LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.     

Glucose and insulin responses to different dietary energy sources in Thoroughbred broodmares grazing cool season pasture

The objectives of this study were to characterize the glycemic and insulinemic responses of Thoroughbred broodmares fed late spring pasture only or a mixture of pasture and a high starch or low starch feed and to test hypotheses about differences in the glycemic and insulinemic effects of these dietary regimes. A group of 15 mares were divided into three treatment groups; pasture and high starch feed (PHS), pasture and low starch feed (PLS), and pasture only (PO) and maintained in these groups for 4.5 months prior to this study. These groups were maintained on a single pasture that was temporarily divided into three sections. The study protocol was conducted over two days. On day 1 the mares were fed their respective treatments and on day 2 all mares were allowed access to pasture only. On both days plasma glucose and insulin were measured in samples taken over a 7.5 h period. Baseline measurements for glucose and insulin were not different between any of the treatment groups on either day (P > 0.05). The baseline insulin concentrations of these pasture-kept mares (26.7 ± 8.3 mIU/L) were high compared to those reported from stall-kept horses. Plasma glucose and insulin on day 1 were influenced by treatment group, sample time, and an interaction between treatment and time (P < 0.05). On day 2 there was no significant influence of treatment group (P > 0.05). Glucose and insulin rose to higher (P < 0.01) peak concentrations in the PHS group on day 1 when compared to the PLS and PO groups, with no difference (P > 0.05) detected between the PLS and PO groups. These results are reflected in greater areas under the concentration-time curves for glucose and insulin in the PHS group on day 1 (P < 0.05). On day 2 there were no differences in any of the glucose and insulin characteristics for any of the treatment groups (P > 0.05). These results indicate a clear difference in the glycemic and insulinemic effect of the PHS feed compared to the PLS and PO groups. Of further interest are the glucose and insulin characteristics of these pasture-kept mares that indicate a low insulin sensitivity and high insulin secretory response. This study provides further information on factors influencing glycemic and insulinemic responses in horses.     

Comparing the 2000 and 2005 factors affecting the selling price of feeder cattle sold at Arkansas livestock auctions

The objectives of the study were to determine how factors affecting the selling price of feeder calves changed from 2000 to 2005 and to examine the perception that discounts narrow or even disappear as calf supplies decrease and selling prices increase. Data from weekly Arkansas livestock auctions were collected from January 1 to December 31 in 2000 and 2005. Data included calf sex, breed type, color, muscle score, horn status, frame score, fill, condition, health, and BW. Mean selling prices for 2000 and 2005 were $92.91 +/- 15.05 and $118.32 +/- 15.13 (mean +/- SD; $/45.45 kg), respectively. Individual price observations were subtracted from the respective annual means and became the dependent variable. The selling prices for feeder calves sold in groups of 2 to 5 calves and in groups of >/= 6 calves were greater in 2005 than 2000 (P < 0.001). Steers received a greater premium ($6.48 +/- 0.09 vs. $6.02 +/- 0.08; mean +/- SE) and bull calves received greater discounts ($0.30 +/- 0.14 vs. $1.68 +/- 0.09) in 2005 than in 2000. Breeds types that increased in value from 2000 to 2005 were Angus x Hereford, Angus, Angus x Charolais, and Brahman (P < 0.001). Breed types that received a reduced selling price in 2005 compared with 2000 (P < 0.001) were one-fourth Brahman Cross, Charolais, Charolais x Limousin, Hereford x Limousin, Limousin, Limousin x one-fourth Brahman, Longhorn, Saler and Simmental. Yellow-white face, black-white face, black, and gray feeder calves received an increase in selling price from 2000 to 2005 (P < 0.001). Although fewer horned feeder calves were sold in 2005 (P < 0.01), they received greater discounts in 2005 than 2000 (-$2.86 +/- 0.16 and -$0.51 +/- 0.09; P < 0.001). In 2005, large-framed feeder calves did not receive the premium detected in 2000, but medium-framed feeder calves in 2005 received a greater selling price compared with 2000. Feeder calves with a muscle score of 1 received a greater premium in 2005 compared with 2000 ($2.58 +/- 0.06 and $0.02 +/- 0.09, respectively; P < 0.001). Feeder calves with a muscle score of 2 were discounted in both years, but the discount in 2005 was not as great as in 2000 (P < 0.001). Full and tanked feeder calves received greater discounts in 2005 than in 2000 (P < 0.001). Discounts for fleshy and fat feeder calves were greater in 2005 than in 2000. Most factors affecting the selling price of Arkansas feeder calves in 2000 affected the selling price in 2005. Although feeder calf supplies were smaller in 2005 than 2000, many discounts increased.     

