Residual feed intake and gain alters the performance and carcass traits in Nellore cattle.

The residual intake and gain (RIG) aims to select animals that present low feed intake in relation to the expected. This study aimed to evaluate the associations of selection for RIG with performance and carcass traits in Nellore cattle. Initially, residual feed intake (RFI) and residual gain (RG) were determined. From this, the RIG was calculated, and the animals were classified as efficient and inefficient for RIG. The efficient animals for RIG showed higher daily weight gain (DWG), Longissimus muscle area (LMA), and mid-test metabolic body weight (MMBW) than the inefficient ones. No significant correlations were found between subcutaneous fat thickness (SFT), marbling (MAR), LMA, MMBW, and the RIG. Thus, it's concluded that the RIG is a measure that can be used to identify and select animals with higher rates of DWG and LMA without changes in the dry matter intake (DMI), SFT, and MAR. However, this index should still be observed with caution, as it may be dependent on body size. Based on the findings, the selection of animals according to the RIG can be an important factor to generate phenotypic evolution in characteristics such as weight gain and rib eye area without adverse effects on the carcass fat deposition.

Integrated multi-omics reveals the relationship between growth performance, rumen microbes and metabolic status of Hu sheep with different residual feed intakes.

Residual feed intake (RFI) is a metric that provides a more accurate measure of feed efficiency. The lower the RFI, the higher the feed efficiency. The changes in the host microbiome and metabolome contribute to the greater feed efficiency of low RFI (LRFI) animals. The aim of this study was to explore the differences in rumen microorganisms, rumen metabolites and plasma metabolites of Hu sheep with differing RFI through the microbiome and metabolome. A total of 80 Hu sheep were used. The experiment consisted of a 15-d pretrial period and a 128-d experimental period. The RFI in the experimental period was calculated for all sheep, and the sheep were screened into high RFI (HRFI, n = 8) and LRFI (n = 8) groups. The HRFI and LRFI sheep did not differ in their initial and final body weights, average daily gain and body measurements, but the dry matter intake of LRFI sheep was significantly decreased (28.4%, P < 0.001). The sheep with LRFI had higher digestibility of crude protein (P = 0.010) and ether extract (P = 0.010) compared to HRFI group. The concentrations of acetate (P = 0.036), propionate (P = 0.010), valerate (P = 0.027) and total volatile fatty acids (P = 0.048) in rumen of LRFI group were higher compared to HRFI group. The results of 16S rDNA sequencing indicated that the sheep with LRFI had higher proportions of Prevotella genus in rumen liquid (P = 0.031). The rumen metabolome and plasma metabolome results showed that the citrate cycle, pyruvate metabolism and alanine, aspartate and glutamate metabolism processes were more active for sheep in LRFI group, which provided more energy substrate such as malic acid, oxoglutaric acid and citric acid. In conclusion, sheep with LRFI can utilize feed more efficiently, and the more active energy metabolism pathway and the production of energy substances may account for the higher feed efficiency.

Multi-omics revealed the mechanism of feed efficiency in sheep by the combined action of the host and rumen microbiota.

This study was conducted to investigate potential regulatory mechanisms of feed efficiency (FE) in sheep by linking rumen microbiota with its host by the multi-omics analysis. One hundred and ninety-eight hybrid female sheep (initial body weight = 30.88 ± 4.57 kg; 4-month-old) were selected as candidate sheep. Each test sheep was fed in an individual pen for 60 days, and the residual feed intake (RFI) was calculated. The ten candidate sheep with the highest RFI were divided into the Low-FE group, and the ten with the lowest RFI were divided into the High-FE group, all selected for sample collection. The RFI, average daily gain and average daily feed intake were highly significantly different between the two experimental groups (P < 0.05). Compared with Low-FE group, the insulin-like growth factor-1 and very low-density lipoprotein in serum and the propionate in rumen significantly increased in High-FE group (P < 0.01), but the acetate:propionate ratio in rumen significantly decreased in High-FE group (P = 0.034). Metagenomics revealed Selenomonas ruminantium, Selenomonas sp. and Faecalibacterium prausnitzi i were key bacteria, and increased abundance of the genes encoding the enzymes for cellulose degradation and production of propionate in High-FE group. The results of proteomics and section showed the rumen papilla length (P < 0.001) and expression of carbonic anhydrase and Na+/K+-ATPase were significantly higher in High-FE group (P < 0.05). On the other hand, the acetyl-CoA content significantly increased in the liver of High-FE group (P = 0.002). The relative expression levels of insulin-like growth factor-1 and apolipoprotein A4 genes were significantly up-regulated in the liver of High-FE group (P < 0.01), but relative expression level of monoacylglycerol O-acyltransferase 3 gene was significantly down-regulated (P = 0.037). These findings provide the mechanism by which the collaborative interaction between rumen microbiota fermentation and host uptake and metabolism of fermentation products impacts feed efficiency traits in sheep.

