Cattle selected for lower residual feed intake have reduced daily methane production

Ruminant enteric methane mitigation: a review

In Australia, agriculture is responsible for ~17% of total greenhouse gas emissions with ruminants being the largest single source. However, agriculture is likely to be shielded from the full impact of any future price on carbon. In this review, strategies for reducing ruminant methane output are considered in relation to rumen ecology and biochemistry, animal breeding and management options at an animal, farm, or national level. Nutritional management strategies have the greatest short-term impact. Methanogenic microorganisms remove H2 produced during fermentation of organic matter in the rumen and hind gut. Cost-effective ways to change the microbial ecology to reduce H2 production, to re-partition H2 into products other than methane, or to promote methanotrophic microbes with the ability to oxidise methane still need to be found. Methods of inhibiting methanogens include: use of antibiotics; promoting viruses/bacteriophages; use of feed additives such as fats and oils, or nitrate salts, or dicarboxylic acids; defaunation; and vaccination against methanogens. Methods of enhancing alternative H2 using microbial species include: inoculating with acetogenic species; feeding highly digestible feed components favouring ‘propionate fermentations’; and modifying rumen conditions. Conditions that sustain acetogen populations in kangaroos and termites, for example, are poorly understood but might be extended to ruminants. Mitigation strategies are not in common use in extensive grazing systems but dietary management or use of growth promotants can reduce methane output per unit of product. New, natural compounds that reduce rumen methane output may yet be found. Smaller but more permanent benefits are possible using genetic approaches. The indirect selection criterion, residual feed intake, when measured on ad libitum grain diets, has limited relevance for grazing cattle. There are few published estimates of genetic parameters for feed intake and methane production. Methane-related single nucleotide polymorphisms have yet to be used commercially. As a breeding objective, the use of methane/kg product rather than methane/head is recommended. Indirect selection via feed intake may be more cost-effective than via direct measurement of methane emissions. Life cycle analyses indicate that intensification is likely to reduce total greenhouse gas output but emissions and sequestration from vegetation and soil need to be addressed. Bio-economic modelling suggests most mitigation options are currently not cost-effective.

Measurement and prediction of enteric methane emission

The greenhouse gas (GHG) emissions from the agricultural sector account for about 25.5% of total global anthropogenic emission. While CO(2) receives the most attention as a factor relative to global warming, CH(4), N(2)O and chlorofluorocarbons (CFCs) also cause significant radiative forcing. With the relative global warming potential of 25 compared with CO(2), CH(4) is one of the most important GHGs. This article reviews the prediction models, estimation methodology and strategies for reducing enteric CH(4) emissions. Emission of CH(4) in ruminants differs among developed and developing countries, depending on factors like animal species, breed, pH of rumen fluid, ratio of acetate:propionate, methanogen population, composition of diet and amount of concentrate fed. Among the ruminant animals, cattle contribute the most towards the greenhouse effect through methane emission followed by sheep, goats and buffalos, respectively. The estimated CH(4) emission rate per cattle, buffaloe, sheep and goat in developed countries are 150.7, 137, 21.9 and 13.7 (g/animal/day) respectively. However, the estimated rates in developing countries are significantly lower at 95.9 and 13.7 (g/animal/day) per cattle and sheep, respectively. There exists a strong interest in developing new and improving the existing CH(4) prediction models to identify mitigation strategies for reducing the overall CH(4) emissions. A synthesis of the available literature suggests that the mechanistic models are superior to empirical models in accurately predicting the CH(4) emission from dairy farms. The latest development in prediction model is the integrated farm system model which is a process-based whole-farm simulation technique. Several techniques are used to quantify enteric CH(4) emissions starting from whole animal chambers to sulfur hexafluoride (SF6) tracer techniques. The latest technology developed to estimate CH(4) more accurately is the micrometeorological mass difference technique. Because the conditions under which animals are managed vary greatly by country, CH(4) emissions reduction strategies must be tailored to country-specific circumstances. Strategies that are cost effective, improve productivity, and have limited potential negative effects on livestock production hold a greater chance of being adopted by producers. It is also important to evaluate CH(4) mitigation strategies in terms of the total GHG budget and to consider the economics of various strategies. Although reductions in GHG emissions from livestock industries are seen as high priorities, strategies for reducing emissions should not reduce the economic viability of enterprises.

