VTechWorks Repository :: Browsing by Author "Lewis, Ronald M."

Browsing by Author "Lewis, Ronald M."

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Assessing Hepatic Gene Expression in Response to Xenobiotic Exposure in Mice
Boorgula, Smitha (Virginia Tech, 2007-04-12)
Xenobiotics are plant derived compounds metabolized by phase I and II liver enzymes. Phase I enzymes increase, and phase II enzymes decrease, xenobiotic toxicity. Xenobiotics considered were ergotamine, associated with fescue toxicosis, and sulforaphane, a phase II inducer. Hypothesized responses in liver gene expression and enzyme activity due to exposure to these xenobiotics were tested. Polymorphic mice were gavaged with sulforaphane, ergotamine or control over four daily dosing periods (2, 5, 8 and 11 d), with at least 5 mice per treatment. Mice were killed and livers collected 24 h after last dosing. With ergotamine, expression of phase II genes catecholâ Oâ amine methyltransferase 1 (P = 0.009) on d 8, and glutathioneâ Sâ transferase (Gst) mu1 (Gstm1; P = 0.049) on d 11 was increased, and sulfotransferase 5a1 on d 11 decreased (P = 0.02). Sulforaphane increased expression of cytochrome P450 1a2 on d 5 (P = 0.02) and flavin containing monooxygenases 1 on d 11 (P = 0.002), both phase I genes. It also increased expression of a phase II gene transcription factor (P = 0.03) and quinone reductase 02 (P = 0.007) on d 5, and Gstm1 on d 8 (P = 0.04) and d 11 (P = 0.01). Moreover, sulforaphane treated mice had higher (P < 0.05) Gstm1 expression across days. Among enzymes, only sufloraphane treated mice had higher (P < 0.05) Gst activity. The increase in both Gstm1 expression and Gst activity indicate a consistent benefit of sufloraphane on phase II enzyme activity.
Assessing the reliability of plant-wax markers to delineate diet choice and feed efficiency in beef heifers
Vargas Jurado, Napoleon (Virginia Tech, 2012-07-24)
Estimating feed efficiency in grazing environments is challenging due to difficulties in quantifying food intakes and diet choices in free-grazing animals. The plant-wax marker technique may be a useful tool to redress this problem. However, its reliability needs to be validated before its wider application. This study was designed to assess the reliability of plant-wax markers for estimating botanical composition of test diets, and diet choices in beef cattle, and provided opportunities to evaluate efficiency in growing heifers. To test estimation of botanical composition, samples of red clover and fescue hay were mixed to form test diets containing 0-100% of either forage. To test estimation of diet choices, 24 heifers from large and moderate frame size lines were evaluated at two instances. Cubed red clover and fescue hays were offered ad libitum. After an acclimation period, feed intakes and body weights were collected for 10 days; fecal samples were collected for the final 5 days. Hydrocarbons and alcohols were quantified with gas chromatography. Estimates were based on least squares. Operator expertise affected measured concentrations of shorter-chained n-alkanes (P<0.041) and long-chain alcohols (P<0.02). Still, overall reliability of the technique was unaffected. Large and moderate framed animals did not differ in efficiency (P>0.05), although large framed animals had increased red clover intakes (P<0.01). Once corrected for fecal losses of n-alkanes, diet choices were estimated accurately. Plant-wax markers provided reliable estimates of botanical composition of diets, and diet choices of animals, suggesting it is a valuable tool to assess efficiencies of grazing cattle.
Cattle acclimate more substantially to repeated handling when confined individually in a pen than when assessed as a group
Parham, Jamie T.; Tanner, Amy E.; Blevins, Sarah R.; Wahlberg, Mark L.; Lewis, Ronald M. (Oxford University Press, 2022-03-01)
Chute (CS) and exit (ES) scores are common subjective methods used to evaluate temperament in cattle production systems. A pen test, which allows behavior to be observed in a non-restrained setting, may also be an effective method to evaluate temperament by allowing more variation among animals to be expressed. The merit of pen scores in assisting producers in evaluating temperament is equivocal. The objectives of this study were to validate the usefulness of a pen score in delineating temperamental cattle and to determine whether these behavioral scores change under repeated and routine management. Over 3 consecutive years, a factorial design of two measurement protocols (frequent [F], infrequent [IN]) and three recording periods was used. The F measurements were collected over 3 consecutive days and IN measurements only on day 1 within a recording period. Each year, 20 mostly Angus commercial Bos taurus heifers were randomly assigned to each protocol. Behavior was measured using a CS, ES, and exit velocity. Body temperature and heart rate also were recorded. A fecal and blood sample were collected and analyzed for levels of various metabolites including glucose concentration and serum cortisol. Following routine handling, each heifers' response to 30 s of exposure to a human stressor was recorded both individually and in groups of four. An individual (IPS) and group (GPS) pen scores were assigned from 1 (docile) to 6 (aggressive). For all heifers, protocol, event, and their interaction, were compared on the first day of an event. For F heifers, event and day within event were instead used. Body weight was included as a covariate, with sire and year fitted as random effects. Reliability of IPS and GPS were determined using a kappa (K) coefficient. Both IPS and GPS were reliably assigned (K = 0.64 and 0.44 for IPS and GPS, respectively) and positively correlated with body temperature, heart rate, glucose, and serum cortisol (r = 0.28 to 0.37). Furthermore, F heifers acclimated to repeated handling in an individual pen setting (P < 0.05) while acclimation to handling within groups was not evident (P > 0.14). IPS provides a reliable evaluation of temperament in a non-restrained setting that is indicative of an animal's response to stress and may be useful when attempting to make phenotypic selection decisions. However, temperamental heifers became calmer with repeated gentle handling. Pen scores collected on heifers either individually or as a group can be reliably assigned and are indicative of an animal's response to stress during normal handling practices. Lay Summary Chute and exit scores are common subjective methods used to evaluate temperament in cattle production systems. A pen test, which allows behavior to be observed in a non-restrained setting, may also be an effective method to evaluate temperament by allowing more variation among animals to be expressed. However, the merit of pen scores in assisting producers in evaluating temperament has yet to be discerned. Therefore, the objectives of this study were to validate the usefulness of pen scores in delineating temperamental cattle and to determine whether these behavioral scores change under repeated and routine management. Pen scores collected on heifers either individually or as a group could be assigned reliably and were indicative of an animal's response to stress during normal handling practices. Temperamental heifers, when handled more frequently, acclimated to repeated handling in an individual pen setting but not in a group. Therefore, regardless of method, when cattle are excitable during their first handling experience, more than one observation of temperament may be beneficial before assessing temperament.
