@article{jiao_maltecca_gray_cassady_2014, title={Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: I. Genetic parameter estimation and accuracy of genomic prediction}, volume={92}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84901594245&partnerID=MN8TOARS}, DOI={10.2527/jas.2013-7338}, abstractNote={The efficiency of producing salable products in the pork industry is largely determined by costs associated with feed and by the amount and quality of lean meat produced. The objectives of this paper were 1) to explore heritability and genetic correlations for growth, feed efficiency, and real-time ultrasound traits using both pedigree and marker information and 2) to assess accuracy of genomic prediction for those traits using Bayes A prediction models in a Duroc terminal sire population. Body weight at birth (BW at birth) and weaning (BW at weaning) and real-time ultrasound traits, including back fat thickness (BF), muscle depth (MD), and intramuscular fat content (IMF), were collected on the basis of farm protocol. Individual feed intake and serial BW records of 1,563 boars obtained from feed intake recording equipment (FIRE; Osborne Industries Inc., Osborne, KS) were edited to obtain growth, feed intake, and feed efficiency traits, including ADG, ADFI, feed conversion ratio (FCR), and residual feed intake (RFI). Correspondingly, 1,047 boars were genotyped using the Illumina PorcineSNP60 BeadChip. The remaining 516 boars, as an independent sample, were genotyped with a low-density GGP-Porcine BeadChip and imputed to 60K. Magnitudes of heritability from pedigree analysis were moderate for growth, feed intake, and ultrasound traits (ranging from 0.44 ± 0.11 for ADG to 0.58 ± 0.09 for BF); heritability estimates were 0.32 ± 0.09 for FCR but only 0.10 ± 0.05 for RFI. Comparatively, heritability estimates using marker information by Bayes A models were about half of those from pedigree analysis, suggesting "missing heritability." Moderate positive genetic correlations between growth and feed intake (0.32 ± 0.05) and back fat (0.22 ± 0.04), as well as negative genetic correlations between growth and feed efficiency traits (-0.21 ± 0.08, -0.05 ± 0.07), indicate selection solely on growth traits may lead to an undesirable increase in feed intake, back fat, and reduced feed efficiency. Genetic correlations among growth, feed intake, and FCR assessed by a multiple-trait Bayes A model resulted in increased genetic correlation between ADG and ADFI, a negative correlation between ADFI and FCR, and a positive correlation between ADG and FCR. Accuracies of genomic prediction for the traits investigated, ranging from 9.4% for RFI to 36.5% for BF, were reported that might provide new insight into pig breeding and future selection programs using genomic information.}, number={6}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Jiao, S. and Maltecca, C. and Gray, K. A. and Cassady, J. P.}, year={2014}, month={Jun}, pages={2377–2386} }
 @article{jiao_maltecca_gray_cassady_2014, title={Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: II. Genomewide association}, volume={92}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84905009876&partnerID=MN8TOARS}, DOI={10.2527/jas.2014-7337}, abstractNote={Efficient use of feed resources has become a clear challenge for the U.S. pork industry as feed costs continue to be the largest variable expense. The availability of the Illumina Porcine60K BeadChip has greatly facilitated whole-genome association studies to identify chromosomal regions harboring genes influencing those traits. The current study aimed at identifying genomic regions associated with variation in feed efficiency and several production traits in a Duroc terminal sire population, including ADFI, ADG, feed conversion ratio, residual feed intake (RFI), real-time ultrasound back fat thickness (BF), ultrasound muscle depth, intramuscular fat content (IMF), birth weight (BW at birth), and weaning weight (BW at weaning). Single trait association analyses were performed using Bayes B models with 35,140 SNP on 18 autosomes after quality control. Significance of nonoverlapping 1-Mb length windows (n = 2,380) were tested across 3 QTL inference methods: posterior distribution of windows variances from Monte Carlo Markov Chain, naive Bayes factor, and nonparametric bootstrapping. Genes within the informative QTL regions for the traits were annotated. A region ranging from166 to 140 Mb (4-Mb length) on SSC 1, approximately 8 Mb upstream of the MC4R gene, was significantly associated with ADFI, ADG, and BF, where SOCS6 and DOK6 are proposed as the most likely candidate genes. Another region affecting BW at weaning was identified on SSC 4 (84-85 Mb), harboring genes previously found to influence both human and cattle height: PLAG1, CHCHD7, RDHE2 (or SDR16C5), MOS, RPS20, LYN, and PENK. No QTL were identified for RFI, IMF, and BW at birth. In conclusion, we have identified several genomic regions associated with traits affecting nutrient utilization that could be considered for future genomic prediction to improve feed utilization.}, number={7}, journal={Journal of Animal Science}, author={Jiao, S. and maltecca and Gray, K. A. and Cassady, J. P.}, year={2014}, pages={2846–2860} }
 @article{dhakal_maltecca_cassady_baloche_williams_washburn_2013, title={Calf birth weight, gestation length, calving ease, and neonatal calf mortality in Holstein, Jersey, and crossbred cows in a pasture system}, volume={96}, ISSN={["0022-0302"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84871620780&partnerID=MN8TOARS}, DOI={10.3168/jds.2012-5817}, abstractNote={Holstein (HH), Jersey (JJ), and crosses of these breeds were mated to HH or JJ bulls to form purebreds, reciprocal crosses, backcrosses, and other crosses in a rotational mating system. The herd was located at the Center for Environmental Farming Systems in Goldsboro, North Carolina. Data for calf birth weight (CBW), calving ease (0 for unassisted, n=1,135, and 1 for assisted, n=96), and neonatal calf mortality (0 for alive, n=1,150, and 1 for abortions recorded after mid-gestation, stillborn, and dead within 48 h, n=81) of calves (n=1,231) were recorded over 9 calving seasons from 2003 through 2011. Gestation length (GL) was calculated as the number of days from last insemination to calving. Linear mixed models for CBW and GL included fixed effects of sex, parity (first vs. later parities), twin status, and 6 genetic groups: HH, JJ, reciprocal F(1) crosses (HJ, JH), crosses >50% Holsteins (HX) and crosses >50% Jerseys (JX), where sire breed is listed first. The CBW model also included GL as a covariate. Logistic regression for calving ease and neonatal calf mortality included fixed effects of sex, parity, and genetic group. Genetic groups were replaced by linear regression using percentage of HH genes as coefficients on the above models and included as covariates to determine various genetic effects. Year and dam were included as random effects in all models. Female calves (27.57±0.54 kg), twins (26.39±1.0 kg), and calves born to first-parity cows (27.67±0.56 kg) had lower CBW than respective male calves (29.53±0.53 kg), single births (30.71±0.19 kg), or calves born to multiparous cows (29.43±0.52 kg). Differences in genetic groups were observed for CBW and GL. Increased HH percentage in the calf increased CBW (+9.3±0.57 kg for HH vs. JJ calves), and increased HH percentage in the dams increased CBW (+1.71±0.53 kg for calves from HH dams vs. JJ dams); JH calves weighed 1.33 kg more than reciprocal HJ calves. Shorter GL was observed for twin births (272.6±1.1 d), female calves (273.9±0.6 d), and for first-parity dams (273.8±0.6 d). Direct genetic effects of HH alleles shortened GL (-3.5±0.7 d), whereas maternal HH alleles increased GL (2.7±0.6 d). Female calves had lower odds ratio (0.32, confidence interval=0.10-0.99) for neonatal calf mortality in second and later parities than did male calves. Maternal heterosis in crossbred primiparous dams was associated with reduced calf mortality.}, number={1}, journal={JOURNAL OF DAIRY SCIENCE}, author={Dhakal, K. and Maltecca, C. and Cassady, J. P. and Baloche, G. and Williams, C. M. and Washburn, S. P.}, year={2013}, month={Jan}, pages={690–698} }
