Residual Feed Intake Research Articles

Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency

Identifying and breeding cattle that are more feed efficient is of great benefit to beef production. Additionally, it is crucial that genes contributing to feed efficiency are robust across varying management settings including dietary source as well as being relevant across contrasting breeds of cattle. The aim of this study was to determine miRNAs that are contributing to the expression of residual feed intake (RFI) across two breeds and dietary sources. miRNA profiling was undertaken in Longissimus dorsi tissue of Charolais and Holstein–Friesian steers divergent for RFI phenotype following two contrasting consecutive diets (high-forage and high-concentrate). Ten miRNA were identified as differentially expressed (adj. P < 0.1) across the breed and diet contrasts examined. Of particular interest was the differential expression of miR-2419-5p and miR-2415-3p, both of which were up-regulated in the Low-RFI Charolais steers across each dietary phase. Pathway analysis of target mRNA genes of differentially expressed miRNA revealed enrichment (P < 0.05) for pathways including metabolic related pathways, insulin receptor signalling, adipogenesis as well as pathways related to skeletal muscle growth. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential molecular regulatory mechanisms relating to feed efficiency in beef cattle.

Impact of feed efficiency on young beef animals on adult resilience: From field challenge experiments to modelling approaches

The relationship between feed efficiency at young ages and resilience as cows has been examined using an experiment that combines residual feed intake (RFI) evaluation of beef heifers and subsequent dietary challenge as cows. Feed efficiency of 569 heifers of 22 months of age was estimated during a 70-day period. Then a dietary challenge was applied on 303 of these animals after their first calving, half of them being fed 30 % below their expected needs from 10 days after calving up to the start of the grazing period (around mid-April), after which all the animals received the same management. When possible, the animals were kept until third lactation, giving a total of 514 lactations. Dam weight, dam BCS and calf weight were measured regularly, dam milk production was estimated three times during the lactation and resumption of cyclicity was recorded as well. The experimental data were analyzed using linear models including the effects of heifer efficiency (RFI <-0.4 = efficient; RFI >0.4 = inefficient) and interaction of heifer efficiency and diet group. The data were also used to calibrate a herd dynamics model representing management-nutrition and reproduction interactions at animal level. The experiment data showed that the efficient heifers were 18 kg heavier as cows when fed ad libitum (P = 0.04) but no difference was observed when restricted. Within both diets, heifers classified as efficient produced between 6 and 12 % less milk as cows than inefficient heifers depending on the lactation stage (P < 0.01), with a subsequent effect on calf weight. Finally, the resumption of cyclicity was one week shorter for the efficient animals when fed ad libitum but the opposite was observed within the restricted group, representing a complete ovarian cycle difference between diet groups within the efficient class (P = 0.001). In the lifetime modelling approach, two clusters of animals with different characteristics, including RFI, were simulated under both a non-restricted and restricted feeding environment. In this simulation, efficient heifers produced lighter cows with lower intake and higher body reserves from second calving until culling. Non-efficient heifers had better productive (kg of weaned calf) performance as cows independently of environment. The simulated reproductive performance of cows was equal for animals coming from efficient and non-efficient heifers under the non-restricted environment whereas efficient heifers perform better in the restricted environment, especially when parity increases. Both approaches showed that the interplay between efficiency at young ages and short- and long-term resilience depends on the environment. It can be concluded that the selection for efficiency at young ages has a negative impact on lactational performance as cows but not necessarily on reproductive resilience.

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.

Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition

The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.

Selection indices for residual feed intake derived from milk spectra

Improving production efficiency and minimizing the environmental impact of dairy farming are 2 important goals of the dairy industry. Achieving these objectives requires improving the feed-to-milk conversion efficiency. One way to achieve this goal is through genetic selection. However, measuring feed efficiency in commercial herds is currently not feasible. As such, we conducted a study to evaluate the genetic accuracy of various selection indices derived from Fourier transform mid-infrared (FTIR)-spectra or milk composition. We use 7,793 weekly records on 537 genotyped cows (78,964 SNPs), with information on residual feed intake (RFI), and FTIR-spectra. We fitted various types of selection indexes using the complete FTIR-spectra of milk samples. The estimated heritability of RFI was 0.12 ± 0.02. The accuracy of indirect selection using the FTIR-spectra was maximized using a principal components selection index (0.16 ± 0.07), followed by a Lasso-type penalized selection index (0.14 ± 0.06). We determined that an index based on milk spectral data recorded on ~25 daughters produced a progeny average with an accuracy comparable to direct phenotypic selection for RFI. We conclude that indirect selection for RFI using FTIR-spectra data can be effective for sires with progeny; however, future studies with a larger sample size are needed to validate these results.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population

BackgroundThe selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1–2 Mb), FROH2 (2–4 Mb), FROH3 (4–8 Mb), FROH4 (8–16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits.ResultsThe correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits.ConclusionsInbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data

BackgroundA heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data.ResultsThe parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima’s D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds.ConclusionsThe detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.