Characterizing Compensatory Effects of Silymarin on Gossypol Toxicosis in Lines of Chickens Divergently Selected for Humoral Immune Response
Blevins, Sarah (Virginia Tech, 2009-08-04)
Feed costs are approximately 70% of total production cost for poultry producers. Poultry diets in the United States generally consist of 2 grains: corn and soybean meal. In recent years, the cost of these grains has dramatically increased. Due to these price increases, producers seek alternative feeds that provide adequate nutrition, and are also more affordable than "traditional" grains. Cottonseed meal is one alternative that is both affordable and an excellent source of crude protein. However, cottonseed meal contains gossypol, a pigment toxic to chickens. This study had two main objectives. The first objective was to determine if silymarin, an extract from milk thistle, could offset or prevent gossypol toxicosis. The second objective was to determine if divergent selection for humoral immune response would have an impact on the ability of the chicken to cope with gossypol toxicosis. Two preliminary studies were conducted. One determined basal activities of liver detoxification enzymes at various ages. The other determined concentrations of gossypol and silymarin that should be added to the diet to elicit a response. The information gathered from the second preliminary study was used to conduct the final experiment. In the final experiment, chickens from each of 2 lines selected for humoral immunity were exposed to diets containing gossypol, silymarin, gossypol and silymarin, and a control. Humoral immunity had no impact on the ability of the chicken to cope with gossypol toxicosis. Silymarin did not alleviate gossypol toxicosis. Future studies will focus on using a lower gossypol concentration in the diet.
Developing Breeding Objectives for Targhee Sheep
Borg, Randy Charles (Virginia Tech, 2004-06-08)
Breeding objectives were developed for Targhee sheep at different levels of prolificacy and triplet survival. Economic weights (EW) were derived for estimated breeding values (BV) from National Sheep Improvement Program genetic evaluations for 120 d weaning weight (WW), maternal milk (MM), yearling weight (YW), fleece weight (FW), fiber diameter (FD), staple length (SL), and prolificacy (PLC; lambs born/100 ewes lambing). A commercial flock was simulated, accounting for nonlinear relationships between performance and profit. Ewes were assumed mated to sires of specified BV and profit was derived from lifetime performance of lambs and replacement females from that lamb crop. Economic weights were determined as change in profit from use of sires with BV that were one additive standard deviation above the mean for each trait [1.98 kg for WW, 1.62 kg for MM, 2.90 kg for YW, 0..36 kg for FW, 0.99 microns for FD, 0.74 cm for SL, and 17.58 lambs/100 ewes for LC], while holding all other BV at breed average. Separate breeding objectives were derived for different ways of meeting increased nutrient needs (P = purchase hay, R = rent pasture, and L= limited flock size) and for different market lamb values (D = discounting lamb value for heavy weights, ND = no discount for heavy lambs). Based on replicated simulations, relative EW did not vary with prolificacy or triplet survival (P > 0.15) but were affected by feed costs and lamb market values (P < 0.01). Selection indexes were derived within and across simulated scenarios, and correlation (r) among indexes of > 0.90 indicated that an index could be used across multiple scenarios with little loss of selection efficiency. Indexes derived within feed cost scenarios (P, R, and L) and lamb value scenarios (D, ND) were strongly intercorrelated (r > 0.97). Correlations among average indexes for feed cost scenarios (0.97 for R and P, 0.70 for R and L; 0.85 for P and L) indicated that two feed cost scenarios could be used depending on whether winter forage was limited (L) or not (NL). The correlation between average indexes for these two scenarios was 0.78. Indexes were presented for combinations of feed cost and lamb value scenarios. Two indexes were suggested, representing the scenarios that apply to a large portion of Targhee producers. These indexes were for discounting heavy lambs with limited winter forage (D-L: 1.0 WW + 0.14 MM __ 0.76 YW + 1.22 FW __ 0.36 FD - 0.09 SL + 0.25 LC) and discounting heavy lambs with additional available forage (D-NL: 1.0 WW + 0.24 MM __ 0.34 YW + 1.65 FW __ 0.41 FD - 0.14 SL + 0.33 LC). For a standardized selection differential of one for the index, the expected changes in mean index value were $2.17 and $1.92 per ewe per generation for D-L and D-NL, respectively.