 @article{ashwell_gonda_gray_maltecca_audrey t. o'nan_cassady_mente_2013, title={Changes in chondrocyte gene expression following in vitro impaction of porcine articular cartilage in an impact injury model}, volume={31}, ISSN={["1554-527X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84872761673&partnerID=MN8TOARS}, DOI={10.1002/jor.22239}, abstractNote={Abstract}, number={3}, journal={JOURNAL OF ORTHOPAEDIC RESEARCH}, author={Ashwell, Melissa S. and Gonda, Michael G. and Gray, Kent and Maltecca, Christian and Audrey T. O'Nan and Cassady, Joseph P. and Mente, Peter L.}, year={2013}, month={Mar}, pages={385–391} }
 @article{maltecca_parker_cassady_2012, title={Application of multiple shrinkage methods to genomic predictions}, volume={90}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84861848308&partnerID=MN8TOARS}, DOI={10.2527/jas.2011-4350}, abstractNote={New challenges have arisen with the development of large marker panels for livestock species. Models easily become overparameterized when all available markers are included. Solutions have led to the development of shrinkage or regularization techniques. The objective of this study was the application and comparison of Bayesian LASSO (B-L), thick-tailed (Student-t), and semiparametric multiple shrinkage methods. The B-L and Student-t methods were also each analyzed within a single shrinkage and a multiple shrinkage framework. Simulated and real data were used to evaluate each method's performance. Real data consisted of SNP genotypes of 4,069 Holstein sires. Traits included in analysis of real data were milk, fat, protein yield, and somatic cell score. The performance of each model was compared based on correlations between true and predicted genomic predicted transmitting abilities. Model performance was also compared with the performance of routinely used methods such as Bayes-A and GBLUP through cross-validation techniques. When using simulated data regardless of shrinkage framework, shrinkage models outperformed genomic BLUP (GBLUP). The average advantage of shrinkage models ranged from 1% to approximately 8% depending on the prior specification. When analyzing real data, shrinkage models slightly outperformed GBLUP for most traits. Shrinkage models were better able to model traits for which 1 or more SNP of large effect have been identified. Overall, results suggested a relatively small advantage in multiple shrinkage models. Multiple shrinkage methods could represent a useful alternative to current methods of prediction; however, their performance in a variety of scenarios needs to be investigated further.}, number={6}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Maltecca, Christian and Parker, Kristen L. and Cassady, Joseph P.}, year={2012}, month={Jun}, pages={1777–1787} }
 @article{huang_maltecca_cassady_alexander_snelling_macneil_2012, title={Effects of reduced panel, reference origin, and genetic relationship on imputation of genotypes in Hereford cattle}, volume={90}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882597849&partnerID=MN8TOARS}, DOI={10.2527/jas.2011-4728}, abstractNote={The objective of this study was to investigate alternative methods of designing and using reduced SNP panels for imputing SNP genotypes. Two purebred Hereford populations, an experimental population known as Line 1 Hereford (L1, n = 240) and registered Hereford with American Hereford Association (AHA, n = 311), were used. Using different reference samples of 62 to 311 animals with 39,497 SNP on 29 autosomes and study samples of 57 or 62 animals for which genotypes were available for ~2,600 SNP (reduced panels), imputations were performed to predict the other ~36,900 loci that had been masked. An imputation package, including LinkPHASE and DAGPHASE, was used for imputation. Four reduced panels differing in minor allele frequency (MAF) and marker spacing were evaluated. Reduced panels included every 15th SNP across the genome (SNP_space), commercial Illumina Bovine3K Beadchip (SNP_3K), SNP with the highest MAF (SNP_MAF), and SNP with high MAF that were also evenly spaced across the genome (SNP_MS). Imputation accuracy was defined as the correlation of imputed genotypes and real genotypes. Reference samples were either from L1 or AHA. Among animals with genotypes, genetic relationships were estimated based on molecular marker genotypes or pedigree. Reduced panel design, number of animals in the reference sample, reference origin and genetic relationship between animals in the reference, and study samples all affected imputation accuracy (P < 0.001). Across genotyping schemes, imputed genotypes from SNP_MS had the greatest accuracy. A 0.1 increase in average pedigree relationship or average molecular relationship between reference and study samples increased imputation accuracy 10 to 20%. Using reference samples from the L1 population resulted in lower imputation accuracy than using reference samples from the admixed population AHA (P < 0.001). Increasing the number of animals in the reference panel by 100 individuals increased imputation accuracy by 8% when pedigree relationship was used as a covariate and 6% when molecular relationship was used as a covariate. We concluded that imputation accuracy would be increased through optimization of reduced panel design and genotyping strategy.}, number={12}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Huang, Y. and Maltecca, C. and Cassady, J. P. and Alexander, L. J. and Snelling, W. M. and MacNeil, M. D.}, year={2012}, month={Dec}, pages={4203–4208} }
