Genetic parameters of a random regression model for daily feed intake of performance tested French Landrace and Large White growing pigs

Daily feed intake data of 1 279 French Landrace (FL, 1 039 boars and 240 castrates) and 2 417 Large White (LW, 2 032 boars and 385 castrates) growing pigs were recorded with electronic feed dispensers in three French central testing stations from 1992–1994. Male (35 to 95 kg live body weight) or castrated (100 kg live body weight) group housed, ad libitum fed pigs were performance tested. A quadratic polynomial in days on test with fixed regressions for sex and batch, random regressions for additive genetic, pen, litter and individual permanent environmental effects was used, with two different models for the residual variance: constant in model 1 and modelled with a quadratic polynomial depending on the day on test d_m as follows in model 2: . Variance components were estimated from weekly means of daily feed intake by means of a Bayesian analysis using Gibbs sampling. Posterior means of (co)variances were calculated using 800 000 samples from four chains (200 000 each). Heritability estimates of regression coefficients were 0.30 (FL model 1), 0.21 (FL model 2), 0.14 (LW1) and 0.14 (LW2) for the intercept, 0.04 (FL1), 0.04 (FL2), 0.11 (LW1) and 0.06 (LW2) for the linear, 0.03 (FL1), 0.04 (FL2) 0.11 (LW1) and 0.06 (LW2) for the quadratic term. Heritability estimates for weekly means of daily feed intake were the lowest in week 4 (FL1: 0.11, FL2: 0.11) and week 1 (LW1: 0.09, LW2: 0.10), and the highest in week 11 (FL1: 0.25, FL2: 0.24) and week 8 (LW1: 0.19, LW2: 0.18), respectively. Genetic eigenfunctions revealed that altering the shape of the feed intake curve by selection is difficult.     

Simultaneous estimation of daily weight and feed intake curves for growing pigs by random regression

In this study, random regression models were used to estimate covariance functions between feed intake and BW in boars from the two breeds: the Norwegian Landrace and the Norwegian Duroc. In total, 1476 animals of the Norwegian Landrace breed and 1300 animals of the Norwegian Duroc breed had registrations on daily feed intake and growth from 54 to 180 days of age. Random regressions on the Legendre polynomials of age were used to describe genetic and permanent environmental curves in BW (up to the second order) and feed intake (up to the first order) for both the breeds. Heritabilities on BW increased over time for the Landrace (0.18 to 0.24), but were approximately constant for the Duroc (0.33 to 0.35). Average heritabilities for feed intake were approximately the same in both the breeds (0.09 to 0.11), and the estimates decreased over time, most pronounced in Duroc. On the basis of the current data, daily feed intake was seemingly controlled by the same genetic factors throughout the test period for Duroc; however, for Landrace, genetic correlations between test days decreased with increasing distance in time. For BW, the genetic correlations between test days were in general high, and did not go below 0.8 for any of the two breeds in this study. For both feed intake and BW, permanent environmental correlations between start and end of the test were reduced with increasing difference in days, most pronounced in Duroc. This study indicates that weight of the animal at the end of the test was more closely genetically correlated to feed intake of earlier periods compared with later periods of growth for both the breeds. This may be explained by the fact that BW is the cumulative growth of an individual, which is likely to be heavily affected by the feed intake during the most intense growth period.     

Quantitative trait loci for chemical body composition traits in pigs and their positional associations with body tissues, growth and feed intake

In this study, quantitative trait loci (QTL) for chemical and physical body composition, growth and feed intake in pigs were identified in a three-generation full-sib population, developed by crossing Pietrain sires with a commercial dam line. Phenotypic data from 315 F₂ animals were available for protein and lipid deposition measured in live animals by the deuterium dilution technique at 30-, 60-, 90-, 120- and 140-kg body weight. At 140-kg body weight, carcass characteristics were measured by the AutoFOM grading system and after dissection. Three hundred and eighty-six animals from 49 families were genotyped for 51 molecular markers covering chromosomes SSC2, SSC4, SSC8, SSC9, SSC10 and SSC14. Novel QTL for protein (lipid) content at 60-kg body weight and protein (lipid) accretion from 120 to 140 kg were detected on SSC9 near several previously detected QTL for lean and fat tissue in neck, shoulder and ham cuts. Another QTL for lipid accretion was found on SSC8, closely associated with a QTL for intramuscular fat content. QTL for daily feed intake were detected on SSC2 and SSC10. The favourable allele of a QTL for food conversion ratio (FCR) on SSC2 was associated with alleles for increased lean tissue and decreased fat tissue. Because no QTL for growth rate were found in the region, the QTL for FCR is most likely due to a change in body composition. These QTL provide insights into the genomic regulation of chemical or physical body composition and its association with feed intake, feed efficiency and growth.     

