BackgroundSingle nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations.ResultsModerate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained).ConclusionsFourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3754-y) contains supplementary material, which is available to authorized users.

BackgroundThe identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental × Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake.ResultsA total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value <0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations.ConclusionsThis GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.

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A series of 3 experiments were conducted to determine the in vitro and in situ disappearance, preference, and performance of steers consuming increasing concentrations of a novel feedstuff called algae meal (ALG). In Exp. 1 and 2, 3 ruminally cannulated steers (998 ± 103 kg BW) and 4 treatments were utilized: a dry-rolled corn-based diet (CON), or 15% ALG (A15), 30% ALG (A30), or 45% ALG (A45) as a DM replacement of corn. Experiment 1 was performed as a 3 × 6 unbalanced Latin square with six 5-d periods, and 6 paired diet combinations to determine steer preference, based on DMI for 4 h after feed delivery. Experiment 2 was conducted as a 3 × 4 unbalanced Latin square with 3 diets fed each period and four 14-d periods to determine in situ disappearance of ALG, soyhulls, corn, and hay as ALG increased in the diet. Experiment 3 utilized 48 individually fed steers (292 ± 22.4 kg; n = 12) in a 55-d grower trial, stratified by BW into 1 of 4 dietary treatments: a control wet corn gluten feed-based diet with no ALG (ALG0), or 15% ALG (ALG15), 30% ALG (ALG30), or 45% ALG (ALG45) in place of wet corn gluten feed on a DM basis. Digestibility of ALG was greater (P < 0.001) than soyhulls at 24 h, but was similar (P = 0.82) at 48 h, with hay being least (P < 0.001) digestible at 24 and 48 h. In Exp. 1, the proportion of total DM consumed by steers during the 4-h postfeeding was affected (P = 0.01) by paired diet combination. Steers preferred A15 or A30 diets over the A45 diet (P ≤ 0.008); however, no difference in preference between CON and A45 was noted (P = 0.76). Steers tended (P = 0.09) to prefer A30 over CON, but A15 and CON were not different (P = 0.75). No other paired diet combinations altered (P ≥ 0.23) DMI. In Exp. 2, inclusion of ALG in the diet did not affect (P ≥ 0.12) rate of, or overall in situ disappearance of, corn, soyhulls, or ALG. In Exp. 3, ADG tended ( = 0.06) to increase as ALG increased in the diet. There was a linear increase ( < 0.001) in DMI as ALG increased in the diet, and as a result, G:F linearly decreased ( = 0.01). In summary, ready consumption of the novel algae meal by steers and support of growth in steers at up to 45% of the diet suggest the algae meal is a viable feedstuff for ruminants.

Eighty Charolais-cross steer calves (283 kg) were fed a moderately high-energy (2.89 Mcal ME/kg) diet for 189 d to examine the effects of reimplantation of 36 mg of zeranol (Ralgro) or 200 mg progesterone plus 20 mg estradiol benzoate (Synovex-S) on the rate, composition and efficiency of gain, skeletal size and carcass parameters in a comparative slaughter trial. The implant treatments included unimplanted controls (C), Ralgro initially (R1), Synovex-S initially (S1), Ralgro initially and a reimplant at 84 d (R2) and Synovex-S initially and a reimplant at 84 d (S2). Both implants increased (P less than .06) gains by 8.1% from 0 to 84 d. Ralgro and Synovex-S increased (P less than .01) daily gains by 11.5% and 25.2%, respectively, from 84 to 189 d. The duration of the response to a single implant appeared to be in excess of 140 d; thus, reimplantation did not further increase daily gains. Reimplantation did improve (P less than .05) feed utilization in Ralgro implanted steers, however. Ralgro and Synovex-S increased (P less than .01) the rate of empty body (EB) protein accretion by 14.1% and 24%, respectively, without affecting EB fat growth. The efficiency of protein gain per unit protein (P less than .05) or energy intake (P less than .04) was improved, but the efficiency of energy gain per unit energy intake was not affected by implantation. Carcass weights of implanted steers were 5% greater (P less than .04) when adjusted to an equal carcass fatness. Both growth stimulants increased hip height (P less than .02), wither height (P less than .08) and body length (P less than .08) over C steers at slaughter.