Effects of source of supplemental zinc on performance and humoral immunity in beef heifers

Two experiments were conducted to evaluate receiving-period performance, morbidity, and humoral immune response, as well as finishing performance and carcass characteristics of heifers fed different sources of supplemental Zn. In Exp. 1, 97 crossbred beef heifers (initial BW = 223.4 kg) were fed a 65% concentrate diet with no supplemental Zn (control) or 75 mg of supplemental Zn/kg of DM from Zn sulfate, Zn methionine, or Zn propionate. During a 35-d receiving period, heifers were monitored daily for signs of bovine respiratory disease. Serum samples were collected for Zn analysis on d 0, 14, and 28. After the receiving period, heifers were adapted to and fed a high-concentrate diet with no supplemental Zn for 42 d. Heifers were then assigned to finishing diet treatments, with the same concentrations and sources of supplemental Zn as during the receiving period and fed for an average of 168 d. Serum samples also were obtained on d 0 and 56 of the finishing period and at the end of the study. During the receiving period, control heifers had a greater (P < or = 0.05) BW and G:F on d 35 than heifers in the other treatments, but no differences were observed among treatments for morbidity or serum Zn concentrations (P > or = 0.50). For the finishing period, DMI and ADG did not differ among treatments; however, overall G:F tended (P = 0.06) to be less for control heifers than for heifers in the 3 supplemental Zn treatments. On d 56 of the finishing period, control heifers tended (P = 0.06) to have a lower serum Zn concentration than heifers in the 3 supplemental Zn treatments. In Exp. 2, 24 crossbred beef heifers (initial BW = 291.1 kg) were fed the same 4 treatments as in Exp. 1 for a 21-d period. The humoral immune response to treatments was determined by measuring specific antibody titers after s.c. injection of ovalbumin on d 0 and 14. Body weights and blood samples for serum Zn concentration and ovalbumin IgG titers were collected on d 0, 7, 14, and 21. Serum Zn concentration and specific ovalbumin IgG titers did not differ (P > 0.10) among the 4 treatments on any sampling day. Results from these 2 studies showed no major differences among the sources of supplemental Zn for receiving period morbidity, ADG, DMI, and humoral immune response of beef heifers; however, a lack of supplemental Zn during an extended finishing period tended to negatively affect G:F.     

Influence of body condition and bovine somatotropin on estrous behavior, reproductive performance, and concentrations of serum somatotropin and plasma fatty acids in postpartum Brahman-influenced cows

Ninety-nine multiparous Brahman-influenced (1/4 to 3/8 Brahman) cows were managed to achieve low (BCS = 4.3 +/- 0.1; n = 50) or moderate (BCS = 6.1 +/- 0.1; n = 49) body condition (BC) to determine the influence of bovine somatotropin (bST) on estrous characteristics, reproductive performance, and concentrations of serum GH and plasma NEFA. Beginning 32 d postpartum, cows within each BC were assigned randomly to treatment with or without bST. Non-bST-treated cows received no treatment, and treated cows were administered bST (Posilac, 500 mg s.c.) on d -35, -21, and -7 before initiation of the breeding season. On d -7, all cows received an intravaginal, controlled internal drug-releasing (CIDR) device. On d 0 (initiation of the 70-d breeding season), the CIDR were removed and cows received prostaglandin F2alpha (PGF2alpha). Blood samples were collected from the median caudal vein of the cows at each bST treatment and at d -28 and 0. Estrous behavior was monitored by radiotelemetry during the first 30 d of the breeding season. Growth hormone was increased (P < 0.05) in low and moderate BC cows treated with bST. The percentage of cows detected in estrus during the first 30 d of the breeding season was decreased (P = 0.05) for low BC (64%) compared with moderate BC (82%) cows. The interval to first estrus tended (P = 0.07) to be shorter in low BC-bST-treated cows (3.7 +/- 1.9 d) than in moderate BC-bST-treated cows (9.6 +/- 1.8 d). During the first 30 d of the breeding season, cows in low BC had a decreased (P = 0.02) number of mounts received and increased (P = 0.001) quiescence between mounts compared with cows in moderate BC. The number of mounts received was reduced (P = 0.04) in bST-treated cows. More (P = 0.02) cows treated with bST became pregnant during the first 3 d of the breeding season compared with non-bST-treated cows. The cumulative first-service conception rate tended (P = 0.07) to be greater for bST-low BC cows than non-bST-treated cows in low or moderate BC. On d 0, NEFA were greater (P < 0.05) in bST-treated vs. non-bST-treated cows. Low BC and bST reduced the intensity of behavioral estrus in postpartum Brahman-influenced cows. However, bST increased the first-service conception rate during the first 30 d of breeding and pregnancy rates during the first 3 d of breeding in postpartum Brahman-influenced cows.     