Review: divergent selection for residual feed intake in the growing pig

This review summarizes the results from the INRA (Institut National de la Recherche Agronomique) divergent selection experiment on residual feed intake (RFI) in growing Large White pigs during nine generations of selection. It discusses the remaining challenges and perspectives for the improvement of feed efficiency in growing pigs. The impacts on growing pigs raised under standard conditions and in alternative situations such as heat stress, inflammatory challenges or lactation have been studied. After nine generations of selection, the divergent selection for RFI led to highly significant (P<0.001) line differences for RFI (−165 g/day in the low RFI (LRFI) line compared with high RFI line) and daily feed intake (−270 g/day). Low responses were observed on growth rate (−12.8 g/day, P<0.05) and body composition (+0.9 mm backfat thickness, P=0.57; −2.64% lean meat content, P<0.001) with a marked response on feed conversion ratio (−0.32 kg feed/kg gain, P<0.001). Reduced ultimate pH and increased lightness of the meat (P<0.001) were observed in LRFI pigs with minor impact on the sensory quality of the meat. These changes in meat quality were associated with changes of the muscular energy metabolism. Reduced maintenance energy requirements (−10% after five generations of selection) and activity (−21% of time standing after six generations of selection) of LRFI pigs greatly contributed to the gain in energy efficiency. However, the impact of selection for RFI on the protein metabolism of the pig remains unclear. Digestibility of energy and nutrients was not affected by selection, neither for pigs fed conventional diets nor for pigs fed high-fibre diets. A significant improvement of digestive efficiency could likely be achieved by selecting pigs on fibre diets. No convincing genetic or blood biomarker has been identified for explaining the differences in RFI, suggesting that pigs have various ways to achieve an efficient use of feed. No deleterious impact of the selection on the sow reproduction performance was observed. The resource allocation theory states that low RFI may reduce the ability to cope with stressors, via the reduction of a buffer compartment dedicated to responses to stress. None of the experiments focussed on the response of pigs to stress or challenges could confirm this theory. Understanding the relationships between RFI and responses to stress and energy demanding processes, as such immunity and lactation, remains a major challenge for a better understanding of the underlying biological mechanisms of the trait and to reconcile the experimental results with the resource allocation theory.     

Analysis of feed intake and energy balance of high-yielding first lactating Holstein cows with fixed and random regression models

At the dairy research farm Karkendamm, the individual roughage intake was measured since 1 September 2005 using a computerised scale system to estimate daily energy balances as the difference between energy intake and calculated energy requirements for lactation and maintenance. Data of 289 heifers with observations between the 11th and 180th day of lactation over a period of 487 days were analysed. Average energy-corrected milk yield, feed intake, live weight and energy balance were 31.8kg, 20.6kg, 584 kg and 13.6 MJ NEL (net energy lactation), respectively, per day. Fixed and random regression models were used to estimate repeatabilities, correlations between cow effects and genetic parameters. The resulting genetic correlations in different lactation stages demonstrate that feed intake and energy balance at the beginning and the middle of lactation are genetically different traits. Heritability of feed intake is low with h2=0.06 during the first days after parturition and increases in the middle of lactation, whereas the energy balance shows the highest heritability with h2=0.34 in the first 30 days of lactation. Genetic correlations between energy balance and feed intake and milk yield, respectively, illustrate that energy balance depends more on feed intake than on milk yield. Genetic correlation between body condition score and energy balance decreases rapidly within the first 100 days of lactation. Hence, to avoid negative effects on health and reproduction as consequences of strong energy deficits at the beginning of lactation, the energy balance itself should be measured and used as a selection criterion in this lactation stage. Since the number of animals is rather small for a genetic analysis, the genetic parameters have to be evaluated on a more comprehensive dataset.     