Feed efficiency differences and reranking in beef steers fed grower and finisher diets

This 3-yr study used 490 steers to determine whether feedlot steers changed their feed efficiency (FE) ranking when fed a grower diet, then a finisher diet. The steers were crossbreds and were between 5 to 7 mo of age. There were 2 feeding periods each year. Within each year, approximately 90 steers had their diet switched from a grower to a finisher diet (feed-swap group), whereas another 90 steers were fed either the grower (grower-fed group) or the finisher (finisher-fed group) diet throughout the feeding trial. Each feeding test lasted for a minimum of 10 wk, and all steers were fed ad libitum. Individual animal feed intakes were collected using the GrowSafe feeding system, and BW were measured every 2 wk. Residual feed intake (RFI), G:F, and Kleiber ratio (KR) were computed at the end of each feeding period. For each measure of efficiency, animals were classified as low, medium, or high based on 0.5 SD from the mean. The majority of steers did not maintain the previous efficiency class in the second period. Approximately 58, 51, and 51% of steers in the feed-swap group, finisher-fed group, and the grower-fed group, respectively, changed their RFI measure by 0.5 SD. A low rank correlation occurred in all test groups but was less in the feed-swap group. Spearman rank correlations between the 2 feeding periods in the feed-swap group were 0.33, 0.20, and 0.31 for RFI, G:F, and KR, respectively. Classifications based on G:F and KR showed that a greater number of steers (P < 0.05) in the feed-swap group did not maintain their FE class from 1 feeding regimen to the other, whereas classification based on RFI did not show any difference (P > 0.05) between the proportions of individuals that changed or maintained their FE class. In the groups without a feed-swap, there was no difference (P > 0.05) in the proportion of steers that changed or maintained the same FE class for all FE measures. Our results suggest that diet type and feeding period affect the FE ranking in beef steers. A feedlot diet is ideal for evaluating the FE potential of steers for feedlot profitability; however, we suggest that tests involving less dense diets should be examined in an effort to understand the relationships between FE and feeder profitability.

Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits

The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.

Repeatability of feed efficiency, carcass ultrasound, feeding behavior, and blood metabolic variables in finishing heifers divergently selected for residual feed intake

This study examined the relationship between feed efficiency and performance, and feeding behavior, blood metabolic variables, and various ultrasonic measurements in finishing beef heifers. Within-animal repeatability estimates of feed intake and behavior, performance, feed efficiency, ultrasonic body measures, and plasma analytes across the growing and finishing stages of the lifespan of the animal were also calculated. Fifty heifers previously ranked as yearlings on phenotypic residual feed intake (RFI) were used. Animals [initial BW = 418 (SD = 31.5) kg] were offered a TMR diet consisting of 70:30 concentrate and corn silage on a DM basis (ME 10.7 MJ/kg of DM; DM 530 g/kg) for 84 d. Feeding duration (min/d) and feeding frequency (events/d) were calculated for each animal on a daily basis using a computerized feeding system. Ultrasonic kidney fat and lumbar and rump fat and muscle depths were recorded on 3 equally spaced occasions during the experimental period. Blood samples were collected by jugular venipuncture on 4 occasions during the experimental period and analyzed for plasma concentrations of IGF-I, insulin, and various metabolites. Phenotypic RFI was calculated for all animals as the residuals from a regression model regressing DMI on ADG and midtest BW(0.75). Repeatability was calculated for several traits both within and between production phase using intraclass correlation and Pearson correlation coefficients as appropriate. Overall ADG, DMI, G:F, and RFI were 1.17 kg/d (SD = 0.19), 10.81 kg/d (SD = 1.02), 0.11 kg of BW gain/kg of DM (SD = 0.02), and 0.00 kg of DM/d (SD 0.59). Daily feeding events and eating rate tended to be positively correlated (P = 0.08) with RFI. Ultrasonic kidney fat depth tended to be related to G:F (r = -0.28; P = 0.07), and kidney fat accretion tended to be related to RFI (r = 0.29; P = 0.08). Plasma urea (r = 0.38; P < 0.01), β-hydroxybutyrate (r = 0.40; P < 0.01), and insulin (r = 0.23; P = 0.07) concentrations were correlated with RFI. Plasma glucose (r = -0.25; P = 0.07), glucose:insulin (r = 0.33; P < 0.05), and insulin (r = -0.30; P < 0.05) were associated with G:F. However, systemic IGF-I was unrelated (P > 0.10) to any measure of feed efficiency. Repeatability estimates within the finishing period for DMI, feeding duration, feeding events, feed intake/feeding event, and eating rate were 0.34, 0.37, 0.60, 0.62, and 0.56, respectively. Repeatability estimates (P < 0.001) between the growing and finishing phases for DMI, G:F, and RFI were r = 0.61, r = 0.37, and r = 0.62, respectively. Moderate to strong repeatability values (ranging from r = 0.40 to 0.76; P < 0.001) were obtained for feeding behavior traits between the yearling and finishing phases. We conclude that RFI and feeding behavior are repeatable traits and that some plasma analytes may be potential indicators of RFI in beef cattle.

Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis

Understanding ruminal methanogens is essential for greenhouse gas mitigation, as well as for improving animal performance in the livestock industry. It has been speculated that ruminal methanogenic diversity affects host feed efficiency and results in differences in methane production. This study examined methanogenic profiles in the rumen using culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis for 56 beef cattle which differed in feed efficiency, as well as diet (the cattle were fed a low-energy diet or a high-energy diet). The methanogenic PCR-DGGE profiles detected were greatly affected by diet, and the major pattern changed from a community containing predominantly Methanobrevibacter ruminantium NT7 with the low-energy diet to a community containing predominantly Methanobrevibacter smithii, Methanobrevibacter sp. AbM4, and/or M. ruminantium NT7 with the high-energy diet. For each diet, the methanogenic PCR-DGGE pattern was strongly associated with the feed efficiency of the host. Diet-associated bands for Methanobrevibacter sp. AbM4 and M. smithii SM9 and a feed efficiency-related band for M. smithii PS were identified. The abundance of total methanogens was estimated by determining the numbers of copies of the 16S rRNA genes of methanogens. However, the size of the methanogen population did not correlate with differences in feed efficiency, diet, or metabolic measurements. Thus, the structure of the methanogenic community at the species or strain level may be more important for determining host feed efficiency under different dietary conditions.

Microbial fuel cells and microbial ecology: applications in ruminant health and production research

Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.

Nutritional and flock management options to reduce methane output and methane per unit product from sheep enterprises

The daily methane output of sheep is strongly affected by the quantity and digestibility of feed consumed. There are few widely applicable technologies that reduce the methane output of grazing ruminants without limiting feed intake per head or animal numbers. In contrast, there are many opportunities to increase the amount of animal product generated per unit of feed eaten. These include improving growth and reproductive rates of livestock and will reduce methane emission per unit of product (called emissions intensity) for individual animals. Producer responses to such improvements through changes to stocking rate and total area grazed will have a major effect on the total emission and profitability of the enterprise. First mating of ewes as lambs (~7 months of age) rather than as hoggets (~19 months of age) reduces the emissions intensity of self-replacing flocks but not that of flocks for which replacement ewes are purchased. Selection of sheep for improved residual feed intake reduces emissions intensity at the individual animal level as well as at the enterprise level. At present, emissions policies that motivate farm managers to consider generating fewer emissions rather than more profit or product are lacking.

