Search

Assisted reproductive technologies are used to propagate desirable genetics in a shortened timeframe. Selected females undergo ovarian stimulation with the use of follicle stimulating hormone (FSH) to increase embryo recovery for subsequent transfer programs. The FSH receptor (FSHR) c.337 C G variant was reported to have a reduction in viable embryo numbers in an ovarian stimulation protocol. We, therefore, hypothesized that FSHR c.337 C G would result in reduced in-vitro blastocyst development. Beef heifers were genotyped and selected based on the c.337 C G FSHR genotype (CC, CG, GG; n = 15-16/genotype). Estrus was synchronized with a Select Synch protocol and heifers were slaughtered 5 days after induced ovulation. Anterior pituitaries, serum and reproductive tracts were collected at slaughter for analysis. Cumulus oocyte complexes (COCs) were collected and pooled within genotype for in-vitro fertilization (IVF) and subsequent blastocyst development. No differences were observed in carcass weights, anterior pituitary weights, serum progesterone, corpus lutea weight, surface follicle counts, histological follicle counts or follicular fluid estradiol concentration (P 0.1) due to FSHR genotype. Differences were observed for ovulation rates in the GG FSHR genotype group (P 0.01). However, cleavage and blastocyst rates were not affected due to FSHR genotype (P 0.1), following standard IVF protocols. The FSHR variant does not influence antral follicle counts, estradiol production, or in-vitro blastocyst development in beef heifers. The GG FSHR genotype had an increased ovulation rate, which may indicate a greater potential for twinning, but research with a larger population is warranted to support this hypothesis.

IntroductionRespiratory disease incidence is intimately associated with an animal’s commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. In addition, viral pathogens affect the immune system and appear to play an integral role in the overall incidence of bovine respiratory disease (BRD); so, an understanding of the interaction of the bacterial and viral pathogens in the upper respiratory tract (URT) may help us to understand the impact of these pathogens on development of BRD. For this research, the overall goal was to characterize bacterial and viral populations in the URT of nursing beef calves at initial vaccination and at the time of a BRD outbreak.MethodsNasal swabs from the URT were collected at initial vaccination (average 45 days of age) and again at the time of the BRD outbreak (average 126 days of age). DNA and RNA were extracted from nasal swabs to evaluate bacterial and viral populations in the URT. Whole blood was also collected at the time of the BRD outbreak for determination of complete blood counts. To evaluate the microbiome, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. To evaluate the viral pathogens, multiplex reverse transcription real-time polymerase chain reaction and next-generation sequencing (Illumina NextSeq) was completed.ResultsOverall, evaluation of these samples revealed that at the time of the BRD outbreak, all calves were nasally shedding bovine coronavirus and a large percentage had a coinfection with Mycoplasma sp., with Mycoplasma bovirhinis being the predominant species. Neither bovine coronavirus nor Mycoplasma sp. were present at high abundance at the earlier timepoint of initial vaccination. When comparing bacterial population diversity between the two sampling timepoints, alpha diversity was significantly greater at initial vaccination compared to the BRD outbreak (P-value DiscussionAnalysis of the respiratory microflora in the URT during initial vaccination and a BRD outbreak will provide insight into the distribution of bacterial and viral populations in nursing beef calves.

Objective Our objective was to evaluate fasting heat production in cattle with and without the GDF8 mutation. Materials and Methods The heifers used in this study were genotyped for the myostatin(MSTN) gene mutation to determine their MSTN genotype as either homozygous normal for phenylalanine at amino acid position 94 of MSTN (0 copy; n = 5) or homozygous for F94L variant in MSTN (2 copy; n = 6). Oxygen consumption was measured using portable headbox respiration calorimeters, and heat production was calculated. Results and Discussion Body weight was not different between treatments (P = 0.33), but it did differ across days (P Implications and Applications Therefore, it is likely that cattle with 2 copies of the F94L MSTN substitution have lower maintenance energy requirements than cattle without the MSTN gene. Thus, genotype, if known, should be considered when assessing energy requirements of beef cattle.

Larkspur (Delphinium spp.) poisoning is a long-term problem for cattle grazing on rangelands of western North America. Recent research has shown that both plant and animal-based factors are critical in understanding and mitigating larkspur poisoning in cattle. Non-toxicological factors including sex, age, cattle breed, and plant chemotype affect cattle responses to larkspur. For example, Angus heifers are more susceptible to larkspur intoxication than are steers or bulls. Young cattle appear to be more susceptible to larkspur poisoning than mature animals. Beef breeds of cattle are more susceptible to larkspur intoxication than dairy breeds. In addition to animal factors, plant alkaloid composition (chemotype) affects the potential toxicity for cattle because of differences in the ratios and concentrations of highly toxic N-(methylsuccinimido) anthranoyllycoctonine (MSAL)-type alkaloids compared to less lethal non-MSAL-type alkaloids. Animal- and plant-based factors can provide substantial information to inform livestock producers on management to reduce risk and cattle losses to various larkspur species in western North America.

Larkspur (Delphinium spp.) poisoning is a long-term problem for cattle grazing on rangelands of western North America. Results from preliminary experiments have suggested that differences in larkspur toxicity may exist between heifers and bulls. The objective of this study was to compare the physiological responses of yearling Angus heifers, steers, and bulls with a standardized dose of Delphinium barbeyi and to test the hypothesis that the response is sex dependent. Clinical signs of intoxication, including muscle coordination and function, were measured 24 h after oral dosing with larkspur by walking the cattle at a pace of 5 to 6 km h-1 for up to 40 min on an oval dirt track. Due to the experimental methods used, the variation in susceptibility to larkspur was not quantifiable for walking times of 0 or 40 min or more. Larkspur susceptible animals that were not able to walk (0 min; 36% of the animals) or larkspur resistant animals that walked the entire test period of 40 min (9% of the animals) resulted in censored or truncated data. The statistical methods (censReg and lmec) were used to adjust for data truncation or censoring. The heifers were only able to walk -8.9 ± 3.9 min (65.5% censored on the left) compared with 13.2 ± 3.7 min for bulls and 15.9 ± 2.7 min for steers. When heifers were compared with bulls and steers together, heifers walked 23.4 ± 4.5 min less (P < 0.0001). Serum alkaloid concentrations were measured immediately before walking, and deltaline concentrations averaged 266 ± 28, 131 ± 20, and 219 ± 28 ng mL-1 for all heifers, steers, and bulls, respectively, and serum methyllycaconitine concentrations averaged 660 ± 46, 397 ± 32, and 612 ± 34 ng mL-1 for all heifers, steers, and bulls, respectively. The relative risk of a zero walk time for yearling heifers is 330% that of yearling bulls (P = 0.0008). These results suggest that yearling Angus heifers are more susceptible to larkspur intoxication and, when possible, heifers should be kept from grazing larkspur-infested rangelands as a simple management tool to reduce the risk of fatal poisoning.