Unravelling the mechanisms underlying the social interaction effects on the feed efficiency of rabbits

The feed consumption and feeding patterns of group-housed livestock and their productive outputs can be affected by interactions among group members, such as competition for feeder access and aggression. The impact of competition is especially significant when feed restriction is implemented during the fattening stage, a common practice in rabbit farms to reduce mortality from digestive disorders during this period. The overall aim was to quantify the importance of social interaction effects at the genetic and environmental level on feed efficiency, feeding behaviour and social ranking traits in rabbit populations having access to electronic feeders whilst they were housed in groups during fattening. This was done by quantifying novel feeding behaviour (FB) and social ranking (SR) traits and by estimating the genetic parameters and genetic correlations between all combinations of direct and social effects of these traits and residual feed intake (RFI), an indicator of feed efficiency. These effects were estimated in animals fed either ad libitum (AL) or on a time-based feed restriction (R) and were selected for feed efficiency on these feeding regimes for six generations. We found that there were substantial social genetic and social litter effects on RFI and FB traits, manifesting as antagonistic relationships between direct and social genetic effects. These effects were stronger amongst the R, as opposed to the AL animals. Despite these antagonistic relationships, the large social genetic effects resulted in substantial heritable variation available for selection of these traits, and therefore feeding behaviour could be changed by genetic selection, especially for R animals. The indicators of an animal’s SR were also heritable and subject to social genetic effects and therefore may respond to selection. However, the phenotypic population mean would not change, because such traits are context−specific. The animals that took most of the feeding resources and had priority access to the feeder had a higher RFI, that is, they were less efficient, but they made their cage mates more efficient. This is the first time that the genetic correlations between direct effects of RFI and direct effects of FB and SR traits, as well as between social effects of RFI and direct effects of FB traits and SR traits, have been quantified. Results could help to understand the mechanisms by which an animal exerts its influence on the feed efficiency of its cage mates under different feeding regimes and assist in the development of breeding strategies.

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.

Milk transcriptome biomarker identification to enhance feed efficiency and reduce nutritional costs in dairy ewes

In recent years, rising prices for high-quality protein-based feeds have significantly increased nutrition costs. Consequently, investigating strategies to reduce these expenses and improve feed efficiency (FE) have become increasingly important for the dairy sheep industry. This research investigates the impact of nutritional protein restriction (NPR) during prepuberty and FE on the milk transcriptome of dairy Assaf ewes (sampled during the first lactation). To this end, we first compared transcriptomic differences between NPR and control ewes. Subsequently, we evaluated gene expression differences between ewes with divergent FE, using feed conversion ratio (FCR), residual feed intake (RFI), and consensus classifications of high− and low-FE animals for both indices. Lastly, we assess milk gene expression as a predictor of FE phenotype using random forest. No effect was found for the prepubertal NPR on milk performance or FE. Moreover, at the milk transcriptome level, only one gene, HBB, was differentially expressed between the NPR (n = 14) and the control group (n = 14). Further, the transcriptomic analysis between divergent FE sheep revealed 114 differentially expressed genes (DEGs) for RFI index (high-FERFI = 10 vs low-FERFI = 10), 244 for FCR (high-FEFCR = 10 vs low-FEFCR = 10), and 1 016 DEGs between divergent consensus ewes for both indices (high-FEconsensus = 8 vs low-FEconsensus = 8). These results underscore the critical role of selected FE indices for RNA-Seq analyses, revealing that consensus divergent animals for both indices maximise differences in transcriptomic responses. Genes overexpressed in high-FEconsensus ewes were associated with milk production and mammary gland development, while low-FEconsensus genes were linked to higher metabolic expenditure for tissue organisation and repair. The best prediction accuracy for FE phenotype using random forest was obtained for a set of 44 genes consistently differentially expressed across lactations, with Spearman correlations of 0.37 and 0.22 for FCR and RFI, respectively. These findings provide insights into potential sustainability strategies for dairy sheep, highlighting the utility of transcriptomic markers as FE proxies.