Effects of early weaning on growth, feed efficiency and carcass traits in Shorthorn cattle

This study aimed to examine the impact of early weaning on residual feed intake, and other production and carcass traits, in a group of cattle subjected to early or conventional weaning treatments, but otherwise managed as contemporaries. Shorthorn (n = 140) calves were randomly allocated by sex and sire to early and conventional weaning treatments. Early weaned animals (n = 69) were weaned at an average of 123 days of age and 145 kg liveweight, while conventionally weaned steers and heifers (n = 71) were 259 days old at weaning and 273 kg. Following conventional weaning, animals were managed as contemporaries through backgrounding, and entered feedlot finishing at a mean age of 353 and 408 days for heifers and steers, respectively, for finishing and feed intake testing. At the conclusion of feed intake testing hip height was measured, and animals were ultrasound scanned to assess fat depth, eye muscle area and percent intramuscular fat. Early weaned animals were significantly lighter (P < 0.001) than their conventionally weaned contemporaries, when weighed at conventional weaning. The weight difference observed at conventional weaning of 19.4 kg between treatment groups persisted throughout the experiment, with significant (P < 0.05) differences of 17.1, 15.6 and 15.8 kg at feedlot entry, and the start and end of the feed intake test period, respectively. Weaning treatment also approached significance for daily feed intake (P = 0.06), with early weaned animals tending to eat less than their conventionally weaned contemporaries (daily feed intake = 11.6 and 12.0 kg, respectively). Weaning treat\ment did not significantly affect feed efficiency whether measured as residual feed intake (P = 0.64) or feed conversion ratio (P = 0.27). None of the other traits measured were significantly affected by weaning treatment. These data showed that early weaning, as implemented for this experiment, resulted in animals that were lighter than their conventionally weaned contemporaries through backgrounding and finishing. Weaning treatment did not, however, influence feed efficiency or the post-weaning growth and carcass composition traits measured for this experiment.

Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies

Cattle with high feed efficiencies (designated "efficient") produce less methane gas than those with low feed efficiencies (designated "inefficient"); however, the role of the methane producers in such difference is unknown. This study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. Two 16S rRNA libraries were constructed using approximately 800-bp amplicons generated from pooled total DNA isolated from efficient (n = 29) and inefficient (n = 29) animals. Sequence analysis of up to 490 randomly selected clones from each library showed that the methanogenic composition was variable: less species variation (22 operational taxonomic units [OTUs]) was detected in the rumens of efficient animals, compared to 27 OTUs in inefficient animals. The methanogenic communities in inefficient animals were more diverse than those in efficient ones, as revealed by the diversity indices of 0.84 and 0.42, respectively. Differences at the strain and genotype levels were also observed and found to be associated with feed efficiency in the host. No difference was detected in the total population of methanogens, but the prevalences of Methanosphaera stadtmanae and Methanobrevibacter sp. strain AbM4 were 1.92 (P < 0.05) and 2.26 (P < 0.05) times higher in inefficient animals, while Methanobrevibacter sp. strain AbM4 was reported for the first time to occur in the bovine rumen. Our data indicate that the methanogenic ecology at the species, strain, and/or genotype level in the rumen may play important roles in contributing to the difference in methane gas production between cattle with different feed efficiencies.

Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattle

Identification of the genes and polymorphisms underlying quantitative traits, and understanding how these genes and polymorphisms affect economic traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle populations. Signal transducer and activator of transcription 6 (STAT6) gene is tightly connected to IL-4 and IL-13 signalling and plays a key role in T(H)2 polarization of the immune system. In addition, STAT6 acts as a mediator of leptin signalling and has been associated with body weight regulation. The objective of this study was to determine if SNPs within the bovine STAT6 gene are associated with economically important traits in feedlot cattle. The approach consisted of resequencing STAT6 using a panel of DNA from unrelated animals of different beef breeds. Specifically, 16 kb of STAT6 was resequenced in 47 animals and the process revealed 39 SNPs. From the 39 SNPs, a panel of 15 tag SNPs was genotyped in 1500 beef cattle samples with phenotypes to perform a marker-trait association analysis. Among the 15 tag SNPs, five and six were polymorphic in Bos taurus and Bos indicus respectively. An association analysis was performed between the 15 tag SNPs and 14 performance and production traits. SNP ss115492459:C > A, ss115492461:A > G and ss115492458:G > C were significantly associated with back fat, calculated yield grade, cutability, hot carcass weight, dry matter intake, days on feed, back fat rate and average daily gain. These three SNPs were present in all Bos taurus beef breeds examined. Our results provide evidence that polymorphisms in STAT6 are associated with carcass and growth efficiency traits, and may be used for marker-assisted selection and management in feedlot cattle.