 @article{velie_cassady_whisnant_2012, title={Endocrine response to acute stress in pigs with differing backtest scores}, volume={145}, ISSN={["1878-0490"]}, DOI={10.1016/j.livsci.2012.01.008}, abstractNote={In an attempt to quantify a pig's behavioral reaction to stress, pigs in previous studies were subjected to a backtest. Pigs scoring high on the backtest were thought to have a greater reaction to stress than those scoring lower on the test. To further understand this reaction eighty-eight gilts from 19 L were tested twice using the backtest. Gilts with the greatest (n = 15, High) and least (n = 15, Low) total time struggling were then selected for acute stress challenges. Pigs, in two replicates, were fitted with jugular cannulas at approximately 150 d of age. An acclimation time of 24 h was given between cannulation, testing and between tests. Blood samples were collected at 10 time points (− 60, − 30, 0, 5, 10, 15, 30, 60, 90, and 120 m relative to the application of the stressor). Pigs were challenged with 0.11 mol/kg BW of corticotropin releasing hormone (CRH) (n = 9 High, n = 9 Low) injected through the cannula to test the proposed model. The first stressor was snaring the pig with a nose-snare for 1 min (n = 10 High, n = 9 Low). The second stressor was depriving the pigs of feed for 24 h followed by placing feed next to the pig but out of reach (n = 6 High, n = 7 Low). Plasma samples were assayed for cortisol, epinephrine, and norepinephrine. Data were analyzed using a model including fixed effects of time, replicate, and group (High or Low) and all two-way interactions. In response to the CRH challenge, cortisol levels peaked at 10 m and returned to basal levels by 90 m. Least squares means response in norepinephrine of the High exceeded Low at 5 m by 376 ± 99 pg/mL. Cortisol, epinephrine, and norepinephrine response to snaring was similar. Cortisol peaked at 10 m and epinephrine and norepinephrine at 5 m. The response to feed deprivation failed to exceed basal levels. Response to the CRH challenge demonstrated the appropriateness of the model and that High and Low pigs were equally capable of responding. The biological significance of differences between High and Low groups in norepinephrine levels at 5 m following snaring is unknown.}, number={1-3}, journal={LIVESTOCK SCIENCE}, author={Velie, B. D. and Cassady, J. P. and Whisnant, C. S.}, year={2012}, month={May}, pages={140–144} }
 @article{gray_maltecca_bagnato_dolezal_rossoni_samore_cassady_2012, title={Estimates of marker effects for measures of milk flow in the Italian brown Swiss dairy cattle population}, volume={8}, ISSN={["1746-6148"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84867661823&partnerID=MN8TOARS}, DOI={10.1186/1746-6148-8-199}, abstractNote={Abstract}, journal={BMC VETERINARY RESEARCH}, author={Gray, Kent A. and Maltecca, Christian and Bagnato, Alessandro and Dolezal, Marlies and Rossoni, Attilio and Samore, Antonia B. and Cassady, Joseph P.}, year={2012}, month={Oct} }
 @article{knauer_cassady_newcom_see_2012, title={Gilt development traits associated with genetic line, diet and fertility}, volume={148}, ISSN={["1871-1413"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84863775012&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2012.05.024}, abstractNote={The objective was to associate gilt development traits with genetic line, diet and fertility group (FG). Gilts (n=1225) were reared from 162 to 265 days of age at a gilt development unit (GDU) and sent to sow farms. Females were Landrace (L), Large White (LW), L and LW F1 or L and LW composite. Estrous traits included age at puberty (AGEPUB), length of estrus (LOE), maximum strength of standing reflex with (MSRBOAR) or without (MSRNOBOAR) a boar present, total strength of standing reflex with (TSRBOAR) or without (TSRNOBOAR) a boar present, vulva redness (VR), strength of vulva reddening and swelling (VISUAL VULVA) and vulva width (VW). Growth and body composition traits were puberty weight, days to 114 kg and 10th rib backfat (BF) and loin muscle area (LMA) at 114 kg and puberty. Structural conformation traits included muscle mass, rib width, front leg side view, rear leg side view, front legs front view, rear legs rear view and locomotion (LOC). Sow farm entry traits were age, weight, BF and LMA. Sow traits included whether or not a gilt farrowed (STAY), age at first farrowing and total number born (TNB). Fertility groups were; FG0=did not reach puberty at the GDU (NOPUB), did not farrow (DNF); FG1=reached puberty at the GDU (YESPUB), DNF; FG2=NOPUB, farrowed; FG3=YESPUB, farrowed. Genetic lines differed (P<0.05) for estrous traits LOE, TSRBOAR, MSRNOBOAR, TSRNOBOAR, VR, VISUAL VULVA and VW. Females fed restrictively vs. ad libitum had a longer (P<0.05) LOE (2.18 vs. 2.03 d), higher (P<0.05) TSRBOAR (15.4 vs. 14.0) and younger (P<0.05) AGEPUB (219 vs. 225 d). Fertility groups 0, 1, 2 and 3 contained 45 (4%), 255 (24%), 66 (6%) and 698 (66%) gilts, respectively. Gilts from FG3 in comparison to FG1 had a longer (P<0.05) LOE (2.16 vs. 2.06 d), greater (P<0.05) MSRBOAR (7.6 vs. 7.4) and greater (P<0.05) TSRBOAR (15.4 vs. 14.6). Fertility group 0 had less (P<0.05) BF, poorer (P<0.05) LOC and was narrower (P<0.05) ribbed compared with the other FG's. Based on these results it was concluded that gilts with LOE ≤1 day or weak standing reflexes were less likely to farrow a litter.}, number={1-2}, journal={LIVESTOCK SCIENCE}, author={Knauer, M. T. and Cassady, J. P. and Newcom, D. W. and See, M. T.}, year={2012}, month={Sep}, pages={159–167} }
 @article{spake_gray_cassady_2012, title={Relationship between backtest and coping styles in pigs}, volume={140}, ISSN={["1872-9045"]}, DOI={10.1016/j.applanim.2012.06.007}, abstractNote={The objective of this study was to examine relationships between behaviors in three different standard tests of temperament in pigs, Sus scrofa. For the backtest, pigs (n = 575) were placed in the supine position for 60 s. Each pig was tested twice. Amount of time struggling and number of struggle attempts during each test was recorded and combined to give total time struggling and total struggle attempts. Increased total time struggling was weakly associated with low preweaning average daily gain (r = −0.24; P < 0.01) and low adjusted 21-day weight (r = −0.19; P < 0.05). Pigs were ranked, within replicate, based on total time struggling. Piglets in the top (longest total time struggling) and bottom (shortest total time struggling) 10% of their respective replicates were selected for additional coping style tests (n = 120). These tests were the resident intruder test, to measure aggression toward other pigs, and novel object test, to measure behavioral and physiological responses to a novel object. Correlations between total time struggling during the backtest and time to contact, time between contact and attack, and time to attack during resident intruder test (r = 0.01, r = −0.03, and r = −0.03, respectively) did not differ from 0. The backtest performance was also not correlated with latency to explore ((r = 0.13), time exploring (r = −0.05), or cardiac response to the novel object during novel object tests (P > 0.1). Pigs grouped based on total time struggling did not differ consistently during resident intruder test or novel object test trials. In conclusion, results of the present study do not support the theory that backtest performance is indicative of behavior in a test of aggression (resident intruder test) or a test of fear/curiosity in response to novelty (novel object test).}, number={3-4}, journal={APPLIED ANIMAL BEHAVIOUR SCIENCE}, author={Spake, Jessica R. and Gray, Kent A. and Cassady, Joseph P.}, year={2012}, month={Sep}, pages={146–153} }