Immune cells phenotype and bioenergetic measures in CD4+ T cells differ between high and low feed efficient dairy cows

Identifying sources of variance that contribute to residual feed intake (RFI) can aid in improving feed efficiency. The objectives of this study were to investigate immune cells phenotype and bioenergetic measures in CD4+ T cells in low feed efficient (LE) and high feed efficient (HE) dairy cows. Sixty-four Holstein cows were enrolled at 93 ± 22 days in milk (DIM) and monitored for 7 weeks to measure RFI. Cows with the highest RFI (LE; n = 14) or lowest RFI (HE; n = 14) were selected to determine immune cells phenotype using flow cytometry. Blood was sampled in the same LE and HE cows at 234 ± 22 DIM to isolate peripheral blood mononuclear cells, followed by magnetic separation of CD4+ T lymphocytes using bovine specific monoclonal antibodies. The metabolic function of isolated CD4+ T lymphocytes was evaluated under resting and activated states. An increased expression of CD62L+ cells within CD8+ T lymphocytes and CD21+ B lymphocytes was observed in HE cows compared to LE cows. CD4+ T lymphocytes of HE cows exhibited an increased mitochondrial and glycolytic activity in resting and activated states compared to LE cows. These data suggest that immune cells in HE cows exhibit an increased metabolic function, which might influence nutrient partitioning and utilization and serve as a source of variation in feed efficiency that warrants future investigation.

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.

Effects of rumen-bypass protein supplement on growth performance, hepatic mitochondrial protein complexes, and hepatic immune gene expression of beef steers with divergent residual feed intake.

We investigated the impact of a rumen-bypass protein (RBP) supplement on growth performance, plasma and urinary N (UN) concentration, hepatic mitochondrial protein complexes, and hepatic mRNA expression of immune genes of beef steers with negative or positive residual feed intake (RFI) phenotype. Forty crossbred beef steers with an average body weight (BW) of 492 ± 36 kg were subjected to a generalized randomized block design over a 42-day experimental period. This study followed a 2 × 2 factorial arrangement of treatments. The factors evaluated were: 1) RFI classification (low-RFI (-2.12 kg/d) vs. high-RFI (2.02 kg/d), and 2) rumen-bypass protein supplement: RBP supplement (RBP; 227 g/steer/d) vs. control diet (CON; 0 g/d), resulting in four distinct treatments: LRFI-CON (n = 10), LRFI-RBP (n = 10), HRFI-CON (n = 10), and HRFI-RBP (n = 10). The RBP supplement (84% crude protein) is a mixture of hydrolyzed feather meal, porcine blood meal, and DL-methionine hydroxy analogue. The beef steers were stratified by BW, randomly assigned to treatments, and housed in four pens (1 treatment/pen) equipped with two GrowSafe feed bunks each to measure individual dry mater intake (DMI). Body weight was measured every 7 d. Liver tissue samples were collected on d 42 from all the beef steers. These samples were used for mRNA expression analysis of 16 immune-related genes and for evaluating the mitochondrial protein complexes I - V. No significant effects due to RBP supplementation or RFI × RBP interactions (P > 0.05) were observed for average daily gain (ADG) and DMI. However, compared to high-RFI steers, low-RFI steers showed a trend towards reduced DMI (12.9 vs. 13.6 kg/d; P = 0.07) but ADG was similar for the two RFI groups. Regardless of RFI status, supplemental RBP increased blood urea nitrogen (BUN) (P = 0.01), with a lower BUN concentration in low-RFI steers compared to high-RFI ones. A tendency for interaction (P = 0.07) between RFI and RBP was detected for the UN concentrations; feeding the dietary RBP increased the UN concentration in high-RFI beef steers (209 vs. 124 mM), whereas the concentration was lower than that of the CON group for low-RFI beef steers (86 vs. 131 mM). Interactions of RBP and RFI were observed (P ≤ 0.05) for mitochondrial activities of complexes IV, V, and mRNA expressions of some immune genes such as TLR2, TLR3, and IL23A. In conclusion, while RBP supplementation did not alter growth performance, its observed effects on hepatic immune gene expression, mitochondrial protein complexes, BUN, and UN depended on the beef steers' RFI phenotype. Therefore, the RFI status of beef steers should be considered in future studies evaluating the effects of dietary protein supplements.

