Selection For Residual Feed Intake Research Articles

Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

BackgroundResidual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency.Methodology/Principal findingsWhole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping.Conclusions/significanceImportant genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.

Divergent genetic selection for residual feed intake impacts mitochondria reactive oxygen species production in pigs1

The objective of this study was to determine the extent to which genetic selection for residual feed intake (RFI) impacts electron leakage and reactive oxygen species (ROS) production in mitochondria from muscle and liver tissue. Understanding how genetic selection for RFI impacts animal physiology and growth efficiency is of the utmost importance as the world population increases. Production efficiency is tied directly to energy use. Mitochondria were used in this study because they produce 90% of the ATP in the body and use a large majority of dietary energy. Mitochondria were isolated from both muscle and liver tissue from pigs genetically selected for RFI (n = 8 per RFI line; 34 ± 4 kg). A 2,7-dichlorofluorscein diacetate assay was used to detect differences in hydrogen peroxide production between the more efficient low RFI line and the less efficient high RFI line. Our hypothesis was that greater efficiency would be linked to less ROS production from the mitochondria. There was less ROS production in mitochondria from the white portion of the semitendinosus in the low RFI line compared with the high RFI line, when both NADH and Flavin Adenine Dinucleotide (FADH2) energy substrates were used (glutamate and succinate, respectively). Additionally, mitochondria from the red portion of the semitendinosus in the low RFI line had less ROS production when succinate was used as an energy substrate (P < 0.05). A positive correlation was observed between RFI and ROS in mitochondria from the LM. These data indicate genetic selection for RFI may influence mitochondrial ROS production and efficiency of pork production.

Selection for residual feed intake alters the mitochondria protein profile in pigs

Residual feed intake (RFI) is a production efficiency measurement used to account for the growth performance of an individual animal. Less efficient animals have greater levels of oxidative stress. A major source of in vivo oxidative stress is the mitochondria. In this study the protein profile of mitochondria was investigated to determine differences between pigs genetically selected for high and low RFI (less and more efficient, respectively). Mitochondria were isolated from the red and white portions of the semitendinosus muscle (STR and STW respectively), from the longissimus dorsi (LD) muscle, and the liver from pigs (n=24, 12 per line) genetically selected for low or high RFI. Mitochondrial protein differences between lines were determined using 2-D DIGE, and spots were identified using electrospray ionization mass spectroscopy. Heat shock protein (HSP) 60 and HSP70, which have been linked to anti-apoptotic pathways in the mitochondria, were increased in the low RFI line. Endoplasmic reticulum oxidase-1 α (ERO1α) was decreased in LD mitochondria from the low RFI line. The protein profile of mitochondria from the more efficient pigs indicates an increase in anti-oxidant defenses and potential modifications of metabolic pathways leading to oxidative stress, metabolism, and cellular repair. Observed shifts in the mitochondria protein profile indicate that pigs divergently selected for low residual feed intake (RFI) may be less prone to muscular oxidative stress, and the liver may have a greater metabolic capacity when compared to their less efficient high RFI contemporaries. Both oxidative stress and metabolic capacity are key areas of interest with regard to increasing the efficiency of pork production. Through the use of divergent selection for RFI and investigation of protein profile and other biological differences between RFI lines of pigs, it is possible to determine biological pathways that affect efficiency of food production.

Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production

Genetic selection for residual feed intake (RFI) is an indirect approach for reducing enteric methane (CH4) emissions in beef and dairy cattle. RFI is moderately heritable (0.26 to 0.43), moderately repeatable across diets (0.33 to 0.67) and independent of body size and production, and when adjusted for off-test ultrasound backfat thickness (RFIfat) is also independent of body fatness in growing animals. It is highly dependent on accurate measurement of individual animal feed intake. Within-animal repeatability of feed intake is moderate (0.29 to 0.49) with distinctive diurnal patterns associated with cattle type, diet and genotype, necessitating the recording of feed intake for at least 35 days. In addition, direct measurement of enteric CH4 production will likely be more variable and expensive than measuring feed intake and if conducted should be expressed as CH4 production (g/animal per day) adjusted for body size, growth, body composition and dry matter intake (DMI) or as residual CH4 production. A further disadvantage of a direct CH4 phenotype is that the relationships of enteric CH4 production on other economically important traits are largely unknown. Selection for low RFIfat (efficient, −RFIfat) will result in cattle that consume less dry matter (DMI) and have an improved feed conversion ratio (FCR) compared with high RFIfat cattle (inefficient; +RFIfat). Few antagonistic effects have been reported for the relationships of RFIfat on carcass and meat quality, fertility, cow lifetime productivity and adaptability to stress or extensive grazing conditions. Low RFIfat cattle also produce 15% to 25% less enteric CH4 than +RFIfat cattle, since DMI is positively related to enteric methane (CH4) production. In addition, lower DMI and feeding duration and frequency, and a different rumen bacterial profile that improves rumen fermentation in −RFIfat cattle may favor a 1% to 2% improvement in dry matter and CP digestibility compared with +RFIfat cattle. Rate of genetic change using this approach is expected to improve feed efficiency and reduce enteric CH4 emissions from cattle by 0.75% to 1.0% per year at equal levels of body size, growth and body fatness compared with cattle not selected for RFIfat.