Phenotypes are necessary for genomic evaluations and management. Sometimes genomics can be used to measure phenotypes when other methods are difficult or expensive. Prolificacy of bulls used in multiple-bull pastures for commercial beef production is an example. A retrospective study of 79 bulls aged 2-year-old and older used 141 times in 4-5 pastures across 4 years was used to estimate repeatability from variance components. Traits available before each season’s use were tested for predictive ability. Sires were matched to calves using individual genotypes and evaluating exclusions. A lower cost method of measuring prolificacy was simulated for 5 pastures using the bulls’ genotypes and pooled genotypes to estimate average allele frequencies of calves and of cows. Repeatability of prolificacy was 0.62 ± 0.09. A combination of age-class and scrotal circumference accounted for less than 5 % of variation. Simulated estimation of prolificacy by pooling DNA of calves was accurate. Adding pooling of cow DNA or actual genotypes both increased accuracy about the same. Knowing a bull’s prior prolificacy would help predict future prolificacy for management purposes and could be used in genomic evaluations and research with coordination of breeders and commercial beef producers.

Fifty-six head of cattle, 28 animals with bovine respiratory disease complex (BRDC), and 28 healthy animals that were matched by treatment, sale barn of origin, day, and interactions among these variables, were identified from a population of 180 animals (60 each purchased at three sale barns located in Missouri, Tennessee, and Kentucky) enrolled in a study comparing animals receiving metaphylaxis to saline-treated controls. Cattle were transported to a feedlot in KS and assigned to treatment group. Blood samples were collected at Day 0 (at sale barn), Day 1, Day 9, and Day 28 (at KS feedlot), and transported to the US Meat Animal Research Center in Clay Center, NE where plasma was harvested and stored at −80°C until assayed for the cytokines IFN-γ, IL-1β, IL-6, and TNF-α, and the acute stress protein haptoglobin (HPT). Our objectives were to determine if cytokine and haptoglobin profiles differed between control and metaphylaxis treatment groups over time, and if profiles differed between animals presenting with BRDC and those that remained healthy. There was no difference between the treated animals and their non-treated counterparts for any of the analytes measured. Sale barn of origin tended to affect TNF-α concentration. Differences for all analytes changed over days, and on specific days was associated with state of origin and treatment. The Treatment by Day by Case interaction was significant for HPT. The analyte most associated with BRDC was HPT on D9, possibly indicating that many of the cattle were not exposed to respiratory pathogens prior to entering the feedlot.

The period of heifer development is a relatively small fraction of a cow’s life; however, her pattern of growth may have permanent effects on her productivity as a cow. We hypothesized that altering the growth pattern during the peri-pubertal period would increase life-time productivity across genetic types of Bos taurus cows. The objective was to determine the stayability, calf production, and weight of calf weaned across six calf crops. Heifers (n = 685) were placed on one of two developmental programs at 256 ± 1 d of age. Control heifers received a diet that provided 228 kcal ME·(body weight [BW], kg) −0.75 daily, and stair-step heifers were allocated 157 kcal ME·(BW, kg)−0.75 daily for 84 or 85 d, and then the daily allocation was increased to 277 kcal ME·(BW, kg)−0.75. Stair-step heifers (0.33 ± 0.02 kg/d) had a lower average daily gain (ADG) than control heifers (0.78 ± 0.02 kg/d; P < 0.001) during Period 1, and stair-step heifers (0.93 ± 0.03 kg/d) had a greater ADG than controls (0.70 ± 0.03 kg/d; P < 0.001) during Period 2. There were no treatment (P = 0.28) or breed type differences (P = 0.42) for the proportion of cows weaning a calf; however, the proportion of cows weaning a calf decreased with cow age (P < 0.001). Calves from stair-step dams had heavier weaning weights (193 ± 1 kg) compared to control calves (191 ± 1 kg; P = 0.007). There was not a treatment (P = 0.25) or breed type differences in cumulative BW weaned (P = 0.59). A diverse genetic population of cattle within B. taurus was tested and responses in calf production did not differ between stair-step growth pattern and a more constant nonobese growth pattern.

One approach to reducing calving difficulty is to select heifers with higher breeding value for calving ease. Calving ease is often associated with lower birth weight and that may result in other possible effects on lifetime productivity. Females from experimental select and control calving ease lines within each of the seven populations were compared. Random samples of 720 heifers from lines selected for better calving ease breeding values and 190 heifers from control lines selected for average birth weights were followed through four parities. Select and control lines within the same population were selected to achieve similar yearling weight breeding values. Weights of sampled heifers in select lines were 2.6 kg (P < 0.01) lighter at birth but not different from control lines at weaning. Select lines had significantly shorter hip height, lighter mature weight, and greater calving success at second parity. Their calves were born significantly earlier with lighter weights and less assistance. Significant interactions with parity showed fewer calves assisted and greater calf survival to weaning as heifers but negligible differences with control lines in later parities. Steer progeny sampled from these dams in select lines (n = 204) were not different from steers in control lines (n = 91) for hot carcass weight but had significantly greater fat depth. Two production systems were compared considering the seven populations as replicates. The systems differed in selection history of females (select and control lines) and the use of bulls within their lines as young cows, but used the same bulls in both lines as older cows. Cows were culled after single unsuccessful breeding and kept for up to four parities. Select line cows tended (P ≤ 0.10) to wean more calves and stay in the herd longer. They were assisted significantly fewer times at calving and had greater calf weight gain to weaning when evaluated over their herd life. Mature weights were lighter in select lines, but marketable cow weight from the systems was nearly identical. Control lines did have more marketable young cow weight and select lines older cow weight. Weaned calf weight per heifer starting the system was significantly greater for the select heifer system due to greater survival of calves from heifers and greater calving success at second parity. No important unfavorable effects of genetic differences in calving ease were identified in this experiment.

Polymorphisms in μ-calpain (CAPN1) that beneficially associate with beef tenderness are reported to antagonistically associate with calving day in beef heifers and post-partum interval to estrus in beef cows. We, therefore, hypothesized that a molecular breeding value for slice shear force, calculated based on CAPN1 and calpastatin (CAST) genotypes, would demonstrate an antagonistic relationship between genomically predicted slice shear force and ordinal calving date in replacement beef heifers. A secondary objective of this study was to evaluate the association of a polymorphism in diacylglycerol O-acyltransferase (DGAT1) with reproductive traits in beef heifers. One hundred eighty-seven MARC III heifers (¼ Angus, ¼ Hereford, ¼ Red Poll, and ¼ Pinzgauer) that had been selectively bred to increase the frequency of these polymorphisms were submitted for monthly ultrasound exams beginning at 333 d of age and continuing until the start of breeding to determine pubertal status. At the last exam before breeding, all antral follicles were counted, and the length and height of each ovary was measured to determine if genomic selection for slice shear force associated with ovarian follicle number. Calving date, calf gender, and calf birth weight were recorded at parturition. Regression analysis of the molecular breeding value for slice shear force of the heifers on ordinal calving date indicated no association between genomic prediction of tenderness and calving date (P = 0.16); however, there was a tendency for age at puberty to be delayed in heifers as genetic merit for tenderness improved (P = 0.09). The results of the present study indicate that within experimental precision, selecting for tenderness using genomic predictions had minimal or no antagonistic association with reproductive performance in heifers. Further analysis of reproductive performance as cows is needed within this population but applying these genetic markers to select for tenderness in steers does not antagonize reproductive traits influencing conception or first calf birth date and birth weight in replacement beef heifers.