Genetic parameters of feeding behaviour traits in ducks bred for foie gras production

The mule duck accounts for over 90% of French foie gras production, a sector where feed represents two-thirds of production costs. This study focuses on analysing the feeding behaviours of the mule duck and its parental populations (Pekin and Muscovy) using automated feeders. To assess feed efficiency, feed conversion ratio and residual feed intake were analysed, along with six traits derived at the daily and meal levels. Genetic parameters were estimated separately in purebred populations, as well as with a joint crossbred model that estimated the parental contributions to the hybrid crossbred performances. In relation to higher feed intakes and much−reduced feeding times (P < 0.001), the feeding rate in the Pekin population was twice as high as in the Muscovy population (19 g/min vs 9 g/min), while the mule duck exhibited a large heterosis for this trait (29 g/min). Feeding traits exhibited moderate (0.38 ± 0.11) to high (0.65 ± 0.11) heritabilities. Similar correlation patterns were observed between feeding traits in the two parental populations. In the Pekin line, the feed conversion ratio did not significantly correlate with feeding traits except for daily feed intake. However, in the Muscovy population, it was negatively correlated with the number of meals (−0.51 ± 0.21) and positively with meal feed intake and meal duration (+0.79 ± 0.17 and + 0.71 ± 0.26, respectively). The contributions of the two parental species to the hybrid’s performance differed, with the Pekin contributing more to feeding and meat traits compared to the Muscovy. They were similar only for liver weight. Additionally, unfavourable correlations between meat traits and liver traits were estimated in both pathways. Genetic relationships between feeding traits and slaughter traits varied by parental origin, suggesting different strategies for improving hybrid performance in the two parental species. However, in both pathways, genetic correlations between feed conversion ratio and meat traits (breast muscle and thigh weights) were favourable (<−0.42 ± 0.18), whereas they were unfavourable (>0.41 ± 0.20) for fatty liver weight. Altogether, improving liver traits and feed efficiency in the hybrid through selection in the parental populations could be enhanced by considering feeding traits recorded with electronic feeders, provided that adverse correlations are properly accounted for in a multitrait index.

Performance, nutrient utilization and meat quality traits in Bos indicus cattle: a meta-analysis examining the effect of residual feed intake.

This meta-analysis aims to investigate the effects of residual feed intake (RFI) phenotype on performance, nutrient utilization and meat quality traits in Zebu (Bos indicus) cattle. Twenty-three peer-reviewed publications with 37 treatment means were included in the dataset. Weighted mean difference analysis compared animals categorized into low RFI (more efficient) versus medium or high RFI (less efficient) groups. Data heterogeneity via meta-regression and subgroup analysis, considering variables such as animal age, sex class, experimental duration, RFI group, dietary concentrate, and estimated metabolizable energy intake were also explored. The predominant genetic group of cattle in the dataset was Nellore (89.18%), followed by Brahman (10.81%). More efficient animals (low RFI phenotype) exhibited less dry matter intake (DMI; P < 0.010) than medium or high RFI animals (-0.95kg vs. -0.42kg/d). Cattle dietary crude protein and fiber digestibility were consistent across RFI groups (P > 0.05), while dietary ether extract digestibility tended to decrease (P = 0.050) in low RFI animals (-13.20g/kg DM). Low RFI animals tended to increased (P = 0.065) ribeye area (REA) compared to the high/medium RFI groups, while carcass backfat thickness (BFT) decreased (P = 0.042) compared to high/medium RFI groups. Moreover, there was an increase (P < 0.001) of 0.22kg in Warner-Bratzler shear force (WBSF) and a reduction (P < 0.001) in the myofibrillar fragmentation index (MFI) in low RFI animals. Meat color parameters (lightness [L*] and yellowness [b*]) and visual marbling scores were consistent (P > 0.05) across RFI groups. In conclusion, Zebu cattle classified as efficient (low RFI) exhibited reduced DMI, which improves their feed efficiency. However, BFT and meat quality parameters such as tenderness (WBSF and MFI) and redness [a*] were compromised by low RFI phenotype, highlighting the challenge of enhancing feed efficiency and meat quality traits in Zebu cattle.

Genome-wide association analysis identify candidate genes for feed efficiency and growth traits in Wenchang chickens

BackgroundWenchang chickens are one of the most popular local chicken breeds in the Chinese chicken industry. However, the low feed efficiency is the main shortcoming of this breed. Therefore, there is a need to find a more precise breeding method to improve the feed efficiency of Wenchang chickens. In this study, we explored important candidate genes and variants for feed efficiency and growth traits through genome-wide association study (GWAS) analysis.ResultsEstimates of genomic heritability for growth and feed efficiency traits, including residual feed intake (RFI) of 0.05, average daily food intake (ADFI) of 0.21, average daily weight gain (ADG) of 0.24, body weight (BW) at 87, 95, 104, 113 days of age (BW87, BW95, BW104 and BW113) ranged from 0.30 to 0.44. Important candidate genes related to feed efficiency and growth traits were identified, such as PLCE1, LAP3, MED28, QDPR, LDB2 and SEL1L3 genes.ConclusionThe results identified important candidate genes for feed efficiency and growth traits in Wenchang chickens and provide a theoretical basis for the development of new molecular breeding technology.