Energy and protein requirements for maintenance and growth of Boer crossbred kids

Meat production by goats has become an important livestock enterprise in several parts of the world. Nonetheless, energy and protein requirements of meat goats have not been defined thoroughly. The objective of this study was to determine the energy and protein requirements for maintenance and growth of 34 (3/4) Boer x (1/4) Saanen crossbred, intact male kids (20.5 +/- 0.24 kg of initial BW). The baseline group was 7 randomly selected kids, averaging 21.2 +/- 0.36 kg of BW. An intermediate group consisted of 6 randomly selected kids, fed for ad libitum intake, that were slaughtered when they reached an average BW of 28.2 +/- 0.39 kg. The remaining kids (n = 21) were allocated randomly on d 0 to 3 levels of DMI (treatments were ad libitum or restricted to 70 or 40% of the ad libitum intake) within 7 slaughter groups. A slaughter group contained 1 kid from each treatment, and kids were slaughtered when the ad libitum treatment kid reached 35 kg of BW. Individual body components (head plus feet, hide, internal organs plus blood, and carcass) were weighed, ground, mixed, and subsampled for chemical analyses. Initial body composition was determined using equations developed from the composition of the baseline kids. The calculated daily maintenance requirement for NE was 77.3 +/- 1.05 kcal/kg(0.75) of empty BW (EBW) or 67.4 +/- 1.04 kcal/kg(0.75) of shrunk BW. The daily ME requirement for maintenance (118.1 kcal/kg(0.75) of EBW or 103.0 kcal/kg(0.75) of shrunk BW) was calculated by iteration, assuming that the heat produced was equal to the ME intake at maintenance. The partial efficiency of use of ME for NE below maintenance was 0.65. A value of 2.44 +/- 0.4 g of net protein/kg(0.75) of EBW for daily maintenance was determined. Net energy requirements for growth ranged from 2.55 to 3.0 Mcal/kg of EBW gain at 20 and 35 kg of BW, and net protein requirements for growth ranged from 178.8 to 185.2 g/kg of EBW gain. These results suggest that NE and net protein requirements for growing meat goats exceed the requirements previously published for dairy goats. Moreover, results from this study suggest that the N requirement for maintenance for growing goats is greater than the established recommendations.     

Use of group-randomized trials in pet population research

Communities invest considerable resources to address the animal welfare and public health concerns resulting from unwanted pet animals. Traditionally, research in this area has enumerated the pet-owning population, described pet population dynamics in individual communities, and estimated national euthanasia figures. Recent research has investigated the human–animal bond and explored the community implications of managed feral cat colonies. These reports have utilized traditional epidemiologic study designs to generate observational data to describe populations and measure associations. However, rigorous scientific evaluations of potential interventions at the group level have been lacking. Group-randomized trials have been used extensively in public health research to evaluate interventions that change a population's behavior, not just the behavior of selected individuals. We briefly describe the strengths and limitations of group-randomized trials as they are used to evaluate interventions that promote social and behavioral changes in the human public health field. We extend these examples to suggest the appropriate application of group-randomized trials for pet population dynamics research.     

Bacterial colonization affects early organ and gastrointestinal growth in the neonate

Enteral nutrition coupled with bacterial colonization has been shown to have major functional and developmental effects during the postnatal period of neonates. In this study, we developed a highly sensitive premature pig model to elucidate the specific developmental impact of initial bacterial colonization on premature neonates by comparing germ-free and conventionally reared pigs. Thirty-eight preterm pigs (93% gestation) were delivered via caesarean section and reared in either germ-free or conventional isolators for 40–48 h. Pigs were fed either infant milk formula or sow's colostrum. Enteral feeding for two days had trophic effects on gastrointestinal weights, particularly for pancreas, stomach and small intestine (SI). The absence of bacteria in formula fed pigs resulted in a mucosa that appeared more robust and had higher weights for both SI and pancreas, compared to conventional formula fed pigs (P < 0.05). Colostrum fed pigs also had markedly increased mucosal SI proportions, lung and spleen weights compared to conventional formula fed pigs. Colostrum fed pigs and germ-free pigs were similar although stomach, pancreas and distal SI weights were highest for germ-free pigs. The results demonstrate that the initial bacterial colonization interacts with diet to modulate the early neonatal organ development, particularly of the GIT.