Metabolomics Profiling of Serum and Urine from Chuanzang Black Pigs with Different Residual Feed Intake.

This study was conducted to evaluate associations of blood variables and urine variables with different residual feed intakes (RFIs) in growing Chuanzang black (CB) pigs. A total of 228 growing CB boars from 99 days were used. The same basal diet was offered ad libitum and individual feed intake and body weight were measured over a period of 181 d. The CB pigs were categorized based on their residual feed intake values, with six individuals each from the high and low ends selected and divided into two groups: the low residual feed intake group (LS) and the high residual feed intake group (HS). Serum and urine samples were collected at the end of the experiment for determination of metabolomics profiling. Results showed that there were significantly different metabolites in serum and urine of different RFI groups (fold-change, FC > 2.0 or FC < 0.5, and p < 0.05), and 21 metabolites were identified in serum and 61 in urine. Cluster analysis showed that 20 metabolites were up-regulated and one metabolite was down-regulated in serum; 44 metabolites were up-regulated and 17 metabolites were down-regulated in urine. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differential metabolites of serum were enriched in linoleic acid metabolism, and the differential metabolites of urine were enriched in steroid hormone biosynthesis, taurine and hypotaurine metabolism, and primary bile acid biosynthesis. The correlations between serum metabolites and urine metabolites indicated a significant positive correlation between all fatty acyls in serum metabolites and L-glutamate in urine. However, no compelling genetic or blood biomarkers have been found to explain the differences in RFI, suggesting multiple approaches to effective feed use in pigs. This study provides new insights into the subsequent assessment of RFI by metabolomics profiling, as well as the development of novel feed additives for the factors that will facilitate future research directions in CB pigs.

Effect of thymol on the efficiency of feed utilization and compensatory growth in severe feed-restricted lambs.

The present study aimed to evaluate the effect of thymol on growth performance and apparent total tract digestibility of nutrients in severely feed-restricted lambs. Twenty-one male Baluchi lambs were randomly blocked by live weight into three groups: control without feed restriction (CON), feed restricted (FR), and feed restricted plus thymol (FR + T). The lambs underwent a four-week feed restriction period followed by four weeks of realimentation. Thymol was administered daily to the FR + T group during the feed restriction period. Average daily gain (ADG), average daily feed intake, feed efficiency (FE), partial efficiency of maintenance (PEM), and residual feed intake (RFI) were measured as growth performance parameters. Results showed that the severe feed restriction had adverse effects on ADG and FE, but improved PEM (P < 0.05). The effects of thymol administration on ADG, FE, PEM, and apparent total tract digestibility were not significant (P > 0.05). However, the lambs that received thymol during the feed restriction period showed a negative RFI during realimentation (P < 0.05). Overall, these findings suggest that feed restriction as well as thymol may have the potential to improve efficiency of feed utilization in growing lambs. However, this positive effect is independent of the improvement in nutrient digestibility.

Feed Efficiency Estimation from Stochastic Feed Requirement Frontier.