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

The current broilers have been greatly optimized for weight gain and breast yield, which necessitates the provision of nutrients-dense diets for maximum potential. 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. 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. 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. 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.

Investigating relationships between the host genome, rumen microbiome, and dairy cow feed efficiency using mediation analysis with structural equation modeling

The rumen microbiome is crucial for converting feed into absorbable nutrients used for milk synthesis, and the efficiency of this process directly impacts the profitability and sustainability of the dairy industry. Recent studies have found that the rumen microbial composition explains part of the variation in feed efficiency traits, including dry matter intake, milk energy, and residual feed intake. The main goal of this study was to reveal relationships between the host genome, rumen microbiome, and dairy cow feed efficiency using structural equation models. Our specific objectives were to (i) infer the mediation effects of the rumen microbiome on feed efficiency traits, (ii) estimate the direct and total heritability of feed efficiency traits, and (iii) calculate the direct and total breeding values of feed efficiency traits. Data consisted of dry matter intake, milk energy, and residual feed intake records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. We implemented structural equation models such that the host genome directly affects the phenotype (GP → P) and the rumen microbiome (GM → P), while the microbiome affects the phenotype (M → P), partially mediating the effect of the host genome on the phenotype (G → M → P). We found that 7 to 30% of microbes within the rumen microbial community had structural coefficients different from zero. We classified these microbes into 3 groups that could have different uses in dairy farming. Microbes with heritability <0.10 but significant causal effects on feed efficiency are attractive for external interventions. On the other hand, 2 groups of microbes with heritability ≥0.10, significant causal effects, and genetic covariances and causal effects with the same or opposite sign to feed efficiency are attractive for selective breeding, improving or decreasing the trait heritability and response to selection, respectively. In general, the inclusion of the different microbes in genomic models tends to decrease the trait heritability rather than increase it, ranging from -15% to +5%, depending on the microbial group and phenotypic trait. Our findings provide more understanding to target rumen microbes that can be manipulated, either through selection or management interventions, to improve feed efficiency traits.

Assessing different cross-validation schemes for predicting novel traits using sensor data: An application to dry matter intake and residual feed intake using milk spectral data

Feed efficiency is important for economic profitability of dairy farms; however, recording daily dry matter intakes (DMI) is expensive. Our objective was to investigate the potential use of milk mid-infrared (MIR) spectral data to predict proxy phenotypes for DMI based on different cross-validation schemes. We were specifically interested in comparisons between a model that included only MIR data (Model M1), a model that incorporated different energy sink predictors, such as body weight, body weight change, and milk energy (Model M2), and an extended model that incorporated both energy sinks and MIR data (Model M3). Models M2 and M3 also included various cow level variables (stage of lactation, age at calving, parity) such that any improvement in model performance from M2 to M3, whether through a smaller root mean squared error (RMSE) or a greater squared predictive correlation (R2), could indicate a potential benefit of MIR to predict residual feed intake. The data used in our study originated from a multi-institutional project on the genetics of feed efficiency in US Holsteins. Analyses were conducted on 2 different trait definitions based on different period lengths: averaged across weeks vs. averaged across 28-d. Specifically, there were 19,942 weekly records on 1,812 cows across 46 experiments or cohorts and 3,724 28-d records on 1,700 cows across 43 different cohorts. The cross-validation analyses involved 3 different k-fold schemes. First, a 10-fold cow-independent cross-validation was conducted whereby all records from any one cow were kept together in either training or test sets. Similarly, a 10-fold experiment-independent cross-validation kept entire experiments together whereas a 4-fold herd-independent cross-validation kept entire herds together in either training or test sets. Based on cow-independent cross-validation for both weekly and 28-d DMI, adding MIR predictors to energy sinks (Models M3 vs M2) significantly (P < 10-10) reduced average RMSE to 1.59 kg and increased average R2 to 0.89. However, adding MIR to energy sinks (M3) to predict DMI either within an experiment-independent or herd-independent cross-validation scheme seemed to demonstrate no merit (P > 0.05) compared with an energy sink model (M2) for either R2 or RMSE (respectively, 0.68 and 2.55 kg for M2 in herd-independent scheme). We further noted that with broader cross-validation schemes, i.e., from cow-independent to experiment-independent to herd-independent schemes, the mean and slope bias increased. Given that proxy DMI phenotypes for cows would need to be almost entirely generated in herds having no DMI or training data of their own, herd-independent cross-validation assessments of predictive performance should be emphasized. Hence, more research on predictive algorithms suitable for broader cross-validation schemes and a more earnest effort on calibration of spectrophotometers against each other should be considered.