Commercially available bovine-specific assays are limited in number, and multiplex assays for this species are rare. Our objective was to develop a multiplex assay for the bovine inflammatory cytokines IL-1β, IL-6, and TNF-α using the Meso Scale Discovery U-PLEX platform. "Do-It-Yourself" ELISA kits that contained polyclonal antibodies, both unlabeled and biotinylated, and the specific recombinant bovine cytokine standard, were purchased for each of these three cytokines. The biotinylated antibodies were coupled to linkers that bind to specific locations within each well of the U-PLEX plate. Unique linkers were used for each of the cytokines. The unlabeled antibodies were conjugated with electrochemiluminescent labels to serve as detection antibodies. Each cytokine assay was optimized individually prior to performing an optimization on the multiplex assay containing reagents for all three cytokines. To calculate cytokine concentrations, standard curves were developed using the recombinant cytokines and were run concurrently on each plate. Standard curves for IL-1β and TNF-α were run at concentrations ranging from 0 to 50,000 pg/mL, and for IL-6 from 0 to 10,000 pg/mL. The average lowest level of detection concentration measured by the standard curves were 5.3 pg/mL, 0.92 pg/mL, and 22.34 pg/mL for IL-1β, IL-6, and TNF-α respectively, as determined by data from seven plates containing bovine plasma samples from a combination of healthy and diseased cattle. The U-PLEX platform was a viable means to develop custom analyte- and species-specific multiplex assays using privately developed or purchased sets of commercially available reagents.

Objectives were to estimate reciprocal effects of Romanov and Rambouillet breeds on survival, growth, and reproductive traits of F1 progeny and direct breed effects (Suffolk and Composite - ½ Columbia, ¼ Hampshire, and ¼ Suffolk) on survival and growth traits of the subsequent terminally sired lambs. Mature Rambouillet ewes (n = 243) were exposed to 20 Romanov rams over two seasons producing 621 lambs for evaluation of growth and survival traits with 274 F1 ewes being evaluated for reproduction traits through 4 yr of age. Similarly, mature Romanov ewes (n = 116) were exposed to 20 Rambouillet rams producing 601 lambs for evaluation of growth and survival traits with 176 F1 ewes being evaluated for reproduction traits through 4 yr of age. A total of 433 of those F1 ewes produced 3,431 lambs (1,552 litters) from 1,634 exposures to terminal sires over 4 yr. Terminal sires consisted of 38 Suffolk and 44 Composite rams. Reciprocal crossbred ewe lambs were produced from dramatically different uterine and neonatal environments, with litter size at birth from Romanov dams exceeding those from Rambouillet dams by 1.52 lambs (P < 0.001) and birth weight of lambs from Romanov dams averaged 3.41 kg compared with 4.26 kg from Rambouillet dams. Differences in BW were still evident at 140 d (P < 0.001) for dam-reared lambs. However, reciprocal ewe first breeding BW of both types were similar (P = 0.38). Minimal differences were observed in performance of reciprocal cross ewes through 4 yr for productivity, longevity, or progeny growth and survival. One exception was BW at 140 d where an interaction of dam breed with terminal sire breed reached significance for both dam-reared (P = 0.05) and nursery-reared (P = 0.02) lambs. This interaction was due to the lower weight of Composite-sired lambs out of reciprocal cross ewes born from Rambouillet dams. Composite rams increased number born (P < 0.01) and number weaned (P < 0.05) of the reciprocal cross ewes. Suffolk rams increased (P < 0.001) BW and growth rates from birth to 140 d of terminal progeny. Thus, there were little cumulative differences accrued over the 4 yr and no differences were detected for cumulative kilogram of lamb generated at 140 d per ewe exposed. The practical outcome of this evaluation was that performance levels of both types of Romanov crossbred ewes was similar allowing the industry to produce the desired crossbred ewes without needing large purebred ewe flocks of the less numerous Romanov breed.

The objective of this study was to enhance estimates of additive, dominance, and epistatic effects of marker polymorphisms on beef carcass and quality traits. Myostatin (MSTN) F94L SNP and the µ-calpain (CAPN1) 316 and 4751 SNP haplotype have previously been associated with fat and muscle traits in beef cattle. Multiyear selection in a composite population segregating these polymorphisms increased minor allele (F94L L) and chosen haplotype (CAPN1 CC and GT) frequencies to intermediate levels resulting in more precise estimates of additive and nonadditive genetic effects. During the 3 yr after selection, 176 steers were evaluated for growth, carcass, meat quality, tenderness (n = 103), and meat color traits. The statistical model included year, age of dam, age of the steer, and genotype in a random animal model. The 9 genotypes (3 CAPN1 diplotypes × 3 F94L genotypes) affected marbling score, ribeye area, adjusted fat thickness, vision yield grade (all P < 0.001), slice shear force (P = 0.03), and CIE L* reflectance (P = 0.01). Linear contrasts of the 9 genotypes estimated additive, recessive, and epistatic genetic effects. Significant additive effects of the F94L L allele decreased marbling score, adjusted fat thickness, vision yield grade, and slice shear force; and increased ribeye area and CIE L* reflectance. The homozygous F94L FF and LL genotypes differed by 1.3 to 1.9 phenotypic SD for most carcass traits and by 0.8 to 0.9 SD for slice shear force and CIE L* reflectance but carcass weight differed by only 3 kg (0.1 SD). The L allele was partially recessive to F for ribeye area (P = 0.02) and the heterozygous FL means tended to be closer to the FF genotype than the LL genotype for other carcass traits but differences from additive were not significant. The CAPN1 additive × F94L additive effect on slice shear force was the only significant epistatic estimate. The F94L L allele is prevalent in Limousin but nearly absent in other U.S. purebreds. This allele had about half of the effects on birth weight, muscle, and fat traits reported for severe MSTN mutations in Belgian Blue and Piedmontese breeds. The interaction between MSTN and CAPN1 genotypes may reflect the strong additive effects of MSTN F94L L allele on fat and muscle traits interfering with the phenotypic effect of CAPN1 genotype on meat tenderness.

Mature weight of beef cows in the United States has been increasing as a correlated response to selection for calf growth. Unfavorable genetic correlations between cow weight and various measures of female fertility, stayability, and lifetime production suggest declining cow productivity might also be expected as a correlated response to growth selection. National cattle evaluations, however, show increasing trends for stayability and sustained fertility. Random regression (RR) models were employed to further examine genetic relationships among cow weight and productivity, and to assess cumulative productivity traits observed throughout cows' productive lives. Records were from 13,707 females born in the Germplasm Evaluation (GPE) project and mated to calve first as 2-yr olds. Weights observed at pregnancy testing (n = 65,086) and calf production from each exposure to breeding (n = 71,583) were included in uni- and bivariate RR analyses. Production following each breeding season was added to previous production to obtain cumulative production records for each season that the female was exposed to breeding. Zero was added if the cow failed to produce after a breeding season. The number of pregnancies, calves born and calves weaned, as well as age and weight of weaned calves, were accumulated. Projected age-specific heritability (h2) estimates for cumulative production were low (

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to equalize CAPN1 haplotypes, CAST, and GHR genetic marker frequencies. The objective was to estimate the pleiotropic effects of these carcass quality oriented markers for body weight, reproduction, and first calf performance traits in 174 replacement beef females which were managed under 2 post-weaning development protocols. Heifers were weighed at 11-, 12-, and 13-mo, at first breeding season pregnancy evaluation, and prior to first calving season. Pubertal status was determined at 11-, 12-, and 13-mo of age. Antral follicles were counted, reproductive tracts were scored, and tract dimensions were measured at 13-mo. Body condition and hip height were scored and measured at pregnancy evaluation and prior to calving season. Heifer pregnancy and weaning rates and ordinal birth date were recorded. Calf body weights at birth and weaning were analyzed. Single df linear contrasts for recessive effects of the GHR heterozygous genotype showed significant decreases of 2.5–3.6% in 11-, 12-, and 13-mo heifer body weights and heifer weight prior to calving. The additive differences between GHR homozygotes were small and not significant for all body weights measured but a 1 wk difference in calf birth date was significant. For all 13-mo uterine measurements, scores, and antral follicle counts, only the CAST dominance contrast for medium antral follicle count was significant. The CAPN1 haplotype with a strong additive effect for increased beef tenderness also had a significant additive effect on calving date. Heifers homozygous for the tender haplotype calved 7.9 days later than heifers homozygous for the tough haplotype. Most heifer reproductive traits were not significantly affected by CAST and CAPN1 markers that are widely used to improve beef tenderness by selection and breeders should not be concerned with how these markers affect reproduction and other heifer traits with the possible exception of CAPN1 effects on calving date.