Feed accounts 40 to 70 percent of livestock production cost. Therefore, improving feed efficiency of production animals will promote farm profitability. To this end, precise estimation of animal level feed efficiency is important. Considering some limitations of residual feed intake (RFI) as indicator of animal level feed efficiency, an alternative approach is suggested. The approach involves estimation of a stochastic feed requirement frontier (SFRF), which explicitly allows for feed efficiency and statistical noise in the same specification. As a result, a SFRF naturally leads to feed efficiency indicator free from statistical noise. Furthermore, the feed efficiency indicator it generates is nonnegative and it can easily be expressed in terms of surplus feed intake (SFI) caused by feed inefficiency. Simulation experiment was used to illustrate the problems that arise from RFI-based feed efficiency estimation and the improvements that can be expected from the alternative approach. The experimental results showed that RFI tends to overestimate feed efficiency of animals. The overestimation gets worse as the contribution of feed inefficiency to feed intake variation increases. The results from the experiment also showed SFRF provides consistent feed efficiency estimates and associated SFI. Finally, further benefits of the alternative approach in feed efficiency estimation at animal level are presented.

Validation of the Residual Feed Intake Model in Brangus Heifers: Determination of the Optimal Days on Feed Interval to Estimate Dry Matter Intake and Average Daily Gain.

Brangus cattle are gaining popularity in the Southeast U.S. due to the desirable heat tolerance from their Brahman influence combined with the superior carcass merit aspects of Angus genetics. However, little is known about the optimal evaluation conditions for this hybrid breed when placed on test for Residual Feed Intake (RFI), a heritable measure of feed efficiency that allows improvement in performance without altering carcass traits. To address this, dry matter intake (DMI) was measured on Brangus heifers for 70-d to determine the optimal days on feed required to estimate feed intake and ADG and assess if inclusion of ultrasound measures of carcass merit into the model impact RFI rankings for this breed. The 56-d test period had a regression coefficient of 0.96 (p < 0.0001), R2 = 0.94, rp = 0.97 (p < 0.0001), and rs = 0.97 (p < 0.0001), indicating little change in rank of cattle for DMI compared to a 70-d test. ADG was the limiting factor in determining test duration. Based upon examining only heifers that calved, ultrasound backfat measures should be included in the RFI model to normalize for differences in heifer maturity. Results from this study indicate that a test duration of 56-d is sufficient to accurately estimate DMI in this population. This data indicates on-test duration can be shortened, enhancing the rate of genetic change by reducing cost and increasing the number of animals that can be tested annually.

Phenotypic relationships between meat quality parameters and residual feed intake in Japanese black Wagyu cattle.

Japanese black Wagyu cattle are renowned for producing some of the world's most highly valued and recognized beef with exceptional marbling. Therefore, the primary focus of genetic selection for Wagyu cattle has historically been on meat quality, particularly achieving high marbling levels. However, even when the price of the final product is high, production costs also remain high, especially considering that most of the feed has to be imported. The objective of this study was to evaluate phenotypic relationships between feed efficiency, specifically residual feed intake (RFI), as the most utilized efficiency index in cattle, and various meat quality parameters in Japanese black cattle in order to determine if a common phenotypic selection for these parameters could be feasible. For this, a total of 39 Wagyu cattle were evaluated for feed efficiency over their entire fattening period (900 d), with a focus on RFI as a key indicator. Animals were fed high-starch diets with vitamin A deprivation to achieve the desired marbling. Results revealed positive correlations between feed efficiency and meat quality in Wagyu cattle. Specifically, animals with higher feed efficiency exhibited superior meat quality traits, including firmness, marbling, and overall meat rating. When comparing the 20 most extreme RFI individuals (10 most and 10 least efficient), we observed that efficient RFI animals showed increased marbling levels (+13.2%, P = 0.05) and ranking quality (+12%, P = 0.06) of the meat. In conclusion, this research contributes to understanding the interplay between feed efficiency and meat quality in Japanese black Wagyu cattle. Phenotypic correlations observed suggest the possibility of incorporating RFI criteria into genetic selection programs without compromising the prized meat quality traits of Wagyu beef.