 @article{maltecca_gray_weigel_cassady_ashwell_2011, title={A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations}, volume={42}, ISSN={["0268-9146"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80255123496&partnerID=MN8TOARS}, DOI={10.1111/j.1365-2052.2011.02188.x}, abstractNote={Direct gestation length influences economically important traits in dairy cattle that are related to birth and peri-natal survival of the calf. The objective of this study was to identify single nucleotide polymorphisms (SNPs) that are significantly associated with direct gestation length through a genome-wide association study. Data used in the analysis included 7,308,194 cow gestation lengths from daughters of 4743 United States Holstein sires in the Cooperative Dairy DNA Repository population and 580,157 gestation lengths from 749 sires in the Italian Brown population. Association analysis included 36,768 and 35,082 SNPs spanning all autosomes for Holstein and Brown Swiss, respectively. Multiple shrinkage Bayesian was employed. Estimates of heritability for both populations were moderate, with values of 0.32 (±0.03) and 0.29 (±0.02) for Holstein and Brown Swiss, respectively. A panel of SNPs was identified, which included SNPs that have significant effects on direct gestation length, of which the strongest candidate region is located on chromosome 18. Two regions not previously linked to direct calving ease and calf survival were identified on chromosome 7 and 28, corresponding to regions that contain genes related to embryonic development and foetal development. SNPs were also identified in regions that have been previously mapped for calving difficulty and longevity. This study identifies target regions for the investigation of direct foetal effects, which are a significant factor in determining the ease of calving.}, number={6}, journal={ANIMAL GENETICS}, author={Maltecca, C. and Gray, K. A. and Weigel, K. A. and Cassady, J. P. and Ashwell, M.}, year={2011}, month={Dec}, pages={585–591} }
 @article{yoder_maltecca_cassady_flowers_price_see_2011, title={Breed differences in pig temperament scores during a performance test and their phenotypic relationship with performance}, volume={136}, ISSN={["1878-0490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79951959362&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2010.08.004}, abstractNote={Nucleus populations of Chester White, Duroc, Landrace, and Yorkshire boars and gilts (n = 4774) were used to estimate breed differences in temperament and the relationship with performance. Adjusted backfat, adjusted loin depth, days to 113.4 kilograms (DAYS), estimated percent fat-free lean (LEAN), and three temperament scores: load score, scale score, and vocal score were recorded, on a scale of 1 (calm) to 5 (highly excited), during a performance test. Logistic regression for temperament scores included fixed effects of breed, sex, contemporary group (barn-farm-test date), and body weight as a covariate was used. Order that a pig was loaded into the scale, within pen, was included as a fixed effect for load score. After initial analysis, it was determined that vocal score was best described as two categories, vocal or non-vocal, and was reanalyzed accordingly. Linear mixed models for backfat, loin depth, DAYS, and LEAN included fixed effects of breed, sex, and load score, scale score, or vocal score. Growth rate was adjusted to 113.4 kg, while backfat and loin depth were adjusted to 113.4 kg through regression on mean body weight of the respective breed. The odds of increased load score were greater for Landrace (1.62, 1.30; P < 0.01) than Duroc and Yorkshire respectively. Landrace had a greater (P < 0.01) probability of a higher scale and vocal scores compared to Chester White (1.77, 2.37), Duroc (3.31, 3.94) and Yorkshire (2.51, 2.46). Yorkshire had greater (P < 0.01) odds of increased load score (1.25), SS (1.32), and vocal score (1.60) than Duroc. Chester White had greater odds of increased load score and scale score than Duroc (1.58, 1.87) and Yorkshire (1.26, 1.42), respectively. Chester White were 1.66 (P < 0.01) times more likely to have a higher vocal scores than Duroc. Phenotypic correlations (P < 0.01) for scale score with load score, vocal score, backfat, loin depth, DAYS, and LEAN were 0.13, 0.32, − 0.15, − 0.07, 0.10 and 0.17, respectively. Landrace were more excited and vocal in the scale than Chester White, Durocs and Yorkshire. Landrace were more difficult to load into the scale than Durocs and Yorkshire. Chester White were more active in the scale than Durocs and Yorshire, and more vocal than Durocs. Yorkshire were harder to load, more active and vocal than Durocs. It was concluded that temperament differs between breeds, and pigs with lower temperament scores were fatter, had greater loin depth and grew faster.}, number={2-3}, journal={LIVESTOCK SCIENCE}, author={Yoder, C. L. and Maltecca, C. and Cassady, J. P. and Flowers, W. L. and Price, S. and See, M. T.}, year={2011}, month={Apr}, pages={93–101} }
 @article{gray_smith_maltecca_overton_parish_cassady_2011, title={Differences in hair coat shedding, and effects on calf weaning weight and BCS among Angus dams}, volume={140}, ISSN={["1871-1413"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79960901958&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2011.02.009}, abstractNote={The objective of the study was to assess variation in hair coat shedding of Angus cows, and its effect on adjusted weaning weight (d205wt) and BCS. Data were available from 532 Angus cows over 3 years of age. Beginning in March and for 5 months at 30-d intervals, trained technicians scored cows on a scale from 1 to 5, with 1 representing slick coats and 5 winter coats. For each cow, the first month with a score of 3 or less (MFS, 5 levels) was considered the beginning of winter coat shedding and used in the analyses. Association between MFS and d205WT or BCS, was investigated using the mixed procedure of SAS. Data were further analyzed by dividing cows into two groups, group one (Group 1) were cows with a shedding score of 3 or less by June 1st and group two (Group 2) consisted of cows with a shedding score of 4 or 5 on June 1st (AS, 2 levels). Calves from Group1 dams were 11.1 ± 2.8 kg heavier at weaning (P < 0.01) than calves from Group 2 dams. No significant differences were found between shedding score and BCS. Variance components were estimated using THRGIBBS1F90 and heritability of AS was calculated (h2 = 0.35) with a moderate genetic correlation with d205WT (rg = − 0.58). Hair coat shedding is a heritable trait and could be altered by selection. Producers within the Southeastern or Southern United States who are concerned about heat stress may want to select for cattle that shed their winter hair coat earlier in the season. In conclusion, cows who shed their winter coat by June 1st will wean heavier calves on average.}, number={1-3}, journal={LIVESTOCK SCIENCE}, author={Gray, K. A. and Smith, T. and Maltecca, C. and Overton, P. and Parish, J. A. and Cassady, J. P.}, year={2011}, month={Sep}, pages={68–71} }