Diversity Relationships in Native, Warm-Season Plant Communities used for Agriculture
Bonin, Catherine Louise (Virginia Tech, 2011-03-21)
Studies suggest that diverse mixtures of plants may improve forage productivity and also be suitable as bioenergy crops. The objectives of this research were: 1) to measure the effects of native, warm-season perennial (NWSP) forage mixtures and management methods on productivity, weed biomass, nutritive value, and community composition, and 2) to identify mechanisms that generate any positive diversity-productivity relationships over a three-year establishment period. In 2008, two experiments were established to evaluate the use of native, warm-season plants in forage-livestock systems using a pool of ten native species. The first, a large-scale, three-year, experiment tested three different NWSP mixtures (switchgrass monoculture, a four-grass mixture, and a ten-species mixture) and two management methods (grazed or biomass crop). Switchgrass monocultures had the lowest forage yield and highest weed biomass in both grazed areas and biomass crop exclosures. Analysis of forage nutritive value did not show many differences among mixtures, although the monoculture tended to have higher crude protein and lower fiber concentrations than the polycultures. Management method affected community composition, with NWSP richness higher and weed species richness lower in biomass crop exclosures than in grazed areas. A second experiment examined if species richness would enhance yields through a positive biodiversity effect. It employed additive partitioning to separate the selection effect (SE) from the complementarity effect (CE) by sowing random assemblages of NWSPs at five levels of richness into small plots. Species richness was associated with increased yields in the first year only, but overyielding and positive diversity effects were present in all three years. On average, over 50% of multi-species plots overyielded and 64% exhibited a positive biodiversity effect. Both SE and CE contributed to the biodiversity effect and the importance of each effect changed over time as communities became better established. All ten species were also individually analyzed for their yield potential, nutritive value, and elemental composition. Warm-season grasses tended to be higher-yielding but of lower nutritive value. All ten NWSPs contained sufficient concentrations of eleven elements to support nonlactating cows. These experiments demonstrated that diverse NWSP mixtures may be a valuable addition to both forage and bioenergy agroecosystems.
Economic Pasture-Based Cow-Calf Systems for Appalachia
Emenheiser, Joseph Carl (Virginia Tech, 2014-01-06)
Pasture-based beef production is well-suited for the Appalachian region of the United States. This research investigated pasture, beef cattle, and economics components within the cow-calf sector of pasture beef production, and presents implications of their interplay for the vitality of the whole system. Samples of forage DM mass and CP, ADF, NDF, and ash contents in each paddock of a rotational stocking system were collected monthly for 4 grazing seasons. Effects of month, stockpiling, hay feeding, temperature, precipitation, and durations of paddock grazing and rest on forage mass and quality measurements were investigated. The system was complex and dynamic; precipitation and rest days in particular showed clear interactions with both month and stockpiling when predicting forage mass and quality. Available DM, TDN, and CP were compared to nutrient density requirements for beef cows to conclude that the system met or exceeded requirements. Six years of production data from a spring-calving cow-calf enterprise that utilized rotational stocking and fall stockpiling were analyzed. Comparisons among 2 cow frame size and 2 calf creep system treatments for production efficiency (total weaning weight per land area), and net returns to the enterprise, were made. Pastures with medium frame cows and designated creep systems had the greatest production efficiency, but also had the highest costs and netted the least returns. Greatest net returns were achieved in large frame, forward creep systems, which had the lowest production efficiency but also the lowest costs. Provided the quality of calves produced is suitable for other phases of the production stream, we conclude that minimizing costs rather than maximizing productive outputs is a better focus for cow-calf enterprises faced with similar decisions among frame size and creep system treatments.
Estimating forage mass of tall fescue pastures and dry matter intake and digestibility of fescue forage by beef steers
Lopez-Guerrero, Isaias (Virginia Tech, 2005-01-13)
A series of three experiments were conducted to evaluate different methods of estimating forage mass of tall fescue pastures, and dry matter intake and digestibility in beef steers under indoor and grazing conditions. Forage mass was estimated with the herbage cutting method (HCM) and three indirect methods; the pasture capacitance meter (PCM), the plate meter (PPM), and the visual estimation (VE). The coefficients of determination from the calibration equations were 0.686, 0.751, and 0.862 for the PCM, PPM, and VE, respectively. There were differences in forage mass estimates due to sampling method, sampling date, and their interaction. The second experiment was a digestion trial conducted with confined animals to determine the recovery rate of chromic oxide and alkanes from controlled release capsules and to evaluate the accuracy of the concurrent estimations of intake and digestibility. No difference was found in the recovery rate of either alkanes or chromic oxide during the 7 d of the collection period. Likewise, actual fecal output, dry matter intake, and digestibility were not different from the estimated values. However, estimated values had to be adjusted for the respective recovery rate. The third experiment was conducted under grazing conditions to evaluate the chromic oxide controlled release capsule technique in estimating intake and digestibilty. In this trial, although the recovery rate of the marker was extremely high (avg. = 1.89), the actual and estimated values of dry matter fecal output, intake, and digestibility were not different. Again the recovery rate had to be used as a correction factor.
Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep
Becker, Gabrielle M.; Thorne, Jacob W.; Burke, Joan M.; Lewis, Ronald M.; Notter, David R.; Morgan, James L. M.; Schauer, Christopher S.; Stewart, Whit C.; Redden, R. R.; Murdoch, Brenda M. (2024-07-30)
Background: Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright’s fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). Results: Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. Conclusions: In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
Genetic evaluation of ewe productivity and its component traits in Katahdin and Polypay sheep
Vanimisetti, Hima Bindu (Virginia Tech, 2006-11-17)
The objectives of this dissertation were to evaluate genetic influences on ewe productivity, its growth and reproductive components, and measures indicative of accelerated lambing performance. Genetic parameters were estimated for total weight of litter weaned per ewe lambing (TW) and its components, number of lambs born (NB), number of lambs weaned (NW) and average weight of lambs weaned (AW), measured as traits of the ewe, and lamb survival (LS) and weaning weight (WW), measured as traits of the lamb, in Katahdin sheep. Heritabilities of TW, NB, NW, and AW, were 0.12, 0.12, 0.09, and 0.13, respectively. Heritability of WW was 0.15 to 0.20. Genetic effects on LS were negligible. Genetic correlation of TW with NB, NW, and AW averaged 0.30, 0.90, and 0.74, respectively, those of NB with NW and AW averaged 0.72 and 0.01, respectively, and that between NW and AW averaged 0.50. Direct genetic effects on WW were independent of NB and NW, but correlation between maternal genetic effects on WW and animal genetic effects on NW averaged 0.35. Ewe fertility, NB, LS, and WW were modeled using stochastic simulation and used to derive NW, AW, and TW to test alternative predictors of genetic merit for TW. A random 8% of WW observations were set to missing values and AW and TW were recalculated to evaluate the effects of data reporting inconsistencies on efficacy of different prediction strategies. Four alternative predictors of estimated breeding values (EBV) for TW involved direct univariate prediction (TW1), an index of EBV for NW and AW (TW2), indirect prediction using data for NW and AW and genetic correlations among NW, AW and TW (TW3), and indirect prediction augmenting TW3 with data and genetic correlations involving NB (TW4). To validate efficacy of predictors, daughter data sets were generated from the original ewes and their realized TW were regressed on alternative predictors. Regression coefficients from TW1, TW3, and TW4 were close to the expected value of 0.50 whereas those from TW2 were less than 0.50. Model Rsquare statistics were similar among predictors when there were no missing WW data but regressions involving TW1 had lowest model R-square when some WW data was missing. Ewe lamb fertility (ELF), ages at first, second, and third lambings (AGE1 to AGE3), first and second lambing intervals (INT1 and INT2), and number of lambings by 38 mo of age (LAMB3) were evaluated for an accelerated lambing Polypay flock. Relationships among these traits and NB and WW were estimated. Heritability of ELF, AGE1, AGE2, AGE3, INT1, INT2, and LAMB3 were 0.14, 0.39, 0.28, 0.36, 0.00, 0.09, and 0.27, respectively. Heritability of AGE2 and AGE3 were negligible after accounting for variation in AGE1. Genetic correlations of ELF with AGE1 and AGE2 were -0.89, -0.91, respectively, and that with LAMB3 was 0.89. Genetic correlations of LAMB3 with AGE1 and AGE2 were -0.49 and -1.00, respectively. Genetic correlations of ELF and LAMB3 with direct genetic effects on WW were close to -0.70, but correlations with maternal genetic effects on WW were 0.88 and 0.58, respectively. Prolificacy was independent of ELF and LAMB3.
Genetic Parameters of Foal Inspection Scores in the International Sporthorse Registry and Oldenburg Registry North America
Bhatnagar, Adrienne Sharda (Virginia Tech, 2010-08-18)
Foal scores from the International Sporthorse Registry and Oldenburg Registry North America were used for statistical and genetic analysis. Scored traits include type and conformation (TC), athletic ability of movement (AM), overall development as related to age (OD), and total score (TS) calculated as a weighted average of TC, AM, and OD. Premium status (PS) was analyzed as a binary trait. Preliminary statistical analysis determined significant fixed effects of sex, year of birth, dam breed, and inspection period. Offspring of stallions with only one offspring in the dataset and non-warmblood sires were deleted. Non-warmblood or non-Thoroughbred dams were also removed. Variance components were estimated using ASReml methodology to obtain genetic parameters. Traits were moderately to highly heritable with heritabilities of 0.45, 0.47, 0.49, and 0.55 for TC, AM, OD, and TS, respectively. PS had a heritability of 0.32 on a binary scale and 0.51 when transformed to the normal scale. Genetic correlations between TC, AM, OD, and TS were all high and favorable, ranging from 0.80 to 0.99. Genetic correlations with PS were inestimable. Foal inspection scores are heritable and should respond to selection. Selection for improvement in one trait should result in improvement in all traits. If genetic parameters can be correlated to data obtained in older horses, incorporating foal scores in selection decisions could improve warmblood breeding programs. Utilizing foal inspection scores should be beneficial to breeding objectives of the International Sporthorse Registry and Oldenburg Registry North America.
Genetics of resistance to Haemonchus contortus infections in sheep
Vanimisetti, Hima Bindu (Virginia Tech, 2003-02-20)
Genetic control of resistance to H. contortus was assessed in 198 ewes and 386 lambs of 50% Dorset, 25% Rambouillet and 25% Finnsheep breeding in fall and spring over 2 yr. After deworming, lambs that were approximately 120 d old and ewes that had weaned their lambs at 60 d and dried off were individually dosed with approximately 10,000 infective larvae. After infection, body weight (BW), fecal egg counts (FEC) and packed cell volume (PCV) were measured weekly for 7 wk in lambs and fortnightly for eleven wk in ewes. Summary traits were defined as initial PCV, mean BW (MBW) across all times, and means for FEC, log-transformed FEC (MLFEC), and PCV (MPCV) at wk 3 to 7 post-infection for lambs and wk 3 to 11 post-infection for ewes. No consistent seasonal variation in FEC was observed. Younger ewes were more susceptible to infection than older ewes. Sex differences in FEC were not observed in lambs. Heritabilities for summary traits were estimated from a REML analysis that included fixed effects of year and season plus effects of either sex (for lambs) or age category (for ewes). Heritability estimates for MBW, MPCV, and MLFEC were 0.74, 0.57, and 0.27 respectively (all P < 0.01), in lambs, and 0.24 (P < 0.1), 0.25 (P < 0.05) and 0.55 (P < 0.01), respectively, in ewes. Across-year repeatability estimates in ewes for MBW, MPCV, and MLFEC were 0.83, 0.54 and 0.56, respectively (all P < 0.01). Resistance was antagonistically associated with estimated breeding values for growth in ewes but not in lambs. Fertility and prolificacy in ewes were not related to resistance. Breed differences in resistance to H. contortus were also evaluated in 4 to 6-mo-old crossbred Dorset and Dorper, straightbred Katahdin, and Barbados Blackbelly x St. Croix lambs. Dorpers were not more resistant than Dorsets but appeared to cope better, with higher PCV and similar BW during infection compared to Dorsets. Katahdin and Barbados Blackbelly x St. Croix lambs were more resistant with lower FEC.