Effect of immune system stimulation and divergent selection for residual feed intake on digestive capacity of the small intestine in growing pigs1

Little is known of the consequences of divergent selection for residual feed intake (RFI) on intestinal digestion capacity, particularly during immune system stimulation (ISS). Our objective was to evaluate the impact of ISS and divergent selection for RFI on apparent ileal digestibility (AID) and apparent fecal digestibility (AFD) of nutrients and intestinal nutrient active transport and barrier function. Twenty-eight gilts (63 ± 4 kg BW) from low RFI (LRFI; n = 14) and high RFI (HRFI; n = 14) Yorkshire lines were randomly selected from the Iowa State University RFI herd. Following adaptation, 8 pigs in each line were injected intramuscularly and every 48 h for 7 d with increasing amounts of Escherichia coli lipopolysaccharide (ISS+). Remaining pigs were injected with saline (ISS-). Pigs were then euthanized and ileal digesta was collected for measuring AID of nutrients. Fecal samples were collected on a daily basis and pooled for measuring AFD of nutrients. A segment of ileum was used to measure nutrient transport and transepithelial resistance (TER) and/or barrier integrity by Ussing chambers. No effects of line or its interaction with ISS on AID of CP (N × 6.25) and OM, TER, and active nutrients transport were observed. However, ISS decreased (P < 0.05) and tended to (P < 0.1) decrease AID of CP and OM, respectively. Decrease in AFD of CP as result of ISS was greater in the LRFI line compared to the HRFI line (P < 0.05). Relative to ISS-, active glucose and P transport was greater in ISS+ pigs (P < 0.05). Genetic selection for LRFI increases the AFD but has no effect on AID of nutrients. It also reduces the total tract digestive capacity of growing pigs during ISS. Immune system stimulation affects both AID and AFD of dietary CP.

JOINT ALPHARMA-BEEF SPECIES SYMPOSIUM: Interactions of feed efficiency with beef heifer reproductive development1

The influence of nutrition on puberty in beef heifers is complex and under neuroendocrine control. The stores of body fat in mammals are a determinant of the onset and maintenance of puberty. Body fat stores are greater in heifers with greater residual feed intake than in their more efficient herdmates. A 1 unit increase in residual feed intake resulted in a reduction of 7.54 d in age at puberty in Bos taurus beef heifers. However, Bos indicus-influenced heifers, which reach puberty at older ages, were not found to have sexual maturity influenced by selection for residual feed intake. The strong influence of body fat stores on return to estrus after calving does indicate that selection for leaner beef heifers could affect reproductive performance relative to puberty and postpartum rebreeding of first calf heifers. The influence of intermediary metabolism, through signals at the central nervous system, regulates the GnRH pulse generator, thereby influencing pituitary and ovarian function culminating with puberty and return to ovarian cyclicity after calving. Tropically adapted cattle (i.e., Santa Gertrudis and Brahman) selected for low residual feed intake had a lesser response of insulin to a glucose challenge than their less efficient herdmates. These studies indicate the possibility that animals with differing residual feed intake (efficiencies) may have differing intermediary metabolism and, therefore, differing rates of reaching puberty. Selection for low residual feed intake results in selection of leaner heifers that reach puberty at older ages. These leaner heifers calve later in their first and subsequent calving seasons. Selection for residual average daily gain has no negative influence on age at puberty or calving interval. Selection for residual ADG has a negative influence on age at first calving but not calving interval. There may be no acceptable method to improve feed efficiency without harming reproductive efficiency.