Shortening the period of recording individual feed intake may improve selection response for feed efficiency by increasing the number of cattle that can be recorded given facilities of fixed capacity. Individual DMI and ADG records of 3,462 steers and 2,869 heifers over the entire intake recording period (range 62 to 154 d; mean 83 d; DMI83 and ADG83, respectively), DMI and ADG for the first 42 d of the recording period (DMI42 and ADG42, respectively), and postweaning ADG based on the difference between weaning and yearling weights (PADG) were analyzed. Genetic correlations among DMI42 and DMI83, ADG42 and ADG83, ADG42 and PADG, and ADG83 and PADG were 0.995, 0.962, 0.852, and 0.822, respectively. Four objective functions [feed:gain ratio in steers (FGS) and heifers (FGH); residual gain (RG); and residual feed intake (RFI)] based on DMI83 and ADG83 were considered. Indices using DMI42 and ADG42 (I42); DMI42 and PADG (IPW); and DMI42, ADG42, and PADG (IALL) were developed. Accuracy of the 5 EBV, 4 objectives, and 12 objective × index combinations were computed for all 12,033 animals in the pedigree. Accuracies of indices (IA) were summarized for animals with accuracies for objectives (OA) of 0.25, 0.5, 0.75, and 1. For the RG objective and animals with OA of 0.75, indices I42, IPW, and IALL had IA of 0.63, 0.55, and 0.67, respectively. Differences in IA increased with increased emphasis on ADG83 in the objective. Differences in IA between I42 and IPW usually increased with OA. Relative efficiency (RE) of selection on 42-d tests compared with 83 d was computed based on differences in IA and selection intensities of 5%, 25%, 50%, and 75% under the 83-d scenario, assuming 65% more animals could be tested for 42 d. For 25% selected for the RG objective, and animals with OA of 0.75, indices I42, IPW, and IALL had RE of 1.02, 0.90, and 1.10, respectively. As % selected, OA, and emphasis on DMI increased, RE increased. Relative efficiency varied considerably according to assumptions. One-half of the scenarios considered had RE > 1.15 with a maximum of 2.02 and 77% RE > 1.0. A shorter period of recording DMI can improve selection response for feed efficiency. Selection for the efficiency objectives would not affect PADG. It will be most effective if ADG over the period coinciding with intake recording and ADG over a much longer period of time are simultaneously included in a multiple-trait genetic evaluation with DMI and used in a selection index for efficiency.

Genomic prediction utilizing causal variants could increase selection accuracy above that achieved with SNPs genotyped by currently available arrays used for genomic selection. A number of variants detected from sequencing influential sires are likely to be causal, but noticeable improvements in prediction accuracy using imputed sequence variant genotypes have not been reported. Improvement in accuracy of predicted breeding values may be limited by the accuracy of imputed sequence variants. Using genotypes of SNPs on a high-density array and non-synonymous SNPs detected in sequence from influential sires of a multibreed population, results of this examination suggest that linkage disequilibrium between non-synonymous and array SNPs may be insufficient for accurate imputation from the array to sequence. In contrast to 75% of array SNPs being strongly correlated to another SNP on the array, less than 25% of the non-synonymous SNPs were strongly correlated to an array SNP. When correlations between non-synonymous and array SNPs were strong, distances between the SNPs were greater than separation that might be expected based on linkage disequilibrium decay. Consistently near-perfect whole-genome linkage disequilibrium between the full array and each non-synonymous SNP within the sequenced bulls suggests that whole-genome approaches to infer sequence variants might be more accurate than imputation based on local haplotypes. Opportunity for strong linkage disequilibrium between sequence and array SNPs may be limited by discrepancies in allele frequency distributions, so investigating alternate genotyping approaches and panels providing greater chances of frequency-matched SNPs strongly correlated to sequence variants is also warranted. Genotypes used for this study are available from https://www.animalgenome.org/repository/pub/;USDA2017.0519/.

Cows selected for heifer calving ease and yearling weight might also show changes in other important traits. Cattle from select and control lines within 7 populations were selected for reduced heifer calving difficulty EPD (select) or for average birth weight EPD (control) and for identical yearling weight EPD (select and control). Heifers randomly sampled within sire and born in the 4th and 5th of 7 years of selection were retained until 6 years of age with culling for once open and health, but not for other performance. Both lines were bred to the same bulls for calves born during the 3 years post-selection. Select line heifers were 7% lighter (-2.6 ± 0.5 kg, P < 0.01) at birth and not different at weaning (0.2 ± 1.5 kg) or yearling ages (-2.1 ± 2.7 kg). Select cow mature weights estimated by Brody growth curves were 5.2% lighter (-32.9 ± 3.7 kg, P < 0.01) and heights were 2.2% shorter (-3.0 ± 0.7 cm, P < 0.01) than controls. Calf weaning weights were not different. Interactions between 1st calving select (bred to select bulls) and control heifers (bred to control bulls) vs. older cows (all bred to the same bulls) were significant for survival (P < 0.01) and calving assistance (P = 0.03). Select line heifers increased calf survival (86.8% vs. 70.9%) and had decreased calving assistance (16.4% vs. 39.3%), but differences in cows for these traits were negligible. Calves born per select cow exposed exceeded those born per control cow only for 2nd calving (7.1%, P = 0.04), possibly due to reduced calving difficulty as heifers. Selection for calving ease and yearling weight resulted in cows with smaller mature size and similar or better calving ease, calf survival, and calf weaning weight. USDA is an equal opportunity provider and employer.

Steers (n = 868) were raised, feedlot-finished with ad libitum access to a high-energy diet and harvested to determine if there is genomic control of fatty acid profile traits in beef breeds common to the United States. Cattle included purebred and crossbred progeny of Angus, Red Angus, Hereford, Shorthorn, Simmental, Charolais, Limousin, Gelbvieh, Maine Anjou, Chiangus, Braunvieh, Salers, Brahman, Brangus, Santa Gertrudis, and Beefmaster as well as three composite lines. Either directly or through imputation, genotypes were determined for > 133,000 functional single nucleotide polymorphisms (SNP). At approximately 38 h postmortem, a 2.54-cm-thick longissimus steak was obtained from the 13th rib region of the left side of each carcass. At 14 d postmortem, steaks were cooked and subsequently longissimus was pulverized in liquid nitrogen. Fatty acid profile was determined by gas chromatography and mass spectrometry. A genome-wide association study was conducted for fatty acid profile traits expressed as a deviation from the contemporary group mean using the Mixed Linear Model Analysis of SNP & Variation Suite 8.8.3 (Golden Helix) and Pre-computed Kinship Matrix using the GBLUP Genomic Relationship Matrix. A SNP in coiled coil domain containing 57 (CCDC57; Chromosome 19 at 51,349,695) affected the percentage of C14:0 (P < 10–46), short-chain fatty acids (P < 10–36), and saturated fatty acids (P < 10–17). Also, a SNP in thyroid hormone responsive (THRSP; Chromosome 29 at 18,090,403) affected the percentage of C14:0 (P < 10–16) and short-chain fatty acids (P < 10-10). The percentage of polyunsaturated fatty acids was affected by SNP in myostatin (Chromosome 2 at 6,213,980; P < 10–15). These results show that fatty acid profile of beef can be changed through genetic selection but, it is not clear if the level of change will be great enough to impact human health.