Implications of Connectedness in the Genetic Evaluation of Livestock
Kuehn, Larry Alexander (Virginia Tech, 2005-11-15)
The reliability of genetic evaluations across separate management units (e.g. flocks) depends on the extent of genetic links or connections among animals in these units. Where poor connectedness exists, comparisons of estimated breeding values (EBV) across units may be biased. The objectives of this study were to identify breeding strategies to increase connectedness among units, to evaluate statistics that may reflect the reduction in bias as connectedness increases in such strategies, and to assess levels of connectedness in Suffolk and Targhee flocks participating in the National Sheep Improvement Program. Expectations of bias when production units have different genetic means were derived for a simple sire model. These expectations were applied to data involving two flocks of animals with three different types of connections: sharing of a common reference sire or use of either a full- or half-sibling sire in each flock. Bias decreased as numbers of progeny in each flock increased for all methods. Linking through a reference sire was most effective and was the only method that eliminated bias as progeny numbers became infinite. Pedigree and performance data on a single trait with heritability 0.25 were then simulated for 15 flocks with 40 to 140 ewes per flock. Each flock was simulated with a different founder genetic mean to introduce bias into the genetic evaluation. Flocks participated in sire referencing schemes by artificial insemination, with varying levels of participation, or by natural service. With sire referencing genetic gain was higher and inbreeding was lower than without, and bias was rapidly reduced to near-zero levels. Discontinuing the schemes led to lower genetic gain, but bias was not reintroduced. The prediction error correlation of flock genetic means was proposed as a connectedness measure because it was strongly associated with bias. Benchmarks of 0.05 and 0.10 for "good" and "superior" connectedness were established. Targhee flocks have increased connectedness across the breed by actively exchanging rams over 15 yr. In the Suffolk breed, connectedness has only improved within segregated clusters of flocks. Suffolk breeders need to engage in active ram exchange to decrease risk of biased across-flock EBV comparisons.
Index selection in terminal sire sheep: implications for genetic improvement in a crossbreeding system
Marquez Betz, Gabriela Carolina (Virginia Tech, 2013-12-30)
Using terminal sires for crossbreeding is standard practice in the UK sheep industry, where over 70% of market lambs have terminal sire breeding. Thus, selection focusing on terminal sires will translate to changes in the entire industry. Consumers perceive lamb meat as fatty and demand for it has decreased. A lean growth index was developed for terminal sire breeds to increase carcass lean content while keeping fat constant at a constant age end point. The purposes of this study were: to evaluate the effects of index selection of terminal sires on their crossbred offspring up to harvest; to evaluate the effectiveness of the index within the terminal sire breeds; to evaluate the presence and consequences of heterogeneous environmental variances and genetics by environment interactions (GxE) on genetic evaluation. The most widely used breeds of terminal sires in the UK are Charollais, Suffolk, and Texel. These breeds participated in sire referencing schemes from the early 1990s by sharing rams selected on the lean growth index. From 1999 to 2002 approximately 15 high and 15 low lean growth index score rams per breed were selected from their sire referencing schemes and mated to Welsh and Scottish Mule ewes. Their crossbred offspring were reared on 3 farms in the UK under commercial conditions. In total, 6,515 lambs were born between 2000 and 2003. Lambs were weighed at birth (BWT), 5 weeks (5WT), and 10 weeks (10WT). The average daily gain (ADG) from birth to 10 weeks was calculated. Lambs were finished to an estimated 11% subcutaneous fat by visual examination. At harvest, they were weighed (HWT), ultrasonically scanned for muscle (UMD) and fat (UFD) depth, and assessed for condition score and conformation. Lambs sired by high index rams were on average, across breeds, heavier at all ages (P < 0.01) with 0.07 ± 0.03, 0.3 ± 0.1, 0.4 ± 0.1, and 1.2 ± 0.2 kg greater BWT, 5WT, 10WT, and HWT respectively. Their ADG was 5.1 ± 1.9 g/d greater than low index sired lambs. They had thicker UMD (0.7 ± 0.2 mm) and thinner UFD (0.08 ± 0.01 mm). High vs. low index sired lambs took the same amount of days to reach harvest fatness. Suffolk-sired lambs were on average heavier, with greater ADG, whereas Charollais-sired lambs were lightest with smallest ADG. Texel-sired lambs had thicker UMD than Charollais (0.7 ± 0.2 mm; P < 0.001) but were not different than Suffolk. Charollais-sired lambs had greater UFD than both Texel- (0.098 ± 0.016 mm) and Suffolk- (0.061 ± 0.017 mm) sired lambs (P < 0.001). Texel-sired lambs reached harvest condition faster than the other breeds (P < 0.01). Index selection produced heavier and leaner lambs at finishing. Producers have flexibility in choosing the terminal sire that best fits their production system. Heteroscedascity and GxE were found to be more important for ultrasonic traits than weight traits. Fitting a farm by sire random interaction component improved model fit, but only accounted for less than 2% of the variation in weight traits. For ultrasonic traits, it accounted for at least 10% of the variation. When fitting traits as separate but correlated by farm, genetic correlations among traits were mostly above 0.8, indicating no GxE. Reactions norms for sires were fitted. For weight traits and UMD, sires had positive slopes (were environmentally sensitive) that were similar in value, thus performance improved with improving environments. For UFD, reaction norm slopes varied form negative to positive, indicating GxE. Consequences of heteroscedasticity are not large for these data, and any consequence of GxE on breeding goals should be evaluated before explicitly modeling it in genetic evaluation. There was evidence of genetic variation in sensitivity of sires; therefore, they could be selected to be more or less sensitive depending on economic considerations.