The Japanese black cattle, or Wagyu, are known because of its exceptional meat quality and its high degree of marbling. However, to achieve this condition, animals are fed with high amount of concentrate and over long periods of time. In order to decrease both environmental impact and economic profitability of Wagyu producers, feed efficiency may be improved. Therefore, the present work evaluates the phenotypic relationship between meat quality variables of Japanese black cattle and their efficiency of feed utilization. Results showed how individuals with improved efficiency of feed utilization present higher degree of marbling than non-efficient, which may represent the footprint of a new genetic selection program which encompasses both meat quality criteria and feed efficiency values. These results have to be confirmed by genetic studies to verify heritability of these treatments.

Effects of finisher diet nutrients density and slaughter age on energy and protein efficiency, productive and economic performance and meat quality of broilers.

BACKGROUND: The current broilers have been greatly optimized for weight gain and breast yield, which necessitates the provision of nutrients-dense diets for maximum potential. OBJECTIVES: The current study aimed to evaluate the effect of finisher diet nutrients density (ND) on energy and protein efficiency, productive and economic performance and breast meat quality of broilers raised until different slaughter age. METHODS: A total of 600 23-day-old broiler male chicks (Cobb-500) were assigned to 10 treatments with six replicates and 10 birds each. Experimental treatments were included factorial arrangement of five increment (2.5%) levels of finisher diet ND (92.5%, 95%, 97.5%, 100% and 102.5% as strain recommendation) and slaughtered at 38 or 46 days of age. The relative difference in the energy level of experimental diets was used to increase ND levels at the same ratio. RESULTS: Feed intake (FI) and breast meat quality traits exception water holding capacity (WHC) were not affected by finisher diet ND. In response to increasing finisher diet ND, energy and protein efficiency, productive traits, bio-economic index (BEI) and breast relative weight (BRW) linearly improved. However, residual feed intake and breast meat WHC improved with a quadratic trend. By using broken-line regression analysis, the optimum dietary ND was obtained at 97.5%-102% of strain recommendation. Energy and protein efficiency, feed conversion ratio and BEI deteriorated by prolonging rearing period. The BRW, meat lightness (L*), redness (a*), hue angle (h*) and WHC values for the birds slaughtered at 46 days of age were significantly higher, and cooking loss was lower than those slaughtered at 38 days old. CONCLUSIONS: Broilers during the finisher period are not able to regulate their FIs with diet ND. The energy and protein efficiency, productive and economic performance were reduced when broilers were fed diluted diet or the rearing period was prolonged.

Effects of residual feed intake on the economic traits of fast-growing meat ducks.

Feed efficiency (FE) is a crucial economic indicator of meat duck production. The objective of this study was to assess the impact of residual feed intake (RFI), defined as the difference between the actual and expected feed intake based on animal's production and maintenance requirements, on the growth performance (GP), slaughter and internal organ characteristics of fast-growing meat ducks. In total, 1,300 healthy 14-day-old male fast-growing meat ducks were housed in individual cages until slaughter at the age of 35 d. The characteristics of the carcass and internal organs of 30 ducks with the highest RFI (HRFI) and the lowest RFI (LRFI) were respectively determined. RFI, the feed conversion ratio (FCR), and average day feed intake (ADFI) were significantly lower in the LRFI group than the HRFI group (P < 0.001), while there were no significant differences in marketing BW or BW gain (BWG) (P > 0.05). The thigh muscle and lean meat yields were higher, and the abdominal fat content was lower (P < 0.001) in the LRFI group, while there were no significant differences in other carcass traits between the groups (P > 0.05). The liver and gizzard yields were significantly higher (P < 0.001) in the LRFI group, while there were no significant differences (P > 0.05) in intestinal length between the groups. RFI was highly positively correlate with FCR and ADFI (P < 0.01), but negatively correlated the yields of thigh muscle, lean meat, liver, and gizzard, and positively correlated with abdominal fat content. These results indicate that selection for low RFI could improve the FE of fast-growing meat ducks without affecting the marketing BW and BWG, while increasing yields of thigh muscle and lean meat and reducing abdominal fat content. These findings offer useful insights into the biological processes that influence FE of fast-growing meat ducks.