Consequences of divergent selection for residual feed intake in pigs on muscle energy metabolism and meat quality

Selection to decrease Residual Feed Intake (RFI) is a relevant way to improve feed efficiency in growing pigs. However, RFI criterion is correlated with body composition and muscle characteristics. Present study evaluated adaptive responses to divergent selection on RFI on muscle metabolism and homeostasis through AMP-activated protein kinase pathway. Consequences on technological and sensory meat quality were also analyzed in two lines of Large White pigs after six generations of divergent selection on RFI.RFI− pigs (n=60) exhibited similar growth rate but lower feed intake and conversion ratio, and were leaner than RFI+ pigs (n=57). Despite higher glycogen content, metabolic enzyme capacities involved in glycolytic, fatty acid oxidation pathway and energy balance were reduced in the Longissimus muscle of the RFI− pigs. Reduced muscle homeostasis in the RFI− line influenced post-mortem metabolism and impaired technological quality traits of loin and ham but had only slight effects on meat eating quality.

Impact of selection for residual feed intake on breeding soundness and reproductive performance of bulls on pasture-based multisire mating1

There is concern in the beef industry that selecting bulls for feed efficiency based on residual feed intake (RFI) may have a negative impact on bull reproductive performance and fertility. Here we investigated the impact of selection of bulls for low RFI on breeding soundness evaluation (BSE), reproductive performance, and fertility of bulls under natural service in multisire mating groups on pasture. Of the 412 RFI-tested bulls available, 98 (23.8%) were culled for performance, type, temperament, or other reasons, and 88 (21.4%) were culled for failing BSE, for an overall cull rate of 45.1%. From among the 314 bulls subjected to BSE, 32 (10.2%), 20 (6.4%), and 36 (11.4%) were culled for poor feet and legs, scrotal circumference, and semen quality, respectively. The BSE traits were not different (P > 0.10) between bulls categorized as either inefficient (+RFI) or efficient (-RFI), but the proportion of bulls that failed to meet the 60% minimum sperm motility requirement tended (P = 0.07) to be greater in the -RFI group than in the +RFI group (10.2% vs. 4.4%, respectively). In a subpopulation of 115 bulls, individual progressive sperm motility was greater (P < 0.05) in +RFI (85%) than -RFI (80%) bulls. A multisire natural mating experiment was conducted during 2 consecutive breeding seasons (2006 to 2007 and 2007 to 2008) using 18 +RFI and 18 -RFI bulls. The overall calving rate (calves born/cows exposed) was 72.9%. Mean number of progeny per sire was significantly greater (P < 0.01) in -RFI bulls (18.3) than in +RFI bulls (11.8). Selection for feed efficiency based on RFI appears to have no detrimental impact on reproductive performance and fertility in beef bulls bred in multisire groups on pasture. However, the decreased sperm motility and the greater number of progeny per sire associated with -RFI status need further investigation.

Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers

Feed makes up a large proportion of variable costs in dairying. For this reason, selection for traits associated with feed conversion efficiency should lead to greater profitability of dairying. Residual feed intake (RFI) is the difference between actual and predicted feed intakes and is a useful selection criterion for greater feed efficiency. However, measuring individual feed intakes on a large scale is prohibitively expensive. A panel of DNA markers explaining genetic variation in this trait would enable cost-effective genomic selection for this trait. With the aim of enabling genomic selection for RFI, we used data from almost 2,000 heifers measured for growth rate and feed intake in Australia (AU) and New Zealand (NZ) genotyped for 625,000 single nucleotide polymorphism (SNP) markers. Substantial variation in RFI and 250-d body weight (BW250) was demonstrated. Heritabilities of RFI and BW250 estimated using genomic relationships among the heifers were 0.22 and 0.28 in AU heifers and 0.38 and 0.44 in NZ heifers, respectively. Genomic breeding values for RFI and BW250 were derived using genomic BLUP and 2 Bayesian methods (BayesA, BayesMulti). The accuracies of genomic breeding values for RFI were evaluated using cross-validation. When 624,930 SNP were used to derive the prediction equation, the accuracies averaged 0.37 and 0.31 for RFI in AU and NZ validation data sets, respectively, and 0.40 and 0.25 for BW250 in AU and NZ, respectively. The greatest advantage of using the full 624,930 SNP over a reduced panel of 36,673 SNP (the widely used BovineSNP50 array) was when the reference population included only animals from either the AU or the NZ experiment. Finally, the Bayesian methods were also used for quantitative trait loci detection. On chromosome 14 at around 25 Mb, several SNP closest to PLAG1 (a gene believed to affect stature in humans and cattle) had an effect on BW250 in both AU and NZ populations. In addition, 8 SNP with large effects on RFI were located on chromosome 14 at around 35.7 Mb. These SNP may be associated with the gene NCOA2, which has a role in controlling energy metabolism.