An Interdisciplinary Approach: Computational Sequence Motif Search and Prediction of Protein Function with Experimental Validation
Choi, Hyunjin (Virginia Tech, 2013-10-29)
Pathogens colonize their hosts by releasing molecules that can enter host cells. A biotrophic oomycete plant pathogen, Phytophthora sojae harbors a superfamily of effector genes whose protein products enter the cells of the host, soybean. Many of the effectors contain an RXLR-dEER motif in their N-terminus. More than 400 members belonging to this family have been previously identified using a Hidden Markov Model. Amino acids flanking the RXLR motif have been utilized to identify effector proteins from the P. sojae secretome, despite the high level of sequence divergence among the members of this protein family. I present here machine learning methods to identify protein candidates that belong to a particular class, such as the effector superfamily. Converting the flanking amino acid sequences of RXLR motifs (or other candidate motifs) into numeric values that reflect their physical properties enabled the protein sequences to be analyzed through these methods. The methods evaluated include Support Vector Machines and a related spherical classification method that I have developed. I also approached the effector prediction problem by building functional linkage networks and have produced lists of predicted P. sojae effector proteins. I tested the best candidate through gene gun bombardment assays using the beta-glucuronidase reporter system, which revealed that there is a high likelihood that the candidate can enter the soybean cells.
Model definition for genetic evaluation of purebred and crossbred lambs including heterosis
Jurado, Napoleon Vargas; Notter, David R.; Taylor, Joshua B.; Brown, Daniel J.; Mousel, Michelle R.; Lewis, Ronald M. (Oxford University Press, 2022-06)
Both direct and maternal heterosis increase birth and post-natal weights in crossbred lambs. Estimates of these heterotic effects can be used as adjustment factors in multi-breed genetic evaluations. Crossbreeding is a common practice among commercial sheep producers to improve animal performance. However, genetic evaluation of U.S. sheep is performed within breed type (terminal sire, semi-prolific, and western range). While incorporating crossbred records may improve assessment of purebreds, it requires accounting for heterotic and breed effects in the evaluation. The objectives of this study were to: 1) describe the development of a paternal composite (PC) line, 2) determine the effect of direct and maternal heterosis on growth traits of crossbred lambs, 3) estimate (co)variance components for direct and maternal additive, and uncorrelated maternal environmental, effects, and 4) provide an interpretation of the estimates of random effects of genetic groups, and to use those solutions to compare the genetic merit of founding breed subpopulations. Data included purebred and crossbred records on birth weight (BN; n = 14,536), pre-weaning weight measured at 39 or 84 d (WN; n = 9,362) depending on year, weaning weight measured at 123 d (WW; n = 9,297), and post-weaning weight measured at 252 d (PW; n = 1,614). Mean (SD) body weights were 5.3 (1.1), 16.8 (3.9) and 28.0 (7.6), 39.1 (7.2), and 54.2 (8.7) kg for BN, WN (at the two ages), WW, and PW, respectively. In designed experiments, the Siremax, Suffolk, Texel, Polypay, Columbia, Rambouillet, and Targhee breeds were compared within the same environment. Estimates of heterotic effects and covariance components were obtained using a multiple trait animal model. Genetic effects based on founders' breeds were significant and included in the model. Percent estimates of direct heterosis were 2.89 +/- 0.61, 2.60 +/- 0.65, 4.24 +/- 0.56, and 6.09 +/- 0.86, and estimates of maternal heterosis were 1.92 +/- 0.87, 4.64 +/- 0.80, 3.95 +/- 0.66, and 4.04 +/- 0.91, for BN, WN, WW, and PW, respectively. Correspondingly, direct heritability estimates were 0.17 +/- 0.02, 0.13 +/- 0.02, 0.17 +/- 0.02, and 0.46 +/- 0.04 for BN, WN, WW, and PW. Additive maternal effects accounted for trivial variation in PW. For BN, WN, and WW, respectively, maternal heritability estimates were 0.16 +/- 0.02, 0.10 +/- 0.02, and 0.07 +/- 0.01. Uncorrelated maternal environmental effects accounted for little variation in any trait. Direct and maternal heterosis had considerable impact on growth traits, emphasizing the value of crossbreeding and the need to account for heterosis, in addition to breed effects, if crossbred lamb information is included in genetic evaluation. Lay Summary Crossbreeding is common in commercial sheep enterprises. It allows breeds with different attributes to be combined to generate crossbred progeny tailored to production environments and customer preferences. Additionally, crossbreds often benefit from heterosis, performing at levels above the average of their parental breeds. Over two decades, body weights were collected at birth and at pre-weaning, weaning, and post-weaning ages on purebred and crossbred lambs from semi-prolific (Polypay), western range (Columbia, Rambouillet, Targhee), and terminal sire (Siremax, Suffolk, Texel) breeds at the U.S. Sheep Experiment Station. When combined, the value of direct heterosis-that due to a lamb being crossbred-and maternal heterosis-that due to the lamb's dam being crossbred-increased birth (5%) and post-natal (up to 10%) weights in crossbred lambs. This highlights the value of crossbreeding to the U.S. sheep industry, especially in western range production systems. Genetic variation between and within breeds also was detected for the purebred parental breeds. Such heterotic and breed effects must be accounted for if crossbred performance is to be incorporated in genetic evaluation of purebreds. Therefore, these results provide the foundation for utilizing crossbred information in the evaluation and selection of purebred sheep in the United States.