Genetic relationships between behavioral traits and feed efficiency traits in lactating Holstein cows.

The evaluation of dairy cow feed efficiency using residual feed intake accounts for known energy sinks. However, behavioral traits may also contribute to the variation in feed efficiency. Our objective was to estimate the heritability and repeatability of behavioral traits and their genetic correlations with feed efficiency and its components in lactating Holstein cows. The first dataset consisted of 36,075 daily rumination and lying time records collected using a SMARTBOW ear-tag accelerometer (Zoetis, Parsippany, NJ) and 6,371 weekly feed efficiency records of 728 cows from the University of Wisconsin-Madison. The second dataset consisted of 59,155 daily activity records, measured as number of steps, recorded by pedometers (AfiAct; SAE Afikim, Kibbutz Afikim, Israel) and 8,626 weekly feed efficiency records of 635 cows from the University of Florida. Feed efficiency and its components included DMI, change in BW, metabolic BW, secreted milk energy, and residual feed intake. The statistical models included the fixed effect of cohort, lactation number, and days in milk, and the random effects of animal and permanent environment. Heritability estimates for behavioral traits using daily records were 0.19 ± 0.06 for rumination and activity, and 0.37 ± 0.07 for lying time. Repeatability estimates for behavioral traits using daily data ranged from 0.56 ± 0.02 for activity to 0.62 ± 0.01 for lying time. Both heritability and repeatability estimates were larger when weekly records instead of daily records were used. Rumination and activity had positive genetic correlations with residual feed intake (0.40 ± 0.19 and 0.31 ± 0.22, respectively) and lying time had a negative genetic correlation with this residual feed intake (-0.27 ± 0.11). These results indicate that more efficient cows tend to spend more time lying and less time active. Additionally, less efficient cows tend to eat more and therefore also tend to ruminate longer. Overall, sensor-based behavioral traits are heritable and genetically correlated with feed efficiency and its components and, therefore, they could be used as indicators to identify feed-efficient cows within the herd.

Multi-omics unveils tryptophan metabolic pathway as a key pathway influencing residual feed intake in Duroc swine.

The genetic trait of residual feed intake (RFI) holds considerable importance in the swine industry. Recent research indicates that the gut microbiota of pigs plays a pivotal role in the manifestation of the RFI trait. Nevertheless, the metabolic pathways involved in the functioning of these microorganisms remain elusive. Thus, based on the ranking of the RFI trait in Duroc pigs, the present study selected the top 10 and bottom 10 pigs as the experimental subjects. The distribution and metabolite differences of cecal microbiota were analyzed using 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. The low RFI cecal group was named LRC, and the high RFI cecal group was named HRC. The results indicate that the LRC group had lower RFI, feed conversion ratio (FCR), average daily feed intake (ADFI) (p < 0.001), and thinner backfat (p < 0.05) compared with the HRC group. We simultaneously recorded the foraging behavior as well, the LRC group had a significant increase in total time spent at the feeder per day (TPD) (p < 0.05) and a significant increase in average feed intake per mins (AFI) and the number of visits to the feeder per day (NVD) compared to the HRC group (p < 0.001). Clostridium_XVIII, Bulleidia, and Intestinimonas were significantly enriched in the LRC group (p < 0.01), while Sutterella, Fusobacterium, and Bacteroides were significantly increased in the HRC group (p < 0.01). In the metabolome, we detected 390 (248 metabolites up and 142 down in the LRC compared with HRC), and 200 (97 metabolites up and 103 down in the LRC compared with HRC) differential metabolites in positive and negative ionization modes. The comprehensive analysis found that in the LRC group, Escherichia and Eubacterium in the gut may increase serotonin content, respectively. Bacteroides may deplete serotonin. We suggest that the RFI may be partly achieved through tryptophan metabolism in gut microbes. In individuals with low RFI, gut microbes may enhance feed efficiency by enhancing host synthesis and metabolism of tryptophan-related metabolites.