Using genes differentially expressed in bulls to classify steers divergently selected for high and low residual feed intake

Feed efficiency is an economically important trait in livestock and residual feed intake (RFI) is a commonly used measure of the trait in beef cattle. Residual feed intake is the difference between the actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. It is a heritable trait, and efficient animals have lower RFI values. Several genes have been identified as being differentially expressed in the liver of Angus bulls that have been divergently selected for RFI. The objective of this study was to use genes that are differentially expressed in bulls to classify Angus steers from the same divergent RFI selection lines. Liver samples were collected at slaughter from 40 high RFI and 40 low RFI steers that were ~23 months old, and had just completed a 251-day feedlot feeding period. RNA samples from the livers were assayed by quantitative real-time PCR for 14 genes, which have been identified previously in bulls. Steers were not measured for RFI, hence the estimated breeding values (EBV) for RFI of their parents were used to calculate their mid-parent (average of the two parents) RFI-EBV. Correlation and discriminant analyses were conducted on the normalised quantitative real-time PCR data from the steers. Discriminant analysis was also conducted on the bull data for comparison. In the steers, 8 out of the 14 genes were significantly (P &lt; 0.05) correlated with RFI-EBV. Two genes from the glutathione S-transferase mu family (GSTM1 and GSTM2) and the S100 calcium-binding protein A10 (S100A10) had the highest correlations with RFI-EBV, with correlation coefficients of 0.59, 0.44 and 0.36, respectively. Based on the 14 expressed genes, 84% of the steers and 98% of the bulls were correctly classified into their respective RFI selection lines. The results of this study indicate that a high proportion of the genes that were differentially expressed in the original study with bulls were also differentially expressed in this study with steers. The high accuracy in classification obtained in this study shows that the transcriptional approach to the study of the biological processes involved in variation in RFI has great potential for identification of candidate genes.

Correlated responses in sow appetite, residual feed intake, body composition, and reproduction after divergent selection for residual feed intake in the growing pig1

Residual feed intake (RFI) has been explored as an alternative selection criterion to feed conversion ratio to capture the fraction of feed intake not explained by expected production and maintenance requirements. Selection experiments have found that low RFI in the growing pig is genetically correlated with reduced fatness and feed intake. Selection for feed conversion ratio also reduces sow appetite and fatness, which, together with increased prolificacy, has been seen as a hindrance for sow lifetime performance. The aims of our study were to derive equations for sow RFI during lactation (SRFI) and to evaluate the effect of selection for RFI during growth on sow traits during lactation. Data were obtained on 2 divergent lines selected for 7 generations for low and high RFI during growth in purebred Large Whites. The RFI was measured on candidates for selection (1,065 pigs), and sow performance data were available for 480 sows having from 1 to 3 parities (1,071 parities). Traits measured were sow daily feed intake (SDFI); sow BW and body composition before farrowing and at weaning (28.4 ± 1.7d); number of piglets born total, born alive, and surviving at weaning; and litter weight, average piglet BW, and within-litter SD of piglet BW at birth, 21 d of age (when creep feeding was available), and weaning. Sow RFI was defined as the difference between observed SDFI and SDFI predicted for sow maintenance and production. Daily production requirements were quantified by litter size and daily litter BW gain as well as daily changes in sow body reserves. The SRFI represented 24% of the phenotypic variability of SDFI. Heritability estimates for RFI and SRFI were both 0.14. The genetic correlation between RFI and SRFI was 0.29 ± 0.23. Genetic correlations of RFI with sow traits were low to moderate, consistent with responses to selection; selection for low RFI during growth reduced SDFI and increased number of piglets and litter growth, but also increased mobilization of body reserves. No effect on rebreeding performance was found. Metabolic changes previously observed during growth in response to selection might explain part of the better efficiency of the low-RFI sows, decreasing basal metabolism and favoring rapid allocation of resources to lactation. We propose to consider SRFI as an alternative to SDFI to select for efficient sows with reduced input demands during lactation.