Phenotypic and genetic evaluation of fitness characteristics in sheep under a range environment
Borg, Randy Charles (Virginia Tech, 2007-04-23)
The objectives of this dissertation were to evaluate genetic and environmental relationships between lamb and ewe traits including body weight, fleece weight and quality, prolificacy, body condition, ewe stayability and lamb survival. Average heritability estimates for lamb birth weight (BWT), weaning weight (WW), maternal weaning weight, yearling body weight, fleece weight, spinning count and staple length were 0.19, 0.09, 0.08, 0.35, 0.38, 0.25, and 0.31 respectively. Heritability estimates for adult traits averaged 0.43 for body weight (AW), 0.13 for body condition (AC), and 0.12 for number of lambs born per ewe lambing (NLB). Correlations between direct additive AW and direct additive and maternal lamb weights ranged from 0.21 to 0.96 (P < 0.05) and 0.29 to 0.53 (P < 0.05), respectively, with residual correlations ranging from 0.05 to 0.95. Correlations of lamb traits with adult body condition and NLB were generally not different from zero; genetic and residual correlations ranged from -0.52 to 0.69 and -.39 to 0.31, respectively. Ewe stayability was analyzed as overall stayability (STAYn|2) which indicated the presence or absence of a ewe at n yrs of age, given that she was present at 2 yrs of age, and marginal stayability (STAYn|1-n) recording the presences of a ewe at n yrs of age, given that she was in the flock the previous year. Additive variance in ewe stayability was only found in stayability at 5 and 6 yr of age (P < 0.05). Heritability estimates for STAY5|4 and STAY6|2 from multiple trait analyses with other traits averaged 0.08 and 0.10, respectively. Phenotypic correlations between STAY and all other traits were near zero, ranging from -0.04 to 0.03. The estimated correlations between additive effects on STAY5|4 and STAY6|2 and additive maternal effects on WW were positive (both 0.46; P < 0.05). Genetic correlations between STAY5|4 and WW, adult weight, and NLB were 0.06, 0.13 and -0.06 (P > 0.10), respectively. However, genetic correlations between STAY6|2 and WW, adult weight, and NLB were negative (-0.17, -0.32 (P < 0.05) and -0.03, respectively). Significant genetic variation was thus present in stayability, with nonzero genetic correlations present between STAY, maternal milk, WW, and adult weight. Survival analysis was performed using a proportional hazards model to measure the probability of lamb death before weaning. Lamb survival was recorded as the day of age at death. Records were censored if a live lamb was artificially removed from their litter before death. Fixed effects on survival included ewe age, litter size, sex, and linear and quadratic BWT. Average age of death was 13.7 d. Censoring of records before weaning occurred in 12.9% of the total lambs born. Risk ratios indicated lambs from yearlings and ewes older than 5 yr had the greater risk of death, as did triplet and quadruplet lambs. Linear and quadratic BWT effects on lamb survival were found (P < 0.05) and accounted for most of the litter size effects in large litters. The influence of informative censoring was considered by assuming that lambs censored by 3 d of age had died at the time of censoring. Heritability of lamb survival at 3 d of age (estimated using an animal model in MTDFREML) was near zero, ranging from 0.00 to 0.01. The lack of additive variance suggests that improvement in lamb survival should be made through changes in management practices.