Incorporating body measurement traits to increase genetic gain of feed efficiency and carcass traits in Japanese Black steers.

The objective of the present study was to comprehensively evaluate whether body measurement traits, including body weight and body size, could be used as indicators of genetic selection for feed efficiency and carcass traits in Japanese Black steers. First, we estimated the genetic parameters for body measurements, feed efficiency, and carcass traits. Second, we estimated the correlated responses in feed efficiency and carcass traits when selection was applied to one or multiple-body measurement traits. In total, 4,578 Japanese Black steers with phenotypic values of residual feed intake (RFI) and residual body weight gain (RG) as feed efficiency traits and carcass weight (CWT) and beef marbling standard (BMS) as carcass traits were used. Eleven body measurement traits were measured at the start and finish of the fattening periods (BMT1 and BMT2, respectively), and their growth during the fattening period (BMT3) was used for genetic analyses. The results of genetic parameters showed that the heritability estimates were low to moderate (0.10 to 0.66), and the genetic correlations among body measurement traits were also estimated to be positively moderate to high in each measuring point (0.23 to 0.99). The genetic correlations of body measurement traits with RFI and BMS were estimated to be low (-0.14 to 0.30 and -0.17 to 0.35, respectively), but those with CWT were positively low to high (0.12 to 0.97). The genetic correlation estimates between BMT3 and RG were moderate to high (0.38 to 0.78). Second, correlated responses were estimated under positive selection for body measurement traits. Positive selection for BMT2 and BMT3 increased CWT and RG; however, positive selection for body measurement traits resulted in no change in RFI and BMS. Favorable directions of genetic gains, which were positive for RG, CWT, and BMS and negative for RFI, were obtained by selection indices, including multiple traits in BMT1. Our results suggest that using only one-body measurement trait as an indicator of genetic selection for RFI is difficult. However, body measurement traits can be indirect indicators of improved RG. Our results also suggest that genetic improvement of both RFI and RG without reducing CWT and BMS could be achieved using selection indices that account for a balance of body conformation using multiple-body measurement traits in Japanese Black cattle.

Improving feed efficiency is a key objective in the beef cattle industry. Still, high costs and logistical efforts make measuring daily feed intake per animal in many cattle difficult. Here, we focused on body measurement traits, including body weight and body size, as indirect indicators of feed efficiency in Japanese Black cattle, as measuring these traits is easy and inexpensive. When selection was applied to one- or multiple-body measurement traits, we estimated the correlated responses in feed efficiency and carcass traits. We also estimated the genetic relationships of body measurement traits with feed efficiency and carcass traits. Our results showed body measurement traits were heritable and had weak genetic relationships with residual feed intake. Regarding the possibility of genetic selection for residual feed intake using body measurement traits as indirect indicators, our results suggest that using a single body measurement trait as an indicator is difficult. However, our results also suggest that the genetic improvement of residual feed intake could be possible using selection indices that account for a balance of body conformation using multiple-body measurement traits in Japanese Black cattle.

Gut-brain bidirectional determination in regulating the residual feed intake of small-sized meat ducks.