Bayesian analysis of the effect of selection for residual feed intake on growth and feed intake curves in Yorkshire swine1

Gompertz growth functions were fitted to longitudinal measurements of daily feed intake (DFI) and BW of 586 boars and 495 gilts from a selection experiment in Yorkshire pigs for residual feed intake (RFI). The selection experiment consists of a line selected for low residual feed intake (LRFI) for 5 generations and a randomly selected control line (CTRL). The objectives of this study were to use Bayesian methods to estimate genetic parameters of the Gompertz curve parameters for DFI and BW, to evaluate the effect of selection for reduced RFI on the Gompertz parameters and shape of curves for DFI and BW, and to develop methodology for quantifying genetic variation at the level of the original phenotypes for DFI and BW based on the Bayesian analysis of the nonlinear model. Separate analyses were done for boars and gilts and for BW and DFI. A hierarchical model was specified in 2 levels: in the first level, the Gompertz function was modeled for each pig, and at the second level, a 3-trait linear mixed model was fitted to the 3 Gompertz parameters (asymptotic value, inflection point, and decay parameter), with fixed effects of line by generation and random effects of additive genetic and environmental effects. Bayesian methods were used to combine the 2 levels of modeling. A total of 30,000 random samples of the posterior distributions after convergence of Markov chains were used for inference. Posterior means of heritability within the first level of the model for the asymptotic value, inflection point, and decay parameter for DFI were 0.74, 0.66, and 0.82 for boars and 0.79, 0.70, and 0.57 for gilts; corresponding estimates for BW were 0.64, 0.58, and 0.60 for boars and 0.46, 0.35, and 0.33 for gilts. For DFI, LRFI boars had a reduced mature DFI (2.91 vs. 3.20 kg/d) and an earlier inflection point (85 vs. 95 d) compared with CTRL boars. For BW, LRFI boars had a lighter mature BW (279 vs. 317 kg), an earlier inflection point (184 vs. 198 d), and a decreased decay parameter (127 vs. 134 d) compared with CTRL boars. In contrast, LRFI gilts had a later inflection point (225 vs. 200 d) and a greater decay parameter (172 vs. 143 d) than CTRL gilts for BW. The other Gompertz curve parameters for DFI and BW for boars and gilts were considered not different between lines, with posterior probabilities of the line differences being greater than zero ranging from 0.1 to 0.9.

Variation in residual feed intake in Holstein-Friesian dairy heifers in southern Australia

Feed conversion efficiency of dairy cattle is an important component of the profitability of dairying, given that the cost of feed accounts for much of total farm expenses. Residual feed intake (RFI) is a useful measure of feed conversion efficiency, as it can be used to compare individuals with the same or differing levels of production during the period of measurement. If genetic variation exists in RFI among dairy cattle, selection for lower RFI could improve profitability. In this experiment, RFI was defined as the difference between an animal's actual feed intake and its expected feed intake, which was determined by regression of dry matter (DM) intake against mean body weight (BW) and growth rate. Nine hundred and three Holstein-Friesian heifer calves, aged between 5 and 7 mo, were measured for RFI in 3 cohorts of approximately 300 animals. Calves were housed under feedlot style conditions in groups of 15 to 20 for 85 to 95 d and had ad libitum access to a cubed alfalfa hay. Intakes of individual animals were recorded via an electronic feed recording system and BW gain was determined by weighing animals once or twice weekly, over a period of 60 to 70 d. Calves had DM intake (mean ± SD) of 8.3±1.37kg of DM/d over the measurement period with BW gains of 1.1±0.17kg/d. In terms of converting feed energy for maintenance and growth, the 10% most efficient calves (lowest RFI) ate 1.7kg of DM less each day than the 10% least efficient calves (highest RFI) for the same rate of growth. Low-RFI heifers also had a significantly lower rate of intake (g/min) than high-RFI heifers. The heritability estimate of RFI (mean ± SE) was 0.27 (±0.12). These results indicate that substantial genetic variation in RFI exists, and that the magnitude of this variation is large enough to enable this trait to be considered as a candidate trait for future dairy breeding goals. A primary focus of future research should be to ensure that calves that are efficient at converting feed energy for maintenance and growth also become efficient at converting feed energy to milk. Future research will also be necessary to identify the consequences of selection for RFI on other traits (especially fertility and other fitness traits) and if any interactions exist between RFI and feeding level.