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

BACKGROUND

Neuropeptide Y is a key neurotransmitter of the central nervous system which plays a vital role in the feed energy homeostasis in mammals. Mutations in the regulatory and coding regions of the bovine NPY gene can potentially affect the neuronal regulation of appetite and feeding behaviour in cattle. The objectives of this experiment were to: a) fully characterize the bovine NPY gene transcript and b) identify the SNP diversity in both coding and non-coding regions of the NPY gene in a panel of Bos taurus and B. indicus cattle.

RESULTS

Bovine NPY gene consists of four exons (99, 188, 81 and 195 nucleotides) and three introns. The promoter region of the NPY gene consists of TATA and GC boxes which are separated from the transcription start site (TSS) by 29 and ~100 nt, respectively. Analyses of the tissue specific expression of the bovine NPY gene revealed the presence of highly abundant NPY gene transcripts in the arcuate nucleus, cerebral and cerebellar regions of the bovine brain. We identified a total of 59 SNPs in the 8.4 kb region of the bovine NPY gene. Seven out of nine total SNPs in the promoter region affect binding of putative transcription factors. A high level of nucleotide diversity was evident in the promoter regions (2.84 x 10(-3)) compared to the exonic (1.44 x 10(-3)), intronic (1.30 x 10(-3)) and 3' untranslated (1.26 x 10(-3)) regions.

CONCLUSION

The SNPs identified in different regions of bovine NPY gene may serve as a basis for understanding the regulation of the expression of the bovine NPY gene under a variety of physiological conditions and identification of genotypes with high feed energy conversion efficiency.

Identification of polymorphisms influencing feed intake and efficiency in beef cattle

Feed efficiency is an economically important trait in beef cattle. Net feed efficiency, measured as residual feed intake (RFI), is the difference between actual feed intake and the predicted feed intake required for maintenance and gain of the animal. SNPs that show associations with RFI may be useful quantitative trait nucleotides for marker-assisted selection. This study identified associations between SNPs underlying five RFI QTL on five bovine chromosomes (BTA2, 5, 10, 20 and 29) with measures of dry matter intake (DMI), RFI and feed conversion ratio (FCR) in beef cattle. Six SNPs were found to have effects on RFI (P < 0.05). The largest single SNP allele substitution effect for RFI was -0.25 kg/day located on BTA2. The combined effects of the SNPs found significant in this experiment explained 6.9% of the phenotypic variation of RFI. Not all the RFI SNPs showed associations with DMI and FCR even though these traits are highly correlated with RFI (r = 0.77 and r = 0.62 respectively). This shows that these SNPs may be affecting the underlying biological mechanisms of feed efficiency beyond feed intake control and weight gain efficiency. These SNPs can be used in marker-assisted selection but first it will be important to verify these effects in independent populations of cattle.

Absence of persistent methane emission differences in three breeds of dairy cows

In the present study, data from an experiment with 10 purebred Holstein, Simmental and Jersey cows each were analysed to test the assumption that there are genetically low methane-producing animals. Methane emission of cows offered forage ad libitum and some concentrate was measured for 3 days in open-circuit respiration chambers in weeks 8, 15, 23, 33 and 41 of lactation. Individual cow data were analysed in five different ways: (i) plotting the trend of methane per unit of dry matter intake (DMI) and milk yield over time; relating measured methane production to estimates derived from equations based on either; (ii) DMI or (iii) nutrient intake; (iv) relating residual feed intake (RFI) to methane emission; and (v) analysis of variance of cow × measurement interactions. The Holstein, Simmental and Jersey cows emitted on average 25, 25 and 26 g methane/kg DMI, respectively. There was no indication of individual cows with persistently low or high methane yield per kg DMI and per kg milk. Measured methane emissions differed from estimated values without a clear pattern, and the relationship between RFI and methane emission of the cows was weak. Finally, analysis of variance failed to show distinct patterns of methane per unit of DMI and milk for individual animals. The apparent lack of persistence of individual animal differences in methane yields suggests that genetic determination of this trait is of minor importance in dairy cows.