The gut-brain axis is essential in maintaining the homeostasis of neuronal system, endocrine system, and intestinal microbiota in both the afferent and efferent directions. This axis is considered to be a key mechanism that regulates feed efficiency (FE). This study aimed to investigate the regulatory mechanisms of gut-brain axis-related genes on the residual feed intake (RFI) in H-strain small-sized meat ducks. A total of 500 ducks with similar initial BW (635.2 ± 15.1 g) were selected and reared in the same experimental facility until slaughter at 42 d of age. RFI was calculated from the average daily gain (ADG), average daily feed intake (ADFI), and metabolic body weight (MBW0.75). Thirty high-RFI (H-RFI) and 30 low-RFI (L-RFI) birds were selected for further evaluation of growth performance, carcass characteristics, and blood biochemical parameter measurements. Six L-RFI and 6 H-RFI birds were then subjected to hypothalamic transcriptomic and cecal microbial sequencing analyses. Results indicated that L-RFI birds exhibited lower production performance (ADFI, FCR, and RFI) and blood biochemical indices (total cholesterol and ghrelin content) compared with H-RFI birds (P < 0.05). Gene expression differed significantly between the L-RFI and H-RFI birds, with 70 upregulated and 50 downregulated genes. The bacterial communities of L-RFI birds showed higher abundances of Bacteroides, Bifidobacterium, and Lactococcus, and lower abundances of Erysipelatoclostridium, Parasutterella, Fournierella, and Blautia compared with H-RFI birds (P < 0.05). Interactive analysis revealed bacterial communities associated with FE were significantly correlated with hypothalamic genes (P < 0.05), for example, Bacteroides was positively correlated with DGKH and LIPT2, while negatively correlated with CAPN9, GABRD, and PDE1A. Bifidobacterium showed significant correlations with ATP2A3, CALHM6, and TMEM121B. Overall, RFI was a crucial indicator of FE, regulated by interactions between brain gene expression and gut microbiota through cAMP signaling, neuroactive ligand-receptor interaction, and calcium signaling pathways. Notably, increased expression of hypothalamic genes and abundance of carbohydrate-utilization microbiota in L-RFI meat ducks improved FE by enhancing energy metabolism and volatile fatty acids absorption.

Behavioral consistency of competitive behaviors and feeding patterns in lactating dairy cows across stocking densities at the feed bunk.

Introduction: High feed bunk stocking densities can differentially impact individual dairy cows' competitive behaviors, feeding patterns, and feed efficiency. Our objective was to manipulate feed bunk stocking densities to evaluate intra-individual behavioral consistency across stocking densities and quantify associations with feed efficiency and production. Methods: Thirty-two primiparous (130.7 ± 29.0 days in milk, DIM) and 32 multiparous (111.3 ± 38.3 DIM) lactating Holstein cows were housed with 32 roughage intake control (RIC) bins. Each cow was assigned to share 8 bins with others of the same parity and similar body weight (16 cows/block; 2:1 feed bunk stocking density except during tests). Competition and feeding patterns were evaluated via video and RIC data, respectively, at 3 stocking densities (1:1, 2:1, 4:1 cows/bin) during 1-h tests (2 tests/stocking density; 6 tests/cow) following 2 h feed deprivation. Residual feed intake (RFI) was calculated across the 45-d study as the difference between observed and predicted dry matter intake (DMI) after accounting for known energy sinks. Linear mixed models were used to evaluate the overall impact of test stocking density on competition and feeding patterns. To evaluate intra-individual consistency between stocking densities, individual stability statistic (ISS) scores were computed. Correlational relationships were determined between RFI and ISS scores. Results and dicsussion: Cows displayed the most competitive behaviors at 2:1 stocking density (p < 0.0001) but experienced the highest rate of contacts per minute of eating time at 4:1 (1:1 vs. 2:1 vs. 4:1: 0.09 vs. 0.95 vs. 1.60 contacts/min; p < 0.0001). Feeding patterns were modulated as stocking density increased; eating rate increased (0.16 vs. 0.18 vs. 0.22 kg/min; p < 0.001) as eating time (40.3 vs. 28.2 vs. 14.6 min; p < 0.001) and DMI decreased (6.3 vs. 5.1 vs. 3.0 kg; p < 0.001). As stocking density doubled, individuals remained consistent (p = 0.018) in time spent near others actively eating and tended to remain consistent in competition behavior and feeding patterns (0.053 ≤ p ≤ 0.094). Between 2:1 and 4:1, cows with higher DMI and milk production were more consistent in first-visit DMI and duration. Feed efficiency was not associated with behavioral consistency across the tests (p ≥ 0.14). Nonetheless, feed bunk stocking density has behavioral implications which should be considered in nutritional management decisions.

Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations.

Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified. Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism. Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.

Metagenomic insights into the relationship between intestinal flora and residual feed intake of meat ducks.