Divergent selection for residual feed intake in group-housed growing pigs: characteristics of physical and behavioural activity according to line and sex

The aim of the study was to assess the impact of selection for residual feed intake (RFI) on the behavioural activity of lines divergently selected for RFI during seven generations. In all, six successive batches from the seventh generation of selection were raised in collective pens equipped with a single-place electronic feeder (SEF) from 10 weeks of age to 100 kg BW. Each batch included four groups of 12 pigs: high RFI (RFI⁺) castrated males, RFI⁺ females, low RFI (RFI⁻) castrated males, RFI⁻ females. At 17 weeks of age, health criteria were evaluated using a gradient scale for increased severity of lameness, body lesions, bursae and tail biting. Individual behavioural activities were recorded by 24-h video tape on the day after health evaluation. The investigative motivation towards unfamiliar objects was quantified at 18 weeks of age. The daily individual feeding patterns were computed from SEF records during the 4 weeks surrounding 12, 17 and 22 weeks of age. All pigs spent significantly most of their time lying in diurnal (80% of total scan) and nocturnal (>89%) periods. The RFI⁻ pigs showed a lower proportion of health problems (P<0.01) than RFI⁺ pigs. The RFI⁻ pigs used the SEF less than the RFI⁺ pigs, in diurnal (5.3% v. 6.4% of video scans, P<0.05) and nocturnal periods (3.6% v. 4.5% of video scans, P<0.05). This was confirmed by a significantly lower daily number and duration of visits to the SEF computed from the SEF data. The feeding activity measured from the video recording was significantly correlated (R>0.34; P<0.05) with feeding patterns computed from the SEF. The RFI⁻ pigs spent less time standing over the 24-h period (9.7% v. 12.2% of scans, i.e. 35 min/day, P<0.05). In terms of energy costs, this amounted to 14% of the line difference in terms of daily metabolizable energy intake. The castrated males used the SEF more than females, especially at night (4.7% v. 3.4% of total scans, P<0.05), whereas females displayed greater investigation of their environment (7.7±0.3% v. 6.6±0.2% of total scans, P<0.05) and the novel objects (10.7% v. 4.9% of total scans, P<0.05). In conclusion, the lower physical activity associated with reduced energy expenditure in RFI⁻ pigs compared with RFI⁺ pigs contributed significantly to their improved efficiency and was not related to worsened health scores.     

Genomic dissection and prediction of feed intake and residual feed intake traits using a longitudinal model in F2 chickens

Feed efficiency traits (FETs) are important economic indicators in poultry production. Because feed intake (FI) is a time-dependent variable, longitudinal models can provide insights into the genetic basis of FET variation over time. It is expected that the application of longitudinal models as part of genome-wide association (GWA) and genomic selection (i.e. genome-wide selection (GS)) studies will lead to an increase in accuracy of selection. Thus, the objectives of this study were to evaluate the accuracy of estimated breeding values (EBVs) based on pedigree as well as high-density single nucleotide polymorphism (SNP) genotypes, and to conduct a GWA study on longitudinal FI and residual feed intake (RFI) in a total of 312 chickens with phenotype and genotype in the F₂ population. The GWA and GS studies reported in this paper were conducted using β-spline random regression models for FI and RFI traits in a chicken F₂ population, with FI and BW recorded for each bird weekly between 2 and 10 weeks of age. A single SNP regression approach was used on spline coefficients for weekly FI and RFI traits, with results showing that two significant SNPs for FI occur in the synuclein (SNCAIP) gene. Results also show that these regions are significantly associated with the spline coefficients (q₂) for 5- and 6-week-old birds, while GWA study results showed no SNP association with RFI in F₂ chickens. Estimated breeding value predictions obtained using a pedigree-based best linear unbiased prediction (ABLUP) model were then compared with predictions based on genomic best linear unbiased prediction (GBLUP). The accuracy was measured as correlation between genomic EBV and EBV with the phenotypic value corrected for fixed effects divided by the square root of heritability. The regression of observed on predicted values was used to estimate bias of methods. Results show that prediction accuracies using GBLUP and ABLUP for the FI measured from 2^nd to 10^th week were between 0.06 and 0.46 and 0.03 and 0.37, respectively. These results demonstrate that genomic methods are able to increase the accuracy of predicted breeding values at later ages on the basis of both traits, and indicate that use of a longitudinal model can improve selection accuracy for the trajectory of traits in F₂ chickens when compared with conventional methods.     

