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.

Basarab, J. A., Colazo, M. G., Ambrose, D. J., Novak, S., McCartney, D. and Baron, V. S. 2011. Residual feed intake adjusted for backfat thickness and feeding frequency is independent of fertility in beef heifers. Can. J. Anim. Sci. 91: 573–584. This study examined the effects of residual feed intake (RFI), RFI adjusted for off-test backfat thickness (RFI_fat) and RFI adjusted for off-test backfat thickness and feeding event frequency (RFI_{fat & activity}) on heifer fertility and productivity. Beef heifers (n=190) were monitored for individual daily feed intake and feeding event activity over 108–112 d using the GrowSafe System® and assessed for age at puberty based on plasma progesterone concentration. Individual animal daily feed intake, feeding event activity and off-test backfat thickness were then used to calculate RFI, RFI_fat and RFI_{fat & activity} and group heifers as either negative ([−], RFI<0.0) or positive ([+], RFI≥0.0) for RFI. Heifers averaged 298 kg (SD=34) in body weight, were 276 days of age (SD=19) at the start of test, grew at 0.90 kg d⁻¹ (SD=0.21), consumed 7.62 kg DM head⁻¹ d⁻¹ (SD=0.84) and had a feed conversion ratio of 8.93 (SD=2.43). Age (351 d, SD=43) and weight (367.3 kg, SD=45.0) at puberty were similar between [−] and [+] RFI heifers, but age at puberty was delayed in [−] RFI_fat (P=0.04) and RFI_{fat & activity} (P=0.08) heifers compared with [+] RFI_fat and RFI_{fat & activity} heifers. Efficient or [−] RFI heifer exhibited a lower pregnancy (76.84 vs. 86.32%, P=0.09) and calving rate (72.63 vs. 84.21%, P=0.05) compared with [+] RFI heifers. These differences were partially removed in [−] RFI_fat and completely removed in [−] RFI_{fat & activity} compared with their [+] RFI counterparts (pregnancy rate, 80.85 vs. 82.29%, P=0.80; calving rate, 75.53 vs. 81.25%, P=0.34). No differences were observed between efficient and inefficient heifers in calving difficulty, average calving date, age at first calving, calf birth weight, calf pre-weaning ADG, calf weaning weight and heifer productivity. However, [+] RFI heifers exhibited a 1.9-fold higher calf death loss compared with [−] RFI heifers (11.11% vs. 5.71%, P=0.24). This difference was more pronounced in [+] RFI_fat and [+] RFI_{fat & activity} heifers, which exhibited 2.2-fold (11.84% vs. 5.33%, P=0.15) and 3.0-fold (12.66% vs. 4.17%, P=0.06) higher calf death loss compared with [−] RFI heifers. There was no relationship of RFI adjusted for backfat thickness and feeding activity on fertility traits indicating that backfat thickness and feeding activity may be associated with feed intake and should be considered when selecting heifers for improved feed efficiency.

Background: MicroRNAs (miRNAs), a family of small non-coding RNA molecules, appear to regulate animal lipid metabolism and preadipocyte conversion to form lipid-assimilating adipocytes (i.e.adipogenesis). However, no miRNA to date has been reported to modulate adipogenesis and lipid deposition in beef cattle.Results: The expression patterns of 89 miRNAs including four bovine specific miRNAs in subcutaneous adipose tissues from three groups of crossbred steers differing in backfat thickness were compared using qRT-PCR analysis. Eighty-six miRNAs were detectable in all samples, with 42 miRNAs differing among crossbreds (P < 0.05) and 15 miRNAs differentially expressed between tissues with high and low backfat thickness (P < 0.05). The expression levels of 18 miRNAs were correlated with backfat thickness (P < 0.05). The miRNA most differentially expressed and the most strongly associated with backfat thickness was miR-378, with a 1.99-fold increase in high backfat thickness tissues (r = 0.72).Conclusions: MiRNA expression patterns differed significantly in response to host genetic components. Approximately 20% of the miRNAs in this study were identified as being correlated with backfat thickness. This result suggests that miRNAs may play a regulatory role in white adipose tissue development in beef animals.

Background: Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted in a population of 7573 animals from multiple beef cattle breeds based on 7,853,211 imputed whole genome sequence variants. The GWAS results were used to elucidate genetic architectures of the feed efficiency related traits in beef cattle.Results: The DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants followed a scaled inverse chi-squared distribution to a greater extent. With a threshold ofP-value < 1.00E-05, 16, 72, 88, and 116 lead DNA variants on multiple chromosomes were significantly associated with RFI, DMI, ADG, and MWT, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on DMI, ADG, and MWT were found on chromosomes 6, 14 and 20. On average, missense, 3’UTR, 5’UTR, and other regulatory region variants exhibited larger allele substitution effects in comparison to other functional classes. Intergenic and intron variants captured smaller proportions of additive genetic variance per DNA variant. Instead 3’UTR and synonymous variants explained a greater amount of genetic variance per DNA variant for all the traits examined while missense, 5’UTR and other regulatory region variants accounted for relatively more additive genetic variance per sequence variant for RFI and ADG, respectively. In total, 25 to 27 enriched cellular and molecular functions were identified with lipid metabolism and carbohydrate metabolism being the most significant for the feed efficiency traits.Conclusions: RFI is controlled by many DNA variants with relatively small effects whereas DMI, ADG, and MWT are influenced by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory region and synonymous functional classes play a more important role per sequence variant in determining variation of the feed efficiency traits. The genetic architecture as revealed by the GWAS of the imputed 7,853,211 DNA variants will improve our understanding on the genetic control of feed efficiency traits in beef cattle.

Background: Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated.Results: The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold ofP-value < 10^–5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3’UTR variants, 5’UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3’UTR variants, 5’UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits.Conclusions: The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.

A spring calving herd consisting of about 350 beef cows, 14–16 breeding bulls, 60 replacement heifers and 112 steers were used to compare the whole-farm GHG emissions among calf-fed vs. yearling-fed production systems with and without growth implants. Carbon footprint ranged from 11.63 to 13.22 kg CO₂e per kg live weight (19.87–22.52 kg CO₂e per kg carcass weight). Enteric CH₄ was the largest source of GHG emissions (53–54%), followed by manure N₂O (20–22%), cropping N₂O (11%), energy use CO₂ (9–9.5%), and manure CH₄ (4–6%). Beef cow accounted for 77% and 58% of the GHG emissions in the calf-fed and yearling-fed. Feeders accounted for the second highest GHG emissions (15% calf-fed; 35–36% yearling-fed). Implants reduced the carbon footprint by 4.9–5.1% compared with hormone-free. Calf-fed reduced the carbon footprint by 6.3–7.5% compared with yearling-fed. When expressed as kg CO₂e per kg carcass weight per year the carbon footprint of calf-fed production was 73.9–76.1% lower than yearling-fed production, and calf-fed implanted was 85% lower than hormone-free yearling-fed. Reducing GHG emissions from beef production may be accomplished by improving the feed efficiency of the cow herd, decreasing the days on low quality feeds, and reducing the age at harvest of youthful cattle.