 @article{knauer_cassady_newcom_see_2011, title={Phenotypic and genetic correlations between gilt estrus, puberty, growth, composition, and structural conformation traits with first-litter reproductive measures}, volume={89}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79960997046&partnerID=MN8TOARS}, DOI={10.2527/jas.2009-2673}, abstractNote={The objective was to estimate correlations of gilt estrus, puberty, growth, composition, and structural conformation traits with first-litter reproductive measures. Four groups of gilts (n = 1,225; Genetic Improvement Services of NC, Newton Grove, NC) entered the NC Swine Evaluation Station (Clayton, NC) averaging 162 d of age and were observed daily for symptoms of estrus. Once symptoms of first estrus were observed in 70% of gilts, recording of symptoms of estrus in all gilts occurred every 12 h for 30 d, utilizing fence-line boar contact. Subjective estrous traits were maximum and total strength of standing reflex, as observed with and without the presence of a boar, and strength of vulva reddening and swelling. Objective estrous traits consisted of vulva redness, vulva width, length of estrus, and age at puberty. Growth and composition traits included BW at puberty, days to 114 kg, and 10th rib backfat and LM area at 114 kg and at puberty. Subjective structural conformation traits were muscle mass, rib width, front leg side view, rear leg side view, front legs front view, rear legs rear view, and locomotion. First-litter sow traits included if gilt farrowed (Stay), age at first farrowing (AFF), total number of piglets born (TNB), and weaning to conception interval (WCI). Variance components were estimated using an animal model with AIREMLF90 for linear traits and THRGIBBS1F90 for categorical traits. Heritability estimates for Stay, AFF, and TNB were 0.14, 0.22, and 0.02, respectively. Genetic correlations between length of estrus, the standing reflex traits, and age at puberty with Stay were 0.34, 0.34 to 0.74, and -0.27, respectively, and with AFF were -0.11, -0.04 to -0.41, and 0.76, respectively. Days to 114 kg had genetic associations with Stay, AFF, and TNB of 0.52, -0.25, and -0.08, respectively. Backfat at 114 kg had genetic correlations with Stay, AFF, and TNB of -0.29, 0.14, and 0.47, respectively. Vulva redness and TNB were negatively correlated phenotypically (r = -0.14) and genetically (r = -0.53). Associations between structural conformation traits with Stay, AFF, TNB, and WCI were generally low to moderate and favorable. Selection for longer length of estrus, stronger standing reflex, or younger age at puberty would increase the proportion of gilts that farrow and reduce age at first farrowing.}, number={4}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Knauer, M. T. and Cassady, J. P. and Newcom, D. W. and See, M. T.}, year={2011}, month={Apr}, pages={935–942} }
 @article{fix_cassady_heugten_hanson_see_2010, title={Differences in lean growth performance of pigs sampled from 1980 and 2005 commercial swine fed 1980 and 2005 representative feeding programs}, volume={128}, ISSN={["1878-0490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-76349085628&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2009.11.006}, abstractNote={The objective of this study was to assess how changes in genetics and feeding programs over 25 years in the U.S. commercial swine industry have impacted lean growth performance. Genetic samples (GS) of pigs (n = 162) from the commercial industries in 1980 and 2005 were randomly assigned to 1 of 2 feeding programs (FP) representative of 1980 or 2005. Pigs were placed 3 per pen (n = 54) at approximately 4 weeks of age and were harvested when average BW of the pen exceeded 116 kg. Real-time ultrasound measures for backfat depth and longissimus muscle area at the 10th rib were collected every 4 weeks, beginning at week 8 (group 1) or week 10 (group 2) until harvest. Average daily gain, ADFI, and G:F were calculated for the nursery period (7.0 ± 0.4 to 26.9 ± 0.7 kg BW), finishing period (26.9 ± 0.7 to 119 ± 0.7 kg BW), and overall (7.0 ± 0.4 to 116 ± 0.7 kg BW). Lean ADG and lean G:F were calculated for the period of first real-time ultrasound to harvest (42.7 ± 1.0 kg to 116 kg BW). Pigs from 2005 vs. 1980 GS and pigs fed 2005 vs. 1980 FP reached final BW of 116 kg sooner; 11 and 12 d, respectively. For ADG during finishing and overall, GS × FP interactions were observed, where 1980 GS pigs fed 1980 vs. 2005 FP showed increases of 7.0 and 6.3%, respectively; however, 2005 GS pigs fed 1980 vs. 2005 FP had increases of 12.6 and 12.3%, respectively. Pigs from the 2005 GS had greater ADG during finishing and overall, increased lean ADG, with no difference in ADFI during finishing, overall, and lean gain period or reduced ADFI during nursery which led to greater G:F and lean G:F. Pigs fed 2005 FP had increased ADG during all periods, with reduced ADFI during finishing, overall, and the lean gain test period which led to greater lean G:F and G:F during all portions of the trial. Although via different methods, changes over the past 25 years in the U.S. swine industry with respect to both genetics and feeding programs have resulted in a 15% reduction in days to harvest and a 45% improvement in lean efficiency.}, number={1-3}, journal={LIVESTOCK SCIENCE}, author={Fix, J. S. and Cassady, J. P. and Heugten, E. and Hanson, D. J. and See, M. T.}, year={2010}, month={Mar}, pages={108–114} }
 @article{fix_cassady_herring_holl_culbertson_see_2010, title={Effect of piglet birth weight on body weight, growth, backfat, and longissimus muscle area of commercial market swine}, volume={127}, ISSN={["1878-0490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70449519415&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2009.08.007}, abstractNote={The objective of this study was to estimate the effect of piglet birth weight on future BW, growth, backfat, and longissimus muscle area of pigs in a commercial U.S. production system. Pigs (n = 5727) at a commercial farm were individually weighed and identified within 24 h of birth. Weights were collected prior to weaning (n = 4108), after finisher placement (n = 3439), and 7 (n = 1622) and 16 (n = 1586) weeks into finishing; hot carcass weight was also collected (n = 1693). Average daily gain during lactation, nursery, finishing, and overall (birth to 16 weeks into finishing) was calculated. During BW collection 16 weeks into finishing, real-time ultrasound backfat thickness and longissimus muscle area were measured. Sex × birth weight (linear and quadratic) interactions were observed for BW at weaning and finisher placement and daily gain during pre-weaning and nursery. Linear birth weight × cross foster interactions were observed for weaning weight and pre-weaning gain. Linear and quadratic effects of birth weight on BW at weaning, finisher placement, 7 and 16 weeks into finishing, and hot carcass weight and average daily gain during pre-weaning, nursery, finishing, and total were observed. For all measures of BW and average daily gain, as birth weight increased subsequent BW and average daily gain increased at a decreasing rate; however, for the sex × birth weight (linear and quadratic) interactions, heavier birth weight barrows were lighter and grew slower than gilts of comparable birth weight. Worth noting, the birth weight × sex interactions described very few pigs in the extreme portion of the birth weight distribution. For birth weight × cross foster interactions, non-cross fostered pigs were increasingly heavier and faster growing as birth weight increased compared to cross fostered pigs. Heavier birth weight pigs tended to have increased backfat depth (P = 0.07). Linear and quadratic effects of birth weight on longissimus muscle area were observed; as birth weight increased muscling increased at a decreasing rate. Regardless of interactions or period of production, increased birth weight resulted in heavier future BW, faster daily gain along with larger longissimus muscle area prior to harvest. In all instances the magnitude of the negative effect of birth weight increased as birth weight decreased.}, number={1}, journal={LIVESTOCK SCIENCE}, author={Fix, J. S. and Cassady, J. P. and Herring, W. O. and Holl, J. W. and Culbertson, M. S. and See, M. T.}, year={2010}, month={Jan}, pages={51–59} }