Associations of marker panel scores with feed intake and efficiency traits in beef cattle using preselected single nucleotide polymorphisms1

Because of the moderate heritability and the expense associated with collecting feed intake data, effective selection for residual feed intake would be enhanced if marker-assisted evaluation were used for accurate estimation of genetic merit. In this study, a suite of genetic markers predictive of residual feed intake, DMI, and ADG were preselected using single-marker regression analysis, and the top 100 SNP were analyzed further to provide prediction equations for the traits. The data used consisted of 728 spring-born beef steers, offspring of a cross between a composite dam line and Angus, Charolais, or University of Alberta hybrid bulls. Feed intake data were collected over a 5-yr period, with 2 groups (fall-winter and winter-spring) tested every year. Training and validation data sets were obtained by splitting the data into 2 distinct sets, by randomly splitting the data into training and testing sets based on sire family (split 1) in 5 replicates or by retaining all animals with no known pedigree relationships as the validation set (split 2). A total of 37,959 SNP were analyzed by single-marker regression, of which only the top 100 that corresponded to a P-value <0.002 were retained. The 100 SNP were then analyzed using random regression BLUP, and only SNP that were jointly significant (P < 0.05) were included in the final marker panels. The marker effects from the selected panels were used to derive the molecular breeding values, which were calculated as a weighted sum of the number of copies of the more frequent allele at each SNP locus, with the weights being the allele substitution effects. The correlation between molecular breeding value and phenotype represented the accuracy of prediction. For all traits evaluated, accuracy across breeds was low, ranging between 0.007 and 0.414. Accuracy was least in data split 2, where the validation individuals had no pedigree relationship with animals in the training data. Given the low predictive ability observed, a large number of individuals may be needed for prediction when using such an admixed population. Further, these results suggest that breed composition of the target population in which the marker panels are likely to be used should be an important consideration when developing prediction equations across breeds, especially where an admixed population is used as the training data set.

Lowering ruminant methane emissions through improved feed conversion efficiency

Improvements in feed conversion efficiency (FCE) can be applied to individual animals as well as to production from land, as in a farm system. Our focus relates mainly to food production from individual animals within any animal population where there is divergence in the efficiency that individuals use ingested feed for maintenance and production; primarily due to differences in digestion and metabolism. Intake variation from the predicted mean for individuals of a similar size and level of production in a population has been termed residual feed intake (RFI), with low values indicating an efficient animal. Efficient animals require less feed than average and can be expected to produce less CH4 and N2O per unit product than the population average at a similar level of production. Selection for this trait will lower CH4 emissions per animal, unless more animals are kept to eat the feed not required by efficient animals. There are few published evaluations of CH4 yields from animals with divergent RFI and there is little evidence that efficient animals have a different CH4 yield expressed as CH4/kg dry matter (DM) intake. Of equal or greater importance than RFI is the need to select high producing animals, as this will reduce emissions/unit of product, referred to as emissions intensity (Ei). Research should identify productive individuals that have a low RFI to minimise Ei and maintain food production. The extent to which CH4 can be reduced by selection for RFI will depend on the heritability of efficiency, dispersal of efficient animals through all populations and their resilience in a production system (i.e., robustness). The benefit of RFI to lowering greenhouse gas (GHG) emissions is its application, irrespective of farming system (i.e., confined, intensive, extensive grazing), especially because efficient animals are likely to increase farm profitability. Efficient animals are already in all herds and flocks and research must identify and remove inefficient individuals, while retaining and ensuring efficient ones are fit to purpose. However, the biggest benefits to reducing emissions and increasing production will be associated with good animal management practice (e.g., appropriate genetics, reproductive performance, longevity) with efficient animals superimposed. Good animal systems management will improve profitability, and apply to both intensive and extensive systems to increase food production and lower Ei. One dilemma for agriculturists will be the practice of feeding grains to ruminants, as gains in animal efficiency, especially in reduction of Ei, are likely to be biggest with high energy density rations, but feeding grain to ruminants may become an unsustainable practice if food supplies for humans are limited.This paper is part of the special issue entitled: Greenhouse Gases in Animal Agriculture – Finding a Balance between Food and Emissions, Guest Edited by T.A. McAllister, Section Guest Editors: K.A. Beauchemin, X. Hao, S. McGinn and Editor for Animal Feed Science and Technology, P.H. Robinson.