Phenotypic Relationships between Lactation persistency and Common Health Disorders in Dairy Cows
Appuhamy, Jayasooriya Arachchige Don Ranga Niroshan (Virginia Tech, 2006-11-10)
Lactation persistency is defined as the ability of a cow to maintain production at a higher level after peak yield. Hypothetically, more persistent cows are less susceptible to health and reproductive disorders. The objective of this research was to investigate the phenotypic relationships of common health disorders in dairy cows to lactation persistency. The relationships with peak yield and days in milk (DIM) at peak yield were also studied. Two separate investigations (Study 1 and Study 2) were performed. Study 1 used treatment incidence data and daily milk weights of 991 lactations from experimental dairy herds at Virginia Tech and Pennsylvania State University. Milk yield persistency (PM) was estimated for individual lactations using daily milk weights. In Study 2, producer recorded health data of 87555 lactations from 398 commercial herds were used. PM, fat (PF), and protein (PP) persistencies were estimated from TD yields. Mastitis only in the first 100 days, only after 100 DIM, and at any stage of lactation, and reproductive disorders including metritis, retained placenta, cystic ovaries, metabolic diseases including ketosis, milk fever and displaced abomasums, and lameness were considered in both studies. Mastitis both before and after 100 DIM was considered only in Study 1. Each disease was defined as a binary trait distinguishing between lactations with at least one incidence (1) and lactations with no incidences (0). Standardized measures of the persistencies, uncorrelated with yield, were calculated as a function of yield deviations from standard curves and DIM deviations around reference dates. Peak milk yield and DIM at peak of individual lactations were computed using Wood's function. Effects of persistency (PM, PF, and PP) on probability of the diseases in current and next lactations were examined through odds ratios from a logistic regression model. Conversely, the effects of diseases on persistencies, peak milk yield, and DIM at peak milk yield were also examined. Increasing PM, PF, and PP tend to reduce the incidence of mastitis, specifically in late stages of current and next lactation. PM and PP appear to have greater impact on mastitis than PF. No other likelihood of a disease was affected by the increasing persistencies. Post partum reproductive and metabolic diseases often had substantially positive effect on persistencies of both primiparous and multiparous cows (p<0.001 in Study 1 and p<0.001 in Study 2). Mastitis in early lactation appeared to increase persistency more often in multiparous cows (p<0.05 in Study 1 and p<0.005 in Study 2). Mastitis in late lactation had considerable but negative impact on persistency in both primiparous and multiparous cows (p<0.05 in Study 1 and p<0.005 in Study 2). Cows, which developed mastitis in both early and late lactations tended to have lower PM (p<0.05 in Study 1). Irrespective to the time of occurrence, effect of mastitis on milk, fat and protein yield persistencies was negative. Most of the diseases significantly affected DIM at peak milk yield in multiparous cows (p<0.05 in Study 1). Reproductive and metabolic disorders tended to delay DIM at peak milk yield while Mastitis in late lactation was associated with early DIM at peak milk yield. Lameness had no phenotypic relationships with shape of the lactation curve. Overall, diseases tend to affect milk, fat, and protein persistencies more strongly than the impact of persistency on likelihood of disease.
Reproductive performance of dorset ewes in the star accelerated lambing system
Lewis, Ronald M. (Virginia Tech, 1990-05-05)
Reproductive performance of Dorset ewes in the Cornell University STAR accelerated lambing program was evaluated. This program consists of five 30-d concurrent breeding and lambing periods per year beginning on January 1 (Sl), March 15 (S2), May 27 (S3), August 8 (S4) and October 20 (S5). Optimally, a ewe could lamb every 7.2 mo beginning at 1 yr of age, Records on 1,084 ewes over 7 yr beginning S1, 1982 Reproductive traits considered were ewe fertility, prolificacy, days to first lambing (DFL) and days between lambing (DBL). Fertility and prolificacy differed (P < .001) by exposure seasons. Exposure during favorable seasons (S1, S4, S5) increased fertility (P < .001) and prolificacy (P < .01) over that observed in unfavorable seasons (S2, S3). On average, first lambing occurred at 476 ± 5 d with ewe lambs first exposed during S1, S4 and S5 lambing at younger ages (P < .001). Ewes had more DBL (P < .001) if initial exposure following lambing occurred during an unfavorable season. A curvilinear relationship of ewe age with fertility (P < .001) , prolificacy (P < .01) and DBL (P < .05) was observed in ewes less than 4 yr old. At first exposure following lambing, fertility was lower (P < .001) than at subsequent exposures and ewes that had nursed lambs were less prolific (P < .01) than those that had not. Prolificacy and nursing status had little effect on fertility or DBL (P > .10). Fertility was transformed to an underlying liability scale based on the expected fertility of ewes of a given age and reproductive history. Variance components were estimated by least-squares (LS) and restricted maximum likelihood (REML) procedures. First-exposure fertility was not heritable. heritabilities for fertility at first post-lambing exposure, first-lambing prolificacy, and second-lambing prolificacy were .191 ± .088 (LS) and .200 ± .132 (REML), .914 ± .091 (LS) and .158 ± .144 (REML), and .168 ± .082 (LS) and .210 ± .137 (REML), respectively. Genetic variation in DFL (P < .01) and DBL (P < .001) was found. Although intrasire ewe variation was detected for prolificacy (P < .001) and DBL (P < .01), repeatability estimates were low and smaller than heritability.
Reproductive Soundness and Egg Quality in Chickens Selected for Low and High Antibody Response
Albrecht, Heather Nicole (Virginia Tech, 2011-08-11)
For 36 generations, White Leghorn chickens were selected for high (HAS) or low (LAS) antibody response to sheep red blood cells. The focus of this thesis was to investigate correlated responses in reproductive soundness and egg quality resulting from that selection. Forty-five hens and 25 roosters from each antibody line were used. In hens, commencement and intensity of lay, and egg quality, were analyzed; in both sexes, length of fertility was considered. Hens and roosters were mated to an intercross line to avoid confounding selection with sex effects. The LAS line was more reproductively sound, commencing lay at a younger age (11.67 ± 3.53 d; P < 0.001), lighter body weight (-169.46 ± 40.20 g; P < 0.001) and with greater intensity (2.68 ± 0.25%; P = 0.001) than the HAS line. Additionally, the LAS line had a greater length of fertility (hens: 2.43 ± 0.55 d; P < 0.001; roosters: 3.11 ± 0.71 d; P < 0.001). In contrast to their poorer reproductive soundness, the HAS line had superior egg quality compared to the LAS line. Egg shape index (4.12 ± 0.55; P < 0.001) and albumen height, measured in both mm (0.27 ± 0.12 mm; P < 0.001) and Haugh units (1.89 ± 0.91; P = 0.04), were superior in HAS hens. Selection for increased antibody response appeared to compromise reproductive soundness, perhaps due to limitations in available resources. However, the selection did not compromise egg quality.

Browsing by Author "Lewis, Ronald M."

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