 @article{fix_cassady_holl_herring_culbertson_see_2010, title={Effect of piglet birth weight on survival and quality of commercial market swine}, volume={132}, ISSN={["1878-0490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77954658643&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2010.05.007}, abstractNote={The objective of this study was to determine the effect of individual piglet birth weight on mortality and pig quality in a U.S. commercial production system. Pigs used in this study were farrowed from Large White × Landrace sows (n = 463) bred to Duroc boars during a 4 week period at a commercial sow farm. Within 24 h of birth, all pigs (born alive = 5727 and stillborns = 513) were weighed and individually indentified. A portion of pigs (16.7%) were cross-fostered to reduce litter size variation during lactation. Individual mortality was recorded daily during the suckling phase. Pigs were weighed 2 days prior to weaning (18.7 ± 2.1 days of age), finisher placement (74.8 ± 1.9 days of age), and 16 weeks into finishing (172.8 ± 1.8 days of age). During BW collections, an inventory of all live pigs was conducted, and pigs were given a quality score based on visual evaluation of BW and health (3 = healthy pig; 2 = slightly small and/or slightly unthrifty; 1 small and/or unthrifty). Survival was analyzed for 4 distinct time periods (prenatal, pre-weaning, nursery phase, and finishing phase). Data were analyzed using a logit (survival) or cumulative logit (quality score) function. Birth weight linear effects on prenatal, pre-weaning, and nursery survival as observed mortality probability increased as birth weight decreased. However birth weight did not impact the likelihood of survival during finishing. As birth weight decreased, the likelihood of pigs being poorer quality, quality score (1 or 2), at weaning, finisher placement, and 16 weeks into finishing, increased. As birth weight increased the likelihood of a pig being full value at the end of the finishing phase increased. Reduced individual piglet birth weight, was associated with reduced pig quality and likelihood of prenatal, pre-weaning, and nursery survival. Because of the negative impact of birth weight on pre-weaning and nursery survival and pig quality in finishing, as birth weight decreased pigs were less likely to be full value at harvest.}, number={1-3}, journal={LIVESTOCK SCIENCE}, author={Fix, J. S. and Cassady, J. P. and Holl, J. W. and Herring, W. O. and Culbertson, M. S. and See, M. T.}, year={2010}, month={Aug}, pages={98–106} }
 @article{knauer_cassady_newcom_see_2010, title={Estimates of variance components for genetic correlations among swine estrus traits}, volume={88}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77955997151&partnerID=MN8TOARS}, DOI={10.2527/jas.2009-2639}, abstractNote={Variance components and genetic correlations were estimated among estrus, puberty, growth, and composition traits in Landrace-Large White gilts (n = 1,225; Genetic Improvement Services, Newton Grove, NC) from 59 sires and 330 dams. Four groups of gilts entered the North Carolina Swine Evaluation Station in Clayton at an average age of 162 d and were checked daily for estrus. Once 70% of gilts had reached puberty, recording of estrus symptoms occurred every 12 h for 30 d, using fence-line boar contact. Subjective estrus traits were maximum strength of standing reflex with or without a boar present, total strength of standing reflex with or without a boar present, and strength of vulva reddening and swelling. Objective estrus traits consisted of vulva redness, vulva width, length of estrus in consecutive days based on 12-h observations, and age at puberty (AGEPUB). Growth and composition traits included puberty weight, days to 114 kg (DYS), 10th-rib backfat, and 10th-rib LM area at 114 kg (BF, LMA) and puberty. Variance components were estimated using AIREMLF90 with an animal model. All models included gilt development diet class and breed composition as fixed effects, entry age as a covariate (except DYS, BF, and LMA), a random common litter effect, and a random animal genetic effect. Heritability estimates for length of estrus, maximum strength of the standing reflex with a boar, total strength of the standing reflex with a boar, maximum strength of the standing reflex without a boar, total strength of the standing reflex without a boar, vulva redness, strength of vulva reddening and swelling, and vulva width were 0.21, 0.13, 0.26, 0.42, 0.42, 0.26, 0.45, and 0.58, respectively. Heritability estimates for AGEPUB, puberty weight, 10th-rib backfat at puberty, 10th-rib LM area at puberty, DYS, BF, and LMA were 0.29, 0.39, 0.41, 0.38, 0.24, 0.47, and 0.39, respectfully. Common litter effect estimates ranged from 0.01 to 0.09. The estimated genetic correlation between length of estrus and maximum strength of standing reflex with a boar was 0.99. Genetic correlations between AGEPUB and length of estrus, maximum strength of standing reflex with a boar, and vulva redness were -0.23, -0.32, and 0.20, respectively. Length of estrus had positive genetic associations with DYS and BF (0.30 and 0.29, respectively). It was concluded that past selection for lean BW gain may have weakened the strength of the standing reflex and that sufficient genetic variation exists to make selection for improved swine estrus traits effective.}, number={9}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Knauer, M. T. and Cassady, J. P. and Newcom, D. W. and See, M. T.}, year={2010}, month={Sep}, pages={2913–2919} }
 @article{ashwell_ceddia_house_cassady_eisen_eling_collins_grissom_odle_2010, title={Trans-10, cis-12-conjugated linoleic acid alters hepatic gene expression in a polygenic obese line of mice displaying hepatic lipidosis}, volume={21}, ISSN={["1873-4847"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77955844665&partnerID=MN8TOARS}, DOI={10.1016/j.jnutbio.2009.06.013}, abstractNote={The trans-10, cis-12 isomer of conjugated linoleic acid (CLA) causes a rapid reduction of body and adipose mass in mice. In addition to changes in adipose tissue, numerous studies have reported alterations in hepatic lipid metabolism. Livers of CLA-fed mice gain mass, partly due to lipid accumulation; however, the precise molecular mechanisms are unknown. To elucidate these mechanisms, we examined fatty acid composition and gene expression profiles of livers from a polygenic obese line of mice fed 1% trans-10, cis-12-CLA for 14 days. Analysis of gene expression data led to the identification of 1393 genes differentially expressed in the liver of CLA-fed male mice at a nominal P value of .01, and 775 were considered significant using a false discovery rate (FDR) threshold of .05. While surprisingly few genes in lipid metabolism were impacted, pathway analysis found that protein kinase A (PKA) and cyclic adenosine monophosphate (cAMP) pathways signaling pathways were affected by CLA treatment and 98 of the 775 genes were found to be regulated by hepatocyte nuclear factor 4alpha, a transcription factor important in controlling liver metabolic status.}, number={9}, journal={JOURNAL OF NUTRITIONAL BIOCHEMISTRY}, author={Ashwell, Melissa S. and Ceddia, Ryan P. and House, Ralph L. and Cassady, Joseph P. and Eisen, Eugene J. and Eling, Thomas E. and Collins, Jennifer B. and Grissom, Sherry F. and Odle, Jack}, year={2010}, month={Sep}, pages={848–855} }
