corp) or choline ion from a concentrated RPC prototype (RPC2RD; Balchem Corp), or a high dose (HD) of RPC2 fed at 22g/d (RPC2HD). From 2 to 6 mo of age, calves were group housed and offered 2.3kg grain/hd/d (42% CP) with ad libitum grass hay, and stepped up to a complete finishing diet by 7 mo (12.0% CP; 1.34 Mcal/kg NEg). Weight and height were measured monthly. Animal FE was measured in individual pens for 35 d at 8 mo. Feed intake was measured daily, and blood was obtained on d 18 during the FE period. Afterwards, cattle were group housed and offered a free-choice finishing diet until slaughter, where carcass yield and quality characteristics were measured. Mixed models were used in PROC MIXED (SAS, 9.4) with the fixed effects of treatment, sex, time, their interactions, and the random effect of calf. Month was the repeated measure, and preplanned contrasts were used. Blood and FE data were analyzed with the fixed effect of dam choline treatment, calf sex, and the interaction. Increasing dose of RPC tended to increase weight over the entire study period. Feeding any RPC increased hip and wither height compared with CTL, and increasing RPC dose linearly increased hip and wither height. Treatment and sex interacted on DMI whereby increasing RPC intake linearly increased DMI for males but not females. Compared with control, feeding any RPC decreased plasma insulin, glucose, and an insulin sensitivity index (RQUICKI). In utero choline exposure increased kidney-pelvic-heart fat and marbling score. Mechanisms of action for intrauterine choline exposure on offspring growth, metabolism, and carcass characteristics should be explored as they have direct implications for profitability for cattle growers and feeders.

Applying assisted reproductive technology and reproductive management to reduce CO2-equivalent emission in dairy and beef cattle: a review.

Methane emission from beef and dairy cattle combined contributes around 4.5-5.0% of total anthropogenic global methane. In addition to enteric methane (CH4) produced by the rumen, cattle production also contributes carbon dioxide (CO2) (feed), nitrous oxide (N2O) (feed production, manure) and other CH4 (manure) to the total greenhouse gas (GHG) budget of beef and dairy production systems. The relative contribution in standard dairy systems is typically enteric CH4 58%, feed 29% and manure 10%. Herds with low production efficiency can have an enteric CH4 contribution up to 90%. Digestibility of feed can impact CH4 emission intensity. Low fertility herds also have a greater enteric CH4 contribution. Animals with good feed conversion efficiency have a lower emission intensity of CH4/kg of meat or milk. Feed efficient heifers tend to be lean and have delayed puberty. Fertility is a major driver of profit in both beef and dairy cattle, and it is highly important to apply multi-trait selection when shifting herds towards improved efficiency and reduced CH4. Single nucleotide polymorphisms (SNPs) have been identified for feed efficiency in cattle and are used in genomic selection. SNPs can be utilized in artificial insemination and embryo transfer to increase the proportion of cattle that have the attributes of efficiency, fertility and reduced enteric CH4. Prepubertal heifers genomically selected for favourable traits can have oocytes recovered to produce IVF embryos. Reproductive technology is predicted to be increasingly adopted to reduce generation interval and accelerate the rate of genetic gain for efficiency, fertility and low CH4 in cattle. The relatively high contribution of cattle to anthropogenic global methane has focussed attention on strategies to reduce enteric CH4 without compromising efficiency and fertility. Assisted reproductive technology has an important role in achieving the goal of multiplying and distributing cattle that have good efficiency, fertility and low CH4.

Use of dry-matter intake recorded at multiple time periods during lactation increases the accuracy of genomic prediction for dry-matter intake and residual feed intake in dairy cattle

Context Feed is the largest expense on a dairy farm, therefore improving feed efficiency is important. Recording dry-matter intake (DMI) is a prerequisite for calculating feed efficiency. Genetic variation of feed intake and feed efficiency varies across lactation stages and parities. DMI is an expensive and difficult-to-measure trait. This raises the question of which time periods during lactation would be most appropriate to measure DMI. Aims The aim was to evaluate whether sequence variants selected from genome-wide association studies (GWAS) for DMI recorded at multiple lactation time periods and parities would increase the accuracy of genomic estimated breeding values (GEBVs) for DMI and residual feed intake (RFI). Methods Data of 2274 overseas lactating cows were used for the GWAS to select sequence variants. GWAS was performed using the average of the DMI phenotypes in a 30-day window of six different time periods across the lactation. The most significant sequence variants were selected from the GWAS at each time period for either first or later parities. GEBVs for DMI and RFI in Australian lactating cows were estimated using BayesRC with 50 k single nucleotide polymorphisms (SNPs) and selected GWAS sequence variants. Key results There were differences in DMI genomic correlations and heritabilities between first and later parities and within parity across lactation time periods. Compared with using 50 k single-nucleotide polymorphisms (SNPs) only, the accuracy of DMI GEBVs increased by up to 11% by using the 50 k SNPs plus the selected sequence variants. Compared with DMI, the increase in accuracy for RFI was lower (by 6%) likely because the sequence variants were selected from GWAS for DMI not RFI. The accuracies for DMI and RFI GEBVs were highest by using selected sequence variants from the DMI GWAS in the mid- to late-lactation periods in later parity. Conclusions Our results showed that DMI phenotypes in late lactation time periods could capture more genetic variation and increase genomic prediction accuracy through the use of custom genotype panels in genomic selection. Implications Collecting DMI at the optimal time period(s) of lactation may help develop more accurate and cost-effective breeding values for feed efficiency in dairy cattle.

Effects of feeding CLOSTAT (Bacillus subtilis PB6) on the clinical health, performance, and carcass characteristics of feedlot steers1.

The objectives of this experiment were to evaluate the effects of feeding Bacillus subtilis PB6 on clinical health, performance, and carcass characteristics of feedlot steers. Bos indicus crossbred steer calves (n = 397; 342 kg initial body weight [BW]) were randomly assigned to pens by initial BW; pens (n = 24) were randomly assigned to one of two of the following experimental treatments: 1) no supplemental dietary direct-fed microbial, control (CON; n = 12 pens) or 2) 13 g/steer daily B. subtilis PB6 (CLO; CLOSTAT, Kemin Industries, Des Moines, IA; n = 12 pens). Steers were housed in 12.2 × 30.5 m soil-surfaced pens; pen served as the experimental unit. The percentage of cattle treated once or twice for bovine respiratory disease (BRD) did not differ among treatments (P ≥ 0.27); BRD mortality also did not differ between CON and CLO (P = 0.34). During the receiving period, final BW (P = 0.97), average daily gain (ADG; P = 0.91), dry matter intake (DMI; P = 0.77), and gain:feed (P = 0.79) were not different among treatments. There was a tendency (P = 0.09) for CLO-supplemented steers to be 14% more efficient from days 0 to 14 of the receiving period. Final BW, overall finishing phase ADG, and DMI did not differ by treatment (P ≥ 0.14); ADG was 0.14 kg greater for CLO than CON (P = 0.03) from days 29 to 56 of the finishing period. Gain: feed tended (P = 0.07) to be 7% greater (0.144 vs. 0.141) for CLO than CON throughout the duration of the finishing period, and 6.7% greater (P = 0.08; 0.152 for CLO vs. 0.150 for CON) for the entirety of the experiment. Carcass traits did not differ among treatments (P ≥ 0.31). The results of this experiment suggest that supplementing 13 g/steer daily B. subtilis PB6 may improve feed efficiency in feedlot cattle.

Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle.

Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.

Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas.

Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.

Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle

BackgroundPotential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs.ResultsThe systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10).ConclusionHere we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.