In this study, we sought to determine the effects of intestinal flora on the feed efficiency of meat ducks by evaluating the correlation between intestinal flora and residual feed intake. The F2 generation of Cherry Valley ducks × Runzhou Crested White ducks was used as the study subjects, and feed consumption being recorded from d 21 to 42. RFI was calculated based on growth performance, and 20 low RFI and 20 high RFI ducks were randomly selected to characterize the effect of RFI on growth performance. To analyze the intestinal flora affecting RFI, 16s rDNA sequencing was performed on the contents of 5 intestinal segments from the HR and LR groups, and macrogenomic sequencing was performed on the cecal contents. Feed intake, average daily feed intake, feed conversion ratio, and residual feed intake were lower in low RFI. Analysis of the intestinal flora revealed the cecum to be more highly enriched in the carbohydrate metabolism pathway and less enriched with potentially pathogenic taxa than the other assessed intestinal regions. Further analysis of the cecal microbiota identified nine significantly differentially enriched intestinal flora. In this study, we accordingly identified a basis for the mechanisms underlying the effects of the intestinal flora on meat duck feed efficiency.

Estimation of genetic parameters for maintenance energy requirements and residual feed intake in Nellore cattle.

We estimated heritabilities and genetic and phenotypic correlation estimates for maintenance energy requirements (NEmR), residual feed intake (RFI), growth, carcass and reproductive indicator traits, using data from 41 feed efficiency trials in Brazil, comprising 4381 males and females. Continuous traits were analysed using a linear animal model and threshold traits were analysed using a threshold animal model. The heritability estimates were low for RFI (0.190) and NEmR (0.193); other heritabilities were mainly moderate (growth and carcass traits) or high (sexual precocity traits). The genetic correlation of RFI with NEmR was high (0.701). The genetic correlations of NEmR were low with carcass and reproductive traits, and moderate with growth traits. Thus, selection to improve weaning weight and female sexual precocity indicator traits would not affect maintenance energy requirement. Genetic selection to reduce maintenance energy requirements is feasible and would also reduce DMI and RFI. Selection to improve RFI can be used to identify animals with lower maintenance energy requirements. Long-term selection to reduce RFI and NEmR would have favourable effects on yearling weight, carcass muscle indicator traits and female sexual precocity. Genetic (co)variance component estimates for NEmR, in conjunction with economic values of selection criteria, may be used to develop novel approaches for genetic selection to improve efficiency of beef production.

Repeatability of feed efficiency and its relationship with carcass traits in Hanwoo steers during their entire growing and fattening period.

OBJECTIVE: This study investigated the repeatability of feed efficiency and its association with carcass traits in Hanwoo steers during the entire growing and fattening periods. METHODS: The growth and intake of thirty-six Hanwoo steers (259±19.7 kg; nine months) were monitored throughout five periods, including two growing periods (GP) and three fattening periods (FP). The steers were fed two types of concentrate mixes with varying nutrient compositions until they reached a target weight of 800 kg for slaughter. For each period, steers were categorized into three classes based on their feed efficiency rankings using residual feed intake (RFI) and feed conversion ratio (FCR). Feed efficiency repeatability was assessed using the Spearman correlation coefficient, decomposition of random errors, and the Theil segregation index (TSI). The Pearson correlation coefficient was used to examine the relationship between feed efficiency and carcass traits. RESULTS: The results demonstrated a significant and high correlation with RFI, but not FCR, during the growing or fattening stages (r>0.5; p<0.01). When steers were classified according to their feed efficiency rankings, 58% of the animals in the high RFI class (low efficient) initially (GP 1) remained in the same class by the last period (FP 3), whereas steers were randomly distributed based on FCR. The repeatability, assessed by the decomposition of random errors, was higher for RFI (0.61) than for FCR (0.15). The TSI also indicated that RFI rankings, rather than FCR rankings, are more likely to be maintained. Moreover, a weak association was observed between feed efficiency and carcass traits. CONCLUSION: In conclusion, RFI repeatability throughout the GP and FP surpassed that of the FCR, with steers classified as high RFI during the GP more likely to remain in the same class during the FP. Feed efficiency was weakly correlated with carcass traits.

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.