Reproduction of heifers sired by high or low residual feed intake angus bulls

Introduction Residual feed intake (RFI) has gained popularity as a selection tool for improving feed efficiency in beef cattle. RFI is the difference between what an animal consumes and what it is predicted to consume based on size and growth rate. Animals with low or negative RFI eat less than predicted and are more efficient. Although RFI is being used by the industry, research on the impact of selection for RFI on female fertility is lacking. The objective of this study is to evaluate the reproductive performance of heifers that have been selected for RFI.

Onset of puberty and early-life reproduction in Angus females divergently selected for post-weaning residual feed intake

Angus cattle that had been divergently selected for Low and High post-weaning residual feed intake (RFI) were used in two projects to evaluate early-life reproductive performance and onset of puberty in females. In the first project, data on the 1999-born females (n = 64) were evaluated for weight, subcutaneous fat (P8 fat depth) and reproductive performance over two breeding cycles. These females that were the result of 1.0–2.5 (mean of 1.8) generations of selection, had mean (±s.e.) post-weaning RFI of –0.82 ± 0.19 kg/day and 0.57 ± 0.18 kg/day for the Low and High RFI selection lines, respectively. In the second project, ultrasonography was used to scan the ovaries of the 2008-born heifers (n = 121) on four occasions following weaning. In these heifers the presence of corpus luteum provided evidence of ovulation, and hence the commencement of onset of puberty. The average of the estimated breeding value (EBV) for RFI of the parents of the Low RFI and the High RFI selection line heifers were –0.72 ± 0.05 and 0.37 ± 0.03 kg/day, respectively. In the first project, no significant selection line differences were evident for weight, age at first mating, pregnancy and calving rates (percentage of females that were pregnant, or the percentage that calved out of the total number used for mating), calf birthweight and weight of calf born per female exposed to bull. Females from the Low RFI line had significantly (P &lt; 0.05) lower P8 fat depth relative to their High RFI contemporaries at most of the measurement dates (e.g. 9.2 ± 0.5 versus 12.0 ± 0.5 mm at the start of first mating). Low RFI females also calved significantly (P &lt; 0.05) later in the calving season than High RFI females (35.7 ± 3.0 versus 27.6 ± 2.4 days). The results indicate that there is a delayed pregnancy date during the first mating season leading to a later calving date for the Low RFI heifers. The later first calving date was then maintained at subsequent calving. The later calving, however, did not impact on pregnancy and calving rates. In the second project, it was observed that irrespective of selection line, heifers that had attained onset of puberty had significantly (P &lt; 0.05) greater P8 fat depth than those that had not. Hence the expectation was that, relative to High RFI heifers, the Low RFI heifers with their lower P8 fat, will attain onset of puberty at a slightly older age. This expected trend was observed but the difference was not significant, and further investigations are recommended.

Effect of selection for residual feed intake on feeding behavior and daily feed intake patterns in Yorkshire swine1

Residual feed intake (RFI) is a measure of feed efficiency defined as the difference between observed and predicted feed intake based on average requirements for growth and maintenance. The objective of this study was to evaluate the effect of selection for decreased RFI on feeding behavior traits and to estimate their relationships with RFI. Three data sets from the 4th and 5th generations of a selection experiment with a line selected for reduced RFI (LRFI) and a randomly selected control line (CTRL) were analyzed. Lines were mixed in pens of 16 and evaluated for feeding behavior traits obtained from a single-space electronic feeder over a growing period of ~3 mo before ~115 kg. The following traits were evaluated as averages over the entire test period and over the first and second half of the test period: number of visits per day and hour; occupation time per day, visit, and hour; feed intake (FI) per day, visit, and hour; and FI rate per visit. Models used included fixed effects of line and feeder, covariates of on-test age and FI per day, and random effects of pen, on-test group, sire, and litter. Repeated measures models were used to analyze feeding patterns during the day. The LRFI pigs had significantly less FI per day than CTRL pigs for all 3 data sets. With adjustment for FI per day, line differences of all traits were in the same direction for all 3 data sets but differed in significance and size. Feed intake per visit and hour and visits per day and hour did not differ between lines, but the trend was for LRFI pigs to have fewer visits, in particular during peak eating times. The LRFI pigs had a greater feeding rate and less occupation time per day, visit, and hour than CTRL pigs, but this was not significant for all data sets. Correlations of RFI with FI per day and visit and visits per day were positive. Average daily gain was positively correlated with FI per day and visit and occupation time per visit but negatively correlated with visits per day. Feed intake per day was positively correlated with backfat. In conclusion, feed efficiency may be affected by FI behavior because selection for decreased RFI has resulted in pigs that spend less time eating and eat faster.