 @article{velie_maltecca_cassady_2009, title={Genetic relationships among pig behavior, growth, backfat, and loin muscle area}, volume={87}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70249140947&partnerID=MN8TOARS}, DOI={10.2527/jas.2008-1328}, abstractNote={The objective of this study was to estimate repeatabilities and heritabilities for measures of pig behavior and their relationship with performance. Measures of behavior and performance included the backtest, resident-intruder test, human approach test (HAT), novel object test (NOT), d 1 BW, backfat depth (BF), loin muscle area (LMA), ADG in the farrowing house, ADG, 21-d BW, and 140-d BW (W). Each behavioral trait was measured twice. The study consisted of 95 litters from 31 sires with an average of 3 litters per sire (n >or= 457). Between 7 and 14 d of age, the backtest was conducted by placing each pig in a supine position for 60 s. Total time spent struggling (TTS) and total number of attempts to struggle (TAS) were recorded. The resident intruder test involved 2 nursery pigs, a resident pig and an unfamiliar intruder pig. The resident pen was divided in half by a solid partition. A resident pig was placed in the test area, and an intruder pig was then introduced. Latency until an attack occurred (LAT) and total number of attacks over 2 tests (RIS) were recorded. Amount of time taken for each finishing pig to make snout contact with an unfamiliar human or object was recorded. Dam and sire effects influenced all traits (P < 0.01). Sex and pen affected LAT, RIS, HAT, and NOT (P < 0.10). Repeatabilities of TTS, TAS, RIS, LAT, HAT, and NOT were 0.38, 0.21, 0.07, 0.08, 0.17, and 0.11, respectively. The phenotypic correlations of TTS with TAS and HAT with NOT were 0.61 and 0.34, respectively. Phenotypic correlation between RIS and LAT was -0.85. Total time spent struggling and TAS tended to be phenotypically correlated with 21-d BW and ADG in the farrowing house. Total attempts to struggle were phenotypically correlated with BF (0.15). Latency until an attack occurred was phenotypically correlated with LMA (0.23). Resident intruder score was phenotypically correlated with ADG (-0.13), W (-0.13), and LMA (-0.21) and estimated to be lowly heritable (h(2) = 0.12). Heritabilities of TTS and TAS were 0.31 and 0.53, respectively. Genetic correlation of TAS with ADG and W was 0.38. Genetic correlations of TTS with BF, W, and TAS were 0.14, 0.18, and 0.81, respectively. The backtest is a heritable and repeatable measure of a behavioral characteristic in pigs that is phenotypically and genetically correlated with performance.}, number={9}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Velie, B. D. and Maltecca, C. and Cassady, J. P.}, year={2009}, month={Sep}, pages={2767–2773} }
 @article{cassady_2007, title={Evidence of phenotypic relationships among behavioral characteristics of individual pigs and performance}, volume={85}, ISSN={["1525-3163"]}, DOI={10.2527/jas.2006-310}, abstractNote={The objective of this research was to estimate phenotypic relationships among backtest scores (BTS), resident-intruder test scores (RIS), growth rate, LM area, and backfat in pigs. Little is known about the relationships among measures of behavioral characteristics of individual pigs and economically important traits. However, it may be expected that a pig's behavior affects its performance and that of its pen mates. The backtest was used in this experiment because it was previously shown to be a measure of individual stress-coping behavior and was related to lean gain. The resident-intruder test was used because it is a measure of a pig's tendency for aggressive behavior toward an unfamiliar pig. Each test was performed twice on pigs (n = 150) from 20 litters, and complete performance data was available on 140 pigs. Between 7 and 14 d of age, the backtest was performed by placing each pig in a supine position and gently restraining it for 60 s. The number of escape attempts (bouts of struggling) and total time spent struggling were recorded. The BTS was the summation of escape attempts during both tests. Resident intruder tests were assessed when pigs were between 30 and 50 d of age. A solid divider was placed in the resident pig's pen. The resident was placed alone on 1 side of the divider, away from its penmates. An intruder pig of the same sex and smaller size was then placed into the pen. When an attack was initiated by the resident, the pigs were immediately separated, the test was terminated, and a score of 1 was recorded. If no attack occurred by 5 min, the test was terminated and was given a score of zero. The cumulative score from both tests was the RIS. Dam effects influenced BTS (P < 0.01) and RIS (P < 0.03). Preweaning ADG of pigs with a BTS of 8 was 120 g greater than that of pigs with a BTS of 2. However, ADG from 20 to 76 d of age was 131 g greater in pigs with BTS = 2 than in pigs with BTS = 8. Lean gain of pigs with RIS = 2 was 25 g/d greater than in those with RIS = 0 or 1. This resulted in pigs with RIS = 2 having 1.6 kg more acceptable, standardized, fat-free lean. Conflicting results were found when relating the BTS to performance. However, with the RIS, greater aggression toward other pigs was associated with better performance. It was concluded that an unfavorable phenotypic relationship existed between RIS and lean growth.}, number={1}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Cassady, J. P.}, year={2007}, month={Jan}, pages={218–224} }
 @article{tsai_cassady_freking_nonneman_rohrer_piedrahita_2006, title={Annotation of the Affymetrix(1) porcine genome microarray}, volume={37}, ISSN={["0268-9146"]}, DOI={10.1111/j.1365-2052.2006.01460.x}, abstractNote={Overview: The Affymetrix porcine genome microarray (http:// www.affymetrix.com/products/arrays/specific/porcine.affx) is minimally annotated. Less than 10% of the probe sets on this array are described with gene names, posing a challenge to biological interpretation of data. Lack of annotation is likely due to the limited availability of full-length porcine cDNA sequence. Presented here is a strategy for improving the annotation of this microarray.}, number={4}, journal={ANIMAL GENETICS}, author={Tsai, S. and Cassady, J. P. and Freking, B. A. and Nonneman, D. J. and Rohrer, G. A. and Piedrahita, J. A.}, year={2006}, month={Aug}, pages={423–424} }
 @article{blowe_boyette_ashwell_eisen_robison_cassady_2006, title={Characterization of a line of pigs previously selected for increased litter size for RBP4 and follistatin}, volume={123}, ISSN={["1439-0388"]}, DOI={10.1111/j.1439-0388.2006.00620.x}, abstractNote={Summary}, number={6}, journal={JOURNAL OF ANIMAL BREEDING AND GENETICS}, author={Blowe, C. D. and Boyette, K. E. and Ashwell, M. S. and Eisen, E. J. and Robison, O. W. and Cassady, J. P.}, year={2006}, month={Dec}, pages={389–395} }
 @article{bender_see_hanson_lawrence_cassady_2006, title={Correlated responses in growth, carcass, and meat quality traits to divergent selection for testosterone production in pigs}, volume={84}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33744943805&partnerID=MN8TOARS}, DOI={10.2527/2006.8461331x}, abstractNote={The objective of this project was to characterize changes in growth, carcass yield, and meat quality traits in castrates and gilts in response to divergent selection for testosterone production. In generation 21, endogenous testosterone concentrations in Duroc boars of the high (HTL) and low (LTL) testosterone lines averaged 49.0 and 27.8 ng/mL (P < 0.01), respectively. Eight LTL and 10 HTL boars were used to sire 29 LTL and 33 HTL litters. To remove the effects of inbreeding, these same boars were mated to females of a Large White x Landrace composite (WC) to generate 11 WC by LTL litters (WLT) and 23 WC by HTL litters (WHT). Castrates and gilts were then allotted to LTL (n = 53), HTL (n = 61), WLT (n = 102), and WHT (n = 101) for testing. Growth and carcass traits analyzed included days to 114 kg (D114), ADG, backfat adjusted to 114 kg (ABF), LM area adjusted to 114 kg and predicted percent lean (PPL). Fat-O-Meater data collected were adjusted fat depth (AFD), adjusted loin depth, and percent lean. Meat quality traits characterized at 24 h postmortem included marbling score, percent lipid, pH, drip loss, color score, and Minolta L*, a*, and b*. Data were analyzed with a mixed model including fixed effects of line, mating type (purebred or crossbred), sex, and the random effect of sire nested within line. All possible interactions among fixed effects were tested. The HTL had fewer D114 (P < 0.05), greater ADG (P < 0.01), greater ABF (P < 0.01), and lower PPL (P < 0.01) than LTL. The WHT and WLT did not differ for D114, ADG, or ABF. The WHT had smaller LM area adjusted to 114 kg (P < 0.05) and greater drip loss (P < 0.05) than WLT. The WLT had lower adjusted loin depth (P < 0.05) than LTL and HTL. The LTL and HTL had greater subjective scores for marbling (P < 0.05) compared with WLT and WHT. The least squares mean for percent lipid for HTL and LTL was 4.00. The WHT had greater means for L*, a*, and b* (P < 0.05) than WLT. Pigs selected for increased testosterone production grew faster and produced fatter carcasses than pigs selected for decreased testosterone. Changes in growth, carcass yield, and meat quality traits were detected in castrates and gilts in response to divergent selection for testosterone production.}, number={6}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Bender, J. M. and See, M. T. and Hanson, D. J. and Lawrence, T. E. and Cassady, J. P.}, year={2006}, month={Jun}, pages={1331–1337} }
 @article{tsai_mir_martin_estrada_bischoff_hsieh_cassady_freking_nonneman_rohrer_et al._2006, title={Detection of transcriptional difference of porcine imprinted genes using different microarray platforms}, volume={7}, journal={BMC Genomics}, author={Tsai, S. and Mir, B. and Martin, A. C. and Estrada, J. L. and Bischoff, S. R. and Hsieh, W. P. and Cassady, J. P. and Freking, B. A. and Nonneman, D. J. and Rohrer, G. A. and et al.}, year={2006} }
 @article{muncie_cassady_ashwell_2006, title={Refinement of quantitative trait loci on bovine chromosome 18 affecting health and reproduction in US Holsteins}, volume={37}, ISSN={["1365-2052"]}, DOI={10.1111/j.1365-2052.2006.01425.x}, abstractNote={Summary}, number={3}, journal={ANIMAL GENETICS}, author={Muncie, S. A. and Cassady, J. P. and Ashwell, M. S.}, year={2006}, month={Jun}, pages={273–275} }
 @misc{house_cassady_eisen_mcintosh_odle_2005, title={Conjugated linoleic acid evokes de-lipidation through the regulation of genes controlling lipid metabolism in adipose and liver tissue}, volume={6}, ISSN={["1467-789X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-22744451979&partnerID=MN8TOARS}, DOI={10.1111/j.1467-789X.2005.00198.x}, abstractNote={Summary}, number={3}, journal={OBESITY REVIEWS}, author={House, RL and Cassady, JP and Eisen, EJ and McIntosh, MK and Odle, J}, year={2005}, month={Aug}, pages={247–258} }
 @article{house_cassady_eisen_eling_collins_grissom_odle_2005, title={Functional genomic characterization of delipidation elicited by trans-10, cis-12-conjugated linoleic acid (t10c12-CLA) in a polygenic obese line of mice}, volume={21}, ISSN={["1531-2267"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-21244497638&partnerID=MN8TOARS}, DOI={10.1152/physiolgenomics.00244.2004}, abstractNote={Gene expression was measured during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. Adult mice ( n = 185) were allotted to a 2 × 2 factorial experiment consisting of either nonobese (ICR-control) or obese (M16-selected) mice fed a 7% fat, purified diet containing either 1% linoleic acid (LA) or 1% t10c12-CLA. Body weight (BW) by day 14 was 12% lower in CLA- compared with LA-fed mice ( P < 0.0001). By day 14, t10c12-CLA reduced weights of epididymal, mesenteric, and brown adipose tissues, as a percentage of BW, in both lines by 30, 27, and 58%, respectively, and increased liver weight/BW by 34% ( P < 0.0001). Total RNA was isolated and pooled (4 pools per tissue per day) from epididymal adipose ( days 5 and 14) of the obese mice to analyze gene expression profiles using Agilent mouse oligo microarray slides representing >20,000 genes. Numbers of genes differentially expressed by greater than or equal to twofold in epididymal adipose ( days 5 and 14) were 29 and 125, respectively. It was concluded that, in adipose tissue, CLA increased expression of uncoupling proteins (1 and 2), carnitine palmitoyltransferase system, tumor necrosis factor-α ( P < 0.05), and caspase-3 but decreased expression of peroxisome proliferator-activated receptor-γ, glucose transporter-4, perilipin, caveolin-1, adiponectin, resistin, and Bcl-2 ( P < 0.01). In conclusion, this experiment has revealed candidate genes that will be useful in elucidating mechanisms of adipose delipidation.}, number={3}, journal={PHYSIOLOGICAL GENOMICS}, author={House, RL and Cassady, JP and Eisen, EJ and Eling, TE and Collins, JB and Grissom, SF and Odle, J}, year={2005}, month={May}, pages={351–361} }
 @article{van vleck_cassady_2005, title={Unexpected estimates of variance components with a true model containing genetic competition effects}, volume={83}, DOI={10.2527/2005.83168x}, abstractNote={Simulation of a model containing genetic competition effects was initiated to determine how well REML could untangle variances due to direct and competition genetic effects and pen effects. A two-generation data set was generated with six unrelated males that were each mated to five unrelated females to produce 300 progeny, from which 30 females (one per mating in previous generation) were mated to six unrelated males to produce 300 more progeny. Progeny were randomly assigned, six per pen, to 50 pens per generation. Parameters were V(g), V(c), C(gc), V(p), and V(e), representing direct and competition genetic variance with covariance, and pen and residual variance. Eight statistical models were used to analyze each of 400 replicates of 16 sets of parameters. Both V(g) and V(e) were fixed at 16.0. Values of C(gc) were -2.0, -1.0, 0.1, 1.0, and 2.0. Values of V(c) were 1.0 and 4.0, and values of V(p) were 0.1, 1.0, and 10.0. With the full model, average estimates resembled true parameters, except that V(p) was consistently overestimated when small (0.1 and 1.0), which in turn slightly changed other estimates. The most unexpected result was overestimation of V(p) when V(c) and Cgc were ignored. Overestimation depended on V(c) and the number of competitors in common between records in a pen. Upward bias was somewhat greater when Cg(c) was positive than when it was negative. For example, with C(gc) = 2, V(c) = 4, and V(p