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for 2 yr to equalize and genetic marker frequencies to evaluate the epistatic and pleiotropic effects of these markers on BW, reproduction, and first calf performance traits in replacement beef females ( = 171) managed under 2 postweaning development protocols. Traits evaluated on the heifers were birth BW, weaning BW, 11-mo BW, 12-mo BW, 13-mo BW, first breeding season pregnancy evaluation BW, first calving season BW, 11-mo puberty, 12-mo puberty, 13-mo puberty, first breeding season pregnancy, and first calf weaning rate. Additionally, heifer's first calf performance traits of ordinal calving date, first calf birth BW, and first calf weaning BW (with and without age adjustment) were analyzed. Selection to increase minor allele frequencies and balanced sampling across genotype classes enhanced the ability to detect all genetic effects except dominance × dominance epistasis. The × genotype effect was significant ( < 0.05) for 11-mo BW and 12-mo BW and tended to be significant ( = 0.08) for 13-mo BW. Consistently, for all 3 traits, the most significant effect among epistatic × genotype effects was the additive effect, with the G allele decreasing BW. There were no associations between × genotype and fertility related traits ( ≥ 0.46) in this study. Additionally, there were no × genotype associations with first progeny performance traits ( ≥ 0.14). The large effect of the additive × additive interaction on first calf weaning BW was imprecisely estimated, which may warrant further investigation.

Background:Mannheimia haemolyticais the major bacterial infectious agent of bovine respiratory disease complex and causes severe morbidity and mortality during lung infections.M. haemolyticasecretes a protein leukotoxin (Lkt) that binds to the CD18 receptor on leukocytes, initiates lysis, induces inflammation, and causes acute fibrinous bronchopneumonia. Lkt binds the 22-amino acid CD18 signal peptide domain, which remains uncleaved in ruminant species. Our aim was to identify missense variation in the bovine CD18 signal peptide and measure the effects on Lkt binding.Methods:Missense variants in the integrin beta 2 gene (ITGB2) encoding CD18 were identified by whole genome sequencing of 96 cattle from 19 breeds, and targeted Sanger sequencing of 1238 cattle from 46 breeds. The ability of different CD18 signal peptide variants to bind Lkt was evaluated by preincubating the toxin with synthetic peptides and applying the mixture to susceptible bovine cell cultures in cytotoxicity-blocking assays.Results:We identified 14 missense variants encoded on 15 predicted haplotypes, including a rare signal peptide variant with a cysteine at position 5 (C5) instead of arginine (R5). Preincubating Lkt with synthetic signal peptides with C5blocked cytotoxicity significantly better than those with R5. The most potent synthetic peptide (C5PQLLLLAGLLA) had 30-fold more binding activity compared to that with R5.Conclusions:The results suggest that missense variants in the CD18 signal peptide affect Lkt binding, and animals carrying the C5allele may be more susceptible to the effects of Lkt. The results also identify a potent class of non-antibiotic Lkt inhibitors that could potentially protect cattle from cytotoxic effects during acute lung infections.

Cattle losses from larkspur (Delphinium spp.) toxicity are a long-term challenge on the rangelands of western North America. In addition to animal factors that affect livestock poisonings, plant alkaloid composition (chemotype) affects the intoxication of cattle because some chemotypes are significantly more toxic. Differences in larkspur chemotype toxicity are due to the ratios of N-(methylsuccinimido) anthranoyllycoctonine (MSAL)-type alkaloids to non-MSAL-type alkaloids and the concentrations of those alkaloids in the plant material. The objective of this study was to compare the responses of 6 Angus heifers to 6 chemotypes of larkspur using a Latin square study design. These Angus heifers from the USDA-ARS, Meat Animal Research Center in Clay Center, NE, were chosen for this research because they are the most larkspur-susceptible cattle observed to date. The 6 heifers were given an oral dose of dried ground larkspur and tested for muscle weakness with an exercise test (i.e., walk time). The 6 chemotypes of larkspur had non-MSAL to MSAL-type alkaloid ratios ranging from 1.4:1 to 6:1 and were administered at an oral dose of 7.5 mg/kg MSAL-type alkaloids BW. There was a treatment effect due to larkspur chemotype (P < 0.0001), and period effects were not significant (P = 0.6). There were also significant correlations between the length of time walking on a dirt track at 5 to 6 km/h, and total alkaloid dose (r = -0.92, P = 0.0045) and alkaloid ratio (r = -0.81, P = 0.0258). Serum alkaloid concentrations at 24 h after dosing were representative of the relative abundance of the alkaloid in the plant material. Results from this work suggest that total alkaloid concentrations in combination with alkaloid ratios can be used together to accurately predict the plant risk component of larkspur poisoning to grazing cattle. Animal factors such as cattle age, breed, and sex must also be considered to comprehensively manage larkspur risk.

Selection for beef carcass traits using SNP may have off-target effects on reproduction. Composite cattle (MARC III) were selected for SNP affecting beef tenderness. Selection increased minor allele frequency of a polymorphism in calpastatin (CAST) and changed frequencies of three common haplotypes in µ-calpain (CAPN1) towards 0.33 resulting in heifers of all 18 (3 CAST × 6 CAPN1) genotypes. The minor allele frequency for a diacylglycerol O-acyltransferase 1 (DGAT1) polymorphism was also increased but was not expected to affect beef tenderness. About 60 heifers were retained over 3 years (N = 187). Retention was based on representing the entire genotypic distribution. Contemporary steers from the population were harvested and measured for meat tenderness using slice shear force. Steer data were used to predict molecular breeding values (MBVSSF; 0.0 to 4.1 kg) for the heifers based on CAST and CAPN1. Traits were analyzed with linear covariates for MBVSSF and number of DGAT1 K alleles (0, 1, or 2), fixed effects appropriate for the trait, and random sire of heifer effects. A 1.0 kg increase in heifer MBVSSF was associated (P ≤ 0.05) with 5.6 ± 2.8 d earlier puberty and a 0.73 ± 0.36 kg increase in birth weight of their first calf. Pregnancy rates were not affected but would have had to exceed 5 to 6 % per kg MBVSSF to be significant. A larger experiment would be needed to detect differences that are smaller but still economically important. Regression coefficients for DGAT1 were significant for pre-calving hip height (0.78 ± 0.37 cm) and 26-mo weight (7.2 ± 3.6 kg). Within the precision of this experiment, selecting for more tender MBVSSF or for DGAT1 appears to have little negative effect on economically important traits in heifers but may increase age at puberty. USDA is an equal opportunity provider and employer.