The effect of selection for residual feed intake on general behavioral activity and the occurrence of lesions in Yorkshire gilts1

The objectives of this study were to determine the effect of selection for improved residual feed intake on behavior, activity, and lesion scores in gilts in their home pen. A total of 192 gilts were used, 96 from a line that had been selected for decreased residual feed intake over 5 generations (LRFI) and 96 from a randomly bred control line. Gilts were housed in 12 pens (16 gilts/pen; 0.82 m(2)/gilt) containing 8 gilts from each line in a conventional grow-finish unit. Twelve hours of video footage were collected on the day of placement and then every 4 wk for 3 more observational periods. Video was scored using a 10-min instantaneous scan sampling technique for 4 postures (standing, lying, sitting, and locomotion) and 1 behavior (at drinker). Categories of active (standing, locomotion, and at drinker) and inactive (sitting and lying) were also created. Lesion scores were collected 24 h after behavior collection had begun. The body of a gilt was divided into 4 regions, with each region receiving a score of 0 (0 lesions) to 3 (5+ lesions). All statistical analyses used Proc Mixed of SAS. Data were analyzed separately for the day of placement and the subsequent 3 rounds. General activity was summarized on a percentage basis by each posture and behavior and subjected to an arcsine square root transformation to normalize data and stabilize variance. Analysis was performed on each behavior and posture. Lesion scores for each region of the body were analyzed as repeated measures. There were no differences (P > 0.05) between genetic lines for all postures and the behavior at drinker on the day of placement. However, over subsequent rounds it was observed that LRFI gilts spent less (P = 0.03) time standing, more time sitting (P = 0.05), and were less active (P = 0.03) overall. Gilts from the LRFI line had decreased (P < 0.045) lesion scores on the day after placement. However, over subsequent rounds there were no (P > 0.05) differences between the genetic lines. In conclusion, on the day of placement there were no postural, behavior, or general activity differences between genetic lines, but LRFI gilts had decreased lesion scores. Behavioral differences were observed between genetic lines over subsequent rounds, with LRFI gilts becoming less active, but there were no differences in lesion scores.

Genetic properties of feed efficiency parameters in meat-type chickens

BackgroundFeed cost constitutes about 70% of the cost of raising broilers, but the efficiency of feed utilization has not kept up the growth potential of today's broilers. Improvement in feed efficiency would reduce the amount of feed required for growth, the production cost and the amount of nitrogenous waste. We studied residual feed intake (RFI) and feed conversion ratio (FCR) over two age periods to delineate their genetic inter-relationships.MethodsWe used an animal model combined with Gibb sampling to estimate genetic parameters in a pedigreed random mating broiler control population.ResultsHeritability of RFI and FCR was 0.42-0.45. Thus selection on RFI was expected to improve feed efficiency and subsequently reduce feed intake (FI). Whereas the genetic correlation between RFI and body weight gain (BWG) at days 28-35 was moderately positive, it was negligible at days 35-42. Therefore, the timing of selection for RFI will influence the expected response. Selection for improved RFI at days 28-35 will reduce FI, but also increase growth rate. However, selection for improved RFI at days 35-42 will reduce FI without any significant change in growth rate. The nature of the pleiotropic relationship between RFI and FCR may be dependent on age, and consequently the molecular factors that govern RFI and FCR may also depend on stage of development, or on the nature of resource allocation of FI above maintenance directed towards protein accretion and fat deposition. The insignificant genetic correlation between RFI and BWG at days 35-42 demonstrates the independence of RFI on the level of production, thereby making it possible to study the molecular, physiological and nutrient digestibility mechanisms underlying RFI without the confounding effects of growth. The heritability estimate of FCR was 0.49 and 0.41 for days 28-35 and days 35-42, respectively.ConclusionSelection for FCR will improve efficiency of feed utilization but because of the genetic dependence of FCR and its components, selection based on FCR will reduce FI and increase growth rate. However, the correlated responses in both FI and BWG cannot be predicted accurately because of the inherent problem of FCR being a ratio trait.