Genetic parameters of a random regression model for daily feed intake of performance tested French Landrace and Large White growing pigs

Some misprints appeared on page 640, in Table II and in the last paragraph of Section 2.2 (line 9). One should read: "3.075 × 10^-2", "-4.900 × 10^-4", "1.440 × 10^-5", "2.500 × 10^-9" and "1.0 × 10^-8", respectively (there are not exponential functions).     

Meta-analysis of feed intake and growth responses of growing pigs after a sanitary challenge

Sanitary challenges negatively affect feed intake and growth, leading to a negative impact on animal well-being and economic losses. The aim of this study was to carry out a meta-analysis to quantify the dynamic feed intake and growth responses of growing pigs after a sanitary challenge. A database was constructed using 122 published experiments reporting the average daily feed intake (ADFI) and the average daily gain (ADG) of pigs subjected to one of six sanitary challenges: digestive bacterial infections, poor housing conditions, lipopolysaccharide (LPS) challenges, mycotoxicoses, parasitic infections and respiratory diseases. The responses to experimental challenges were calculated relative to that of a control group. Statistical analyses were carried out for each challenge to quantify the mean and the dynamic responses in feed intake and growth and to identify the basis of the reduction in growth (i.e. reduction in feed intake or reduction in feed efficiency related to changes in maintenance requirements). All challenges resulted in a reduction in ADFI and ADG, with the strongest responses for mycotoxicoses, respiratory diseases and digestive bacterial infections (8% to 23% reduction in ADFI and 16% to 29% reduction in ADG). The reduction in ADG was linearly related to the reduction in ADFI for digestive bacterial infections, LPS challenge, parasitic infections and respiratory diseases. For poor housing conditions and mycotoxicoses, the relationship was curvilinear. A 10% reduction in ADFI resulted in a reduction in ADG varying from 10% for mycotoxicoses to 43% for digestive bacterial infections. More than 70% of the reduction in ADG could be explained by the reduction in ADFI for mycotoxicoses, LPS challenge and respiratory diseases. For challenges associated with the gastrointestinal tract, a large part of the reduction in ADG was due to an increase in maintenance requirements, suggesting digestive and metabolic changes. A dynamic pattern in the reduction in feed intake and growth rate could be identified for digestive bacterial infections, mycotoxicoses and respiratory diseases. For digestive bacterial infections and mycotoxicoses, pigs did not fully recover from the challenge during the experimental period. The results of this study can be used to quantify the effects of a sanitary challenge in growth models of pigs.     

Grazed grass herbage intake and performance of beef heifers with predetermined phenotypic residual feed intake classification

Data were collected on 85 Simmental and Simmental × Holstein–Friesian heifers. During the indoor winter period, they were offered grass silage ad libitum and 2 kg of concentrate daily, and individual dry matter intake (DMI) and growth was recorded over 84 days. Individual grass herbage DMI was determined at pasture over a 6-day period, using the n-alkane technique. Body condition score, skeletal measurements, ultrasonic fat and muscle depth, visual muscularity score, total tract digestibility, blood hormones, metabolites and haematology variables and activity behaviour were measured for all heifers. Phenotypic residual feed intake (RFI) was calculated for each animal as the difference between actual DMI and expected DMI during the indoor winter period. Expected DMI was calculated for each animal by regressing average daily DMI on mid-test live weight (LW)^0.75 and average daily gain (ADG) over an 84-day period. Standard deviations above and below the mean were used to group animals into high (>0.5 s.d.), medium (±0.5 s.d.) and low (<0.5 s.d.) RFI. Overall mean (s.d.) values for DMI (kg/day), ADG (kg), feed conversion ratio (FCR) kg DMI/kg ADG and RFI (kg dry matter/day) were 5.82 (0.73), 0.53 (0.18), 12.24 (4.60), 0.00 (0.43), respectively, during the RFI measurement period. Mean DMI (kg/day) and ADG (kg) during the grazing season was 9.77 (1.77) and 0.77 (0.14), respectively. The RFI groups did not differ (P > 0.05) in LW, ADG or FCR at any stage of measurement. RFI was positively correlated (r = 0.59; P < 0.001) with DMI during the RFI measurement period but not with grazed grass herbage DMI (r = 0.06; P = 0.57). Low RFI heifers had 0.07 greater (P < 0.05) concentration of plasma creatinine than high RFI heifers and, during the grazed herbage intake period, spent less time standing and more time lying (P < 0.05) than high RFI heifers. However, low and high RFI groups did not differ (P > 0.05) in ultrasonic backfat thickness or muscle depth, visual muscle scores, skeletal size, total tract digestibility or blood hormone and haematology variables at any stage of the experiment. Despite a sizeable difference in intake of grass silage between low and high RFI heifers during the indoor winter period, there were no detectable differences between RFI groupings for any economically important performance traits measured when animals were offered ensiled or grazed grass herbage.     

Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake

Residual feed intake (RFI), defined as the difference between observed and expected feed intake based on growth and backfat, has been used to investigate genetic variation in feed efficiency in cattle, poultry and pigs. However, little is known about the biological basis of differences in RFI in pigs. To this end, the objective of this study was to evaluate the fifth generation of a line of pigs selected for reduced RFI against a randomly selected Control line for performance, carcass and chemical carcass composition and overall efficiency. Here, emphasis was on the early grower phase. A total of 100 barrows, 50 from each line, were paired by age and weight (22.6 ± 3.9 kg) and randomly assigned to one of four feeding treatments in 11 replicates: ad libitum (Ad), 75% of Ad (Ad75), 55% of Ad (Ad55) and weight stasis (WS), which involved weekly adjustments in intake to keep body weight (BW) constant for each pig. Pigs were individually penned (group housing was used for selection) and were on treatment for 6 weeks. Initial BW did not significantly differ between the lines (P > 0.17). Under Ad feeding, the low RFI pigs consumed 8% less feed compared with Control line pigs (P < 0.06), had less carcass fat (P < 0.05), but with no significant difference in growth rate (P > 0.85). Under restricted feeding, low RFI pigs under the Ad75 treatment had a greater rate of gain while consuming the same amount of feed as Control pigs. Despite the greater gain, no significant line differences in carcass composition or carcass traits were observed. For the WS treatment, low RFI pigs had similar BW (P > 0.37) with no significant difference in feed consumption (P > 0.32). Overall, selection for reduced RFI has decreased feed intake, with limited differences in growth rate but reduced carcass fat, as seen under Ad feeding. Collectively, results indicate that the effects of selection for low RFI are evident during the early grower stage, which allows for greater savings to the producer.     

Foraging behaviour,nutrient intake from pasture and performance of free-range growing pigs in relation to feed CP level in two organic cropping systems

In organic pig production one of the major challenges is to be able to fulfil amino acid requirements based on organic and locally grown protein feed crops. The pig is an opportunistic omnivore with a unique capacity for foraging above and below the soil surface. It is hypothesized that direct foraging in the range area can pose an important contribution in terms of fulfilling nutrient requirements of growing pigs. Foraging activity, lucerne nutrient intake and pig performance were investigated in 36 growing pigs, foraging on lucerne or grass and fed either a standard organic pelleted feed mixture (HP: high protein) or a grain mixture containing 48% less CP (LP: low protein) compared with the high protein feed mixture, from an average live weight of 58 kg to 90 kg in a complete block design in three replicates. The pigs were fed 80% of energy recommendations and had access to 4 m² of pasture/pig per day during the 40 days experimental period from September to October 2013. Behavioural observations were carried out 12 times over the entire experimental period. For both crops, LP pigs rooted significantly more compared with HP pigs but the effect of CP level was more pronounced in grass (44% v. 19% of all observations) compared with lucerne (28% v. 16% of all observations). Feed protein level turned out not to have any significant effect on grazing behaviour but pigs foraging on lucerne grazed significantly more than pigs foraging on grass (10% v. 4% of all observations). Daily weight gain and feed conversion ratio were significantly affected by feed protein and forage crop interactions. Compared to HP pigs, LP treated pigs had 33% lower daily weight gain (589 v. 878 g) and 31% poorer feed conversion ratio (3.75 v. 2.59 kg feed/kg weight gain) in grass paddocks, whereas in lucerne paddocks LP pigs only had 18% lower daily weight gain (741 v. 900 g) and a 14% poorer feed conversion ratio (2.95 v. 2.54 kg feed/kg weight gain) compared with HP pigs. LP pigs foraging on lucerne used 169 g less concentrate CP/kg weight gain, compared with HP pigs, indicating the nitrogen efficiency of the system. The results indicate that direct foraging of lucerne may be a valuable strategy in terms of accommodating CP and lysine requirements of organic growing pigs.     

Effect of straw amount on feed intake and weight gain in growing pigs housed in pens with partly slatted floor

The provision of straw to pigs kept in conventional pens with concrete floor improves animal welfare, but the effects of straw on pigs’ performance are unclear. In two steps, we investigated the relationship between amount of straw provided to pigs and measures of performance in a set-up maintaining constant space allowance and controlled room temperature. From approximately 30- to 85-kg BW, pigs were housed in groups of 18 in pens (5.48 m × 2.48 m) with concrete floor (1/3 solid, 1/3 drained and 1/3 slatted). The pens were cleaned manually twice a week, and the designated amount of fresh uncut wheat straw was provided daily onto the solid part of the floor. In the first step, 48 pens were assigned to 10-, 500- or 1000-g straw per pig per day, while in the second step, 90 pens were assigned to 10-, 80-, 150-, 220-, 290-, 360-, 430- or 500-g straw per pig per day. Pigs were weighed at the start of the experimental period at approximately 30 kg and again at approximately 85-kg BW. The average daily gain increased 8.1 g (SEM 17) for every extra 100-g straw added daily (P < 0.001) resulting in 40 g higher average daily gain with 500 compared to 10-g straw per pig per day. The feed conversion ratio was not affected by the amount of straw provided, as the feed intake tended to be higher with increasing amounts of straw. Thus, between 10 and 500 g, the more straw provided, the higher the daily weight gain. As the nutritional value of straw is considered minimal, this result is likely due to improved gut health from the increasing amounts of straw ingested and increased feed intake due to increased stimulation of exploratory behaviour with increasing amounts of straw available, or a combination of these. The observed tendency for a higher feed intake supports this suggestion, but studies are needed to establish the impact of these two contributing factors.     

A new mathematical model for combining growth and energy intake in animals: The case of the growing pig

A simultaneous model for analysis of net energy intake and growth curves is presented, viewing the animal's responses as a two dimensional outcome. The model is derived from four assumptions: (1) the intake is a quadratic function of metabolic weight; (2) the rate of body energy accretion represents the difference between intake and maintenance; (3) the relationship between body weight and body energy is allometric and (4) animal intrinsic variability affects the outcomes so the intake and growth trajectories are realizations of a stochastic process. Data on cumulated net energy intake and body weight measurements registered from weaning to maturity were available for 13 pigs. The model was fitted separately to 13 datasets. Furthermore, slaughter data obtained from 170 littermates was available for validation of the model. The parameters of the model were estimated by maximum likelihood within a stochastic state space model framework where a transform-both-sides approach was adopted to obtain constant variance. A suitable autocorrelation structure was generated by the stochastic process formulation. The pigs’ capacity for intake and growth were quantified by eight parameters: body weight at maximum rate of intake (149-281 kg); maximum rate of intake (25.7-35.7 MJ/day); metabolic body size exponent (fixed: 0.75); the daily maintenance requirement per kg metabolic body size (0.232-0.303 MJ/(day×kg^0.75)); reciprocal scaled energy density ; a dimensional exponent, θ₆ (0.730-0.867); coefficient for animal intrinsic variability in intake (0.120-0.248 MJ^0.5) and coefficient for animal intrinsic variability in growth (0.029-0.065 kg^0.5). Model parameter values for maintenance requirements and body energy gains were in good agreement with those obtained from slaughter data. In conclusion, the model provides biologically relevant parameter values, which cannot be derived by traditional analysis of growth and energy intake data.