The genome sequence was obtained from 270 sires used in the Germplasm Evaluation (GPE) project. These bulls included 154 purebred AI sires from GPE Cycle VII breeds (Hereford, Angus, Simmental, Limousin, Charolais, Gelbvieh, and Red Angus), 83 F crosses of those breeds, and 33 AI sires from 8 other breeds. The exome capture sequence targeting coding regions of the genome was obtained from 176 of these bulls. Sequence reads were mapped to the UMD 3.1 bovine genome assembly; a mean of 2.5-fold (x) coverage per bull was obtained from the genomic sequence, and the targeted exons were covered at a mean of 20.0x. Over 28.8 million biallelic sequence variants were detected where each allele was present in at least 3 different bulls. These included 22.0 million previously reported variants and 94.1% of the 774,660 autosomal and BTA X SNP on the BovineHD BeadChip assay (HD). More than 92% of the variants detected in targeted exons were also detected from the low-coverage genome sequence. Less than 1% of the variants detected from the combined genome and exome sequence occurred in annotated protein-coding sequences and 5' and 3' untranslated regions (UTR) surrounding the 19,994 annotated protein coding regions. Variation was detected in the coding sequence or UTR of 96.8% of the genes: loss-of-function variants were predicted for 3,298 genes, 14,973 contained nonsynonymous variants, 11,276 had variation in UTR, and 17,721 genes contained synonymous variants. Minor allele frequencies (MAF) were

The use of genetic markers to aid in selection decisions to improve carcass and growth characteristics is of great interest to the beef industry. However, it is important to examine potential antagonistic interactions with fertility in cows before widespread application of marker-assisted selection. The objective of the current experiment was to examine the influence of 2 commercially available markers currently in use for improving carcass traits, the myostatin (MSTN) F94L and μ-calpain (CAPN1) 316 and 4751 polymorphisms, on heifer development and reproductive performance. In Exp. 1, beef heifers (n = 146) were evaluated for growth and reproductive traits over a 3-yr period to determine if these polymorphisms influenced reproductive performance. In Exp. 2, heifers representing the 2 homozygous genotypes for the MSTN F94L polymorphism were slaughtered on d 4 of the estrous cycle and reproductive tracts were collected for morphological examination. In Exp. 1, there was a tendency (P = 0.06) for birth BW to be affected by MSTN with the Leu allele increasing birth BW in an additive fashion. Additionally, MSTN significantly affected the proportion of pubertal heifers by the start of the breeding season (P 0.15). The GT haplotype of CAPN1, which was previously associated with decreased meat tenderness, was associated with an additive decrease in birth BW of the first calf born to these heifers (P 0.05). From these results, we concluded that the MSTN F94L and CAPN1 polymorphisms can be used to improve carcass traits without compromising fertility in beef heifers. The influence of these markers on cow performance and herd life remains to be determined. While the delay in puberty associated with the MSTN F94L polymorphism did not negatively impact reproductive performance in heifers, caution should be used when combining this marker with other markers for growth or carcass traits until the potential interactions are more clearly understood.

Background: Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals. Methods: A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams. The animals shared minimal pedigree relationships and represent nine popular U.S. breeds and a composite line. The genomes are viewable online with the user-friendly Integrated Genome Viewer environment, and may be used to identify and decode gene variants present in U.S. sheep. Results: The genomes had a combined average read depth of 16, and an average WGS genotype scoring rate and accuracy exceeding 99%. The utility of this resource was illustrated by characterizing three genes with 14 known coding variants affecting litter size in global sheep populations: growth and differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), and bone morphogenetic protein receptor 1B (BMPR1B). In the 96 U.S. rams, nine missense variants encoding 11 protein variants were identified. However, only one was previously reported to affect litter size (GDF9 V371M, Finnsheep). Two missense variants in BMP15 were identified that had not previously been reported: R67Q in Dorset, and L252P in Dorper and White Dorper breeds. Also, two novel missense variants were identified in BMPR1B: M64I in Katahdin, and T345N in Romanov and Finnsheep breeds. Based on the strict conservation of amino acid residues across placental mammals, the four variants encoded by BMP15 and BMPR1B are predicted to interfere with their function. However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in BMP15 and BMPR1B with daughters of these rams. Conclusions: Collectively, this report describes a new resource for discovering protein variants in silico and identifies alleles for further testing of their effects on litter size in U.S. breeds.

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC III) was subjected to marker-assisted selection for multiple years to equalize specific marker frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits (n=254), 2) estimate pleiotropic effects of previously reported SNP on nontarget performance traits (n=542 or 254), and 3) evaluate tenderness SNP specific residual variance for LM tenderness. Three haplotypes within μ-calpain (CAPN1), a SNP in calpastatin (CAST), and a dinucleotide substitution in diacylglycerol O-acyltransferase 1 (DGAT1) were successfully selected to equalize their frequencies. Traits evaluated were birth BW, weaning BW, yearling BW, final BW, dressing percent, HCW, fat thickness, LM area, USDA marbling score, yield grade, LM slice shear force (SSF), and visible and near-infrared (VISNIR)-predicted SSF. While the CAPN1 genotype effect on SSF was not significant (P=0.12), the direction and size of CAPN1 contrasts were consistent with previous research. Effects on SSF between divergent CAPN1 haplotypes (1.153 kg) and the additive effect of CAST (0.902 kg) were large, and animals homozygous for tender alleles at both CAPN1 and CAST would have 4.11 kg lower SSF (27.5% of the mean) than animals homozygous tough for both markers. Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P=0.40). There were significant effects for DGAT1 on adjusted fat thickness (P=0.02) and VISNIR-predicted SSF (P

Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within μ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an increase in mean and an increase in variation. This work confirms the importance of CAPN1 and CAST for tenderness in beef, provides a new effect of CAST on beef tenderness, and questions the utility of GHR as a selection marker for beef quality.

Bovine respiratory disease (BRD) is the most economically important disease in U.S. feedlots. Infection can result in morbidity, mortality, and reduced average daily gain. Cheap and reliable genetic methods of prediction and protection from BRD would be highly advantageous to the industry. The immune response may correlate with BRD incidence. Cattle (n = 2,182) were vaccinated against common viral and bacterial pathogens of BRD. Two blood samples were collected, one during booster vaccination and one 21d later, enabling 3 phenotypes for each trait [prebooster (pre), postbooster (post), and delta (post minus pre)]. From the blood samples innate and adaptive responses [counts of white blood cells (WBC), neutrophils, lymphocytes, monocytes, eosinophils, and basophils] were measured. In addition, feedlot ADG and binary traits [health records (HR; 0 = healthy, 1 = ill) and lung scores (LS; collected at harvest; 0 = no lesions, 1 = lesions)] were also recorded. Traits ADG, HR, and LS have all been significantly correlated with infection to BRD. In this investigation we aimed to find correlations between the immune response and ADG, HR, and LS to find an easily measurable trait that would be a good predictor of BRD resistance after vaccination. The results showed an average positive delta for the innate immune response (eosinophils, basophils, neutrophils), whereas the adaptive immune response had an average negative delta (lymphocytes). Overall, we discovered that the immune responses had moderately high heritabilities (h(2); lowest: delta monocytes, 0.21 ± 0.05; greatest: pre lymphocytes: 0.5 ± 0.05), with lymphocytes having the greatest h(2) throughout the study (h(2) ≥ 0.41). All genetic correlations were calculated using bivariate REML models. Although LS did not significantly correlate with any of the immune phenotypes, both ADG (post lymphocytes, -0.24 ± 0.12) and HR (pre eosinophils, -0.67 ± 0.29; delta WBC, -0.5 ± 0.24, and delta lymphocytes, -0.67 ± 0.21) did. All the significant genetic correlations with HR were negative; resistance to BRD appears to be a function of greater delta lymphocytes and WBC. The increase in eosinophils may potentially link its role in decreasing lymphocytes. These results may enable producers to predict if revaccination, quarantine, and breeding of animals is required to reduce the incidence of BRD postvaccination. In addition, immunological phenotypes maybe used to aid genomic selection indices to select animals with greater rates of protection after BRD vaccination.

Vitamin D is an important modulator of calcium homeostasis and has several effects on the immune system. The objective of the study was to estimate its heritability and to identify genomic regions associated with concentration of circulating 25-hydroxyvitamin D (25OHD) in beef cattle. Status of vitamin D was measured in crossbred animals from Cycle VII of the United States Meat Animal Research Center (USMARC) Germplasm Evaluation Project. Progeny were born from March through May in 2008 and in 2010. Heritability was estimated and a genomewide association study was conducted on the concentration of 25OHD measured in 1,432 animals at preconditioning and 1,333 animals at weaning. Genotyping of the population was done by imputing from the parental generation genotyped with a high density array (777,000 SNP) to a target population genotyped with a medium density SNP array (50,000 SNP). After imputation, 675,018 SNP were used in the genomewide association study. Heritability of concentration of circulating 25OHD in cattle at preconditioning and at weaning was 0.41 ± 0.08 and 0.32 ± 0.11, respectively. A region on chromosome 3 was associated with circulating 25OHD. The region on BTA3 had 7 SNP significantly (P < 7.4 × 10(-8)) associated at the genomewide level with serum concentrations of serum 25OHD. Genomewide significant SNP spanned the region between 84.93 and 86.65 megabases (Mb); however, 6 SNP reside between 86.64 and 86.65 Mb. The gene CYP2J2 was identified as a candidate gene associated with concentrations of serum 25OHD in cattle. This is 1 of 6 enzymes involved in metabolizing vitamin D to 25OHD. Results from the present study suggest that CYP2J2 is a gene controlling serum 25OHD concentrations in cattle. CYP2J2 should be considered a prime candidate for understanding both genetic and physiological factors affecting serum 25OHD concentrations in cattle and, therefore, vitamin D status.

Genetic markers in casein (CSN1S1) and thyroglobulin (TG) genes have previously been associated with fat distribution in cattle. Determining the nature of these genetic associations (additive, recessive, or dominant) has been difficult, because both markers have small minor allele frequencies in most beef cattle populations. This results in few animals homozygous for the minor alleles. selection to increase the frequencies of the minor alleles for 2 SNP markers in these genes was undertaken in a composite population. The objective was to obtain better estimates of genetic effects associated with these markers and determine if there were epistatic interactions. Selection increased the frequencies of minor alleles for both SNP from 0.10). Additive, dominance, and epistatic SNP association effects were estimated from genotypic effects for adjusted fat thickness and predicted meat tenderness. Adjusted fat thickness showed a dominance association with TG SNP (P < 0.06) and an epistatic additive CSN1S1 × additive TG association (P < 0.03). For predicted meat tenderness, heterozygous TG meat was more tender than meat from either homozygote (P < 0.002). Dominance and epistatic associations can result in different SNP allele substitution effects in populations where SNP have the same linkage disequilibrium with causal mutations but have different frequencies. Although the complex associations estimated in this study would contribute little to within-population selection response, they could be important for marker-assisted management or reciprocal selection schemes.

High energy propellants for human lunar missions are analyzed, focusing on very advanced ozone and atomic hydrogen. One of the most advanced launch vehicle propulsion systems, such as the Space Shuttle Main Engine (SSME), used hydrogen and oxygen and had a delivered specific impulse of 453 seconds. In the early days of the space program, other propellants (or so called metapropellants) were suggested, including atomic hydrogen and liquid ozone. Theoretical and experimental studies of atomic hydrogen and ozone were conducted beginning in the late 1940s. This propellant research may have provided screenwriters with the idea of an atomic hydrogen-ozone rocket engine in the 1950 movie, Rocketship X-M. This paper presents analyses showing that an atomic hydrogen-ozone rocket engine could produce a specific impulse over a wide range of specific impulse values reaching as high as 1,600 s. A series of single stage and multistage rocket vehicle analyses were conducted to find the minimum specific impulse needed to conduct high energy round trip lunar missions.

Genomic selection involves the assessment of genetic merit through prediction equations that allocate genetic variation with dense marker genotypes. It has the potential to provide accurate breeding values for selection candidates at an early age and facilitate selection for expensive or difficult to measure traits. Accurate across-breed prediction would allow genomic selection to be applied on a larger scale in the beef industry, but the limited availability of large populations for the development of prediction equations has delayed researchers from providing genomic predictions that are accurate across multiple beef breeds. In this study, the accuracy of genomic predictions for 6 growth and carcass traits were derived and evaluated using 2 multibreed beef cattle populations: 3,358 crossbred cattle of the U.S. Meat Animal Research Center Germplasm Evaluation Program (USMARC_GPE) and 1,834 high accuracy bull sires of the 2,000 Bull Project (2000_BULL) representing influential breeds in the U.S. beef cattle industry. The 2000_BULL EPD were deregressed, scaled, and weighted to adjust for between- and within-breed heterogeneous variance before use in training and validation. Molecular breeding values (MBV) trained in each multibreed population and in Angus and Hereford purebred sires of 2000_BULL were derived using the GenSel BayesCπ function (Fernando and Garrick, 2009) and cross-validated. Less than 10% of large effect loci were shared between prediction equations trained on (USMARC_GPE) relative to 2000_BULL although locus effects were moderately to highly correlated for most traits and the traits themselves were highly correlated between populations. Prediction of MBV accuracy was low and variable between populations. For growth traits, MBV accounted for up to 18% of genetic variation in a pooled, multibreed analysis and up to 28% in single breeds. For carcass traits, MBV explained up to 8% of genetic variation in a pooled, multibreed analysis and up to 42% in single breeds. Prediction equations trained in multibreed populations were more accurate for Angus and Hereford subpopulations because those were the breeds most highly represented in the training populations. Accuracies were less for prediction equations trained in a single breed due to the smaller number of records derived from a single breed in the training populations.

The promise of genomic selection is accurate prediction of the genetic potential of animals from their genotypes. Simple DNA tests might replace low-accuracy predictions for expensive or lowly heritable measures of puberty and fertility based on performance and pedigree. Knowing with some certainty which DNA variants (e.g., SNP) affect puberty and fertility is the best way to fulfill the promise. Several SNP from the BovineSNP50 assay have tentatively been associated with reproductive traits including age at puberty, antral follicle count, and pregnancy observed on different sets of heifers. However, sample sizes are too small and SNP density is too sparse to definitively determine genomic regions harboring causal variants affecting reproductive success. Additionally, associations between individual SNP and similar phenotypes are inconsistent across data sets, and genomic predictions do not appear to be globally applicable to cattle of different breeds. Discrepancies may be a result of different QTL segregating in the sampled populations, differences in linkage disequilibrium (LD) patterns such that the same SNP are not correlated with the same QTL, and spurious correlations with phenotype. Several approaches can be used independently or in combination to improve detection of genomic factors affecting heifer puberty and fertility. Larger samples and denser SNP will increase power to detect real associations with SNP having more consistent LD with underlying QTL. Meta-analysis combining results from different studies can also be used to effectively increase sample size. High-density genotyping with heifers pooled by pregnancy status or early and late puberty can be a cost-effective means to sample large numbers. Networks of genes, implicated by associations with multiple traits correlated with puberty and fertility, could provide insight into the complex nature of these traits, especially if corroborated by functional annotation, established gene interaction pathways, and transcript expression. Example analyses are provided to demonstrate how integrating information about gene function and regulation with statistical associations from whole-genome SNP genotyping assays might enhance knowledge of genomic mechanisms affecting puberty and fertility, enabling reliable DNA tests to guide heifer selection decisions.

Knowledge of breed composition can be useful in multiple aspects of cattle production, and can be critical for analyzing the results of whole genome-wide association studies currently being conducted around the world. We examine the feasibility and accuracy of using genotype data from the most prevalent bovine genome-wide association studies platform, the Illumina BovineSNP50 array (Illumina Inc., San Diego, CA), to estimate breed composition for individual breeds of cattle. First, allele frequencies (of Illumina-defined allele B) of SNP on the array for each of 16 beef cattle breeds were defined by genotyping a large set of more than 2,000 bulls selected in cooperation with the respective breed associations to be representative of their breed. With these breed-specific allele frequencies, the breed compositions of approximately 2,000 two-, three-, and four-way cross (of 8 breeds) cattle produced at the US Meat Animal Research Center were predicted by using a simple multiple regression technique or Mendel (http://www.genetics.ucla.edu/software/mendel) and their genotypes from the Illumina BovineSNP50 array, and were then compared with pedigree-based estimates of breed composition. The accuracy of marker-based breed composition estimates was 89% when using either estimation method for all breeds except Angus and Red Angus (averaged 79%), based on comparing estimates with pedigree-based average breed composition. Accuracy increased to approximately 88% when these 2 breeds were combined into an aggregate Angus group. Additionally, we used a subset of these markers, approximately 3,000 that populate the Illumina Bovine3K (Illumina Inc.), to see whether breed composition could be estimated with similar accuracy when using this reduced panel of SNP makers. When breed composition was estimated using only SNP in common with the Bovine 3K array, accuracy was slightly reduced to 83%. These results suggest that SNP data from these arrays could be used to estimate breed composition in most US beef cattle in situations where pedigree is not known (e.g., multiple-sire natural service matings, non-source-verified animals in feedlots or at slaughter). This approach can aid analyses that depend on knowledge of breed composition, including identification and adjustment of breed-based population stratification, when performing genome-wide association studies on populations with incomplete pedigrees. In addition, SNP-based breed composition estimates may facilitate fitting cow germplasm to the environment, managing cattle in the feedlot, and tracing disease cases back to the geographic region or farm of origin.

The effects of individual SNP and the variation explained by sets of SNP associated with DMI, metabolic midtest BW, BW gain, and feed efficiency, expressed as phenotypic and genetic residual feed intake, were estimated from BW and the individual feed intake of 1,159 steers on dry lot offered a 3.0 Mcal/kg ration for at least 119 d before slaughter. Parents of these F 1 × F 1 (F 2 1 ) steers were AI-sired F 1 progeny of Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental bulls mated to US Meat Animal Research Center Angus, Hereford, and MARC III composite females. Steers were genotyped with the BovineSNP50 BeadChip assay (Illumina Inc., San Diego, CA). Effects of 44,163 SNP having minor allele frequencies >0.05 in the F 2 1 generation were estimated with a mixed model that included genotype, breed composition, heterosis, age of dam, and slaughter date contemporary groups as fixed effects, and a random additive genetic effect with recorded pedigree relationships among animals. Variance in this population attributable to sets of SNP was estimated with models that partitioned the additive genetic effect into a poly-genic component attributable to pedigree relationships and a genotypic component attributable to genotypic relationships. The sets of SNP evaluated were the full set of 44,163 SNP and subsets containing 6 to 40,000 SNP selected according to association with phenotype. Ninety SNP were strongly associated (P < 0.0001) with at least 1 efficiency or component trait; these 90 accounted for 28 to 46% of the total additive genetic variance of each trait. Trait-specific sets containing 96 SNP having the strongest associations with each trait explained 50 to 87% of additive variance for that trait. Expected accuracy of steer breeding values predicted with pedigree and genotypic relationships exceeded the accuracy of their sires predicted without genotypic information, although gains in accuracy were not sufficient to encourage that performance testing be replaced by genotyping and genomic evaluations.

Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age were identified by marker association using the highly parallel BovineSNP50 BeadChip (50K) assay composed of 54,001 individual SNP. Genotypes were obtained from progeny (F(1); 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F(1)(2) = F(1) x F(1); 1,306 steers and 707 females) of 150 AI sires representing 7 breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Genotypes and birth, weaning, and yearling BW records were used in whole-genome association analyses to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning BW gain (WG), 160-d adjusted postweaning BW gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT + WG) and 365-d adjusted yearling weight (YW = BWT + WG + PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P that may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 231 SNP meeting stringent criteria generally coincided with described previously QTL affecting growth traits. The 12,425 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatal growth relative to BWT.

Selection was used to create select and control lines within 4 purebred and 3 composite cattle populations. Both lines were selected for similar direct yearling weight and maternal weaning weight EBV. Select lines were selected for lower 2-yr-old heifer calving difficulty score EBV and control lines were selected for average birth weight EBV. Select (n = 6,926) and control (n = 2,043) line calves were born from 1993 through 1999 and selection began with the 1992 mating. High replacement rates resulted in 2,188 births to select line and 598 births to control line heifers. Data used to calculate EBV came from these populations and from 15 yr of data preceding the experiment. Calving difficulty was scored from 1 (no assistance) to 7 (cesarean). Calving difficulty scores from all twins, malpresentations, and cows 3 yr old and older were eliminated. Except for the first year, when a single-trait BLUP was used, a multiple-trait BLUP was used to calculate direct and maternal EBV for calving difficulty score, birth weight, and weaning weight, and direct EBV for postweaning gain. Sires (n = 498) were selected from those born in both the preceding populations and the select and control lines. In purebred populations, some industry sires (n = 88) were introduced based on their EPD. Tests of mean select and control line EBV differences of calves born in the final 2 yr were based on population variation. Select line direct EBV were 1.06 lower for heifer calving difficulty score (P < 0.001) and 3.5 kg lower (P < 0.001) for birth weight than controls. Average differences for other EBV were small and not significant. Yearling weight EBV was intentionally increased in both select and control lines of purebred populations. Angus, Hereford, Charolais, and Gelbvieh yearling weight EBV in control lines increased by 32.4, 27.2, 21.0, and 10.5 kg, respectively, from 1991 and 1992 to 1998 and 1999 compared with an average increase of 2.7 kg in composite populations. Birth weight direct EBV in purebred control lines increased by approximately 8% of yearling weight EBV increases. Selection based on a multiple-trait BLUP was able to create lines differing in calving difficulty score and birth weight EBV, but not in weaning weight and postweaning gain EBV. Differences between lines should be useful for evaluating BLUP and other traits and for identifying potential limitations of genetically decreasing calving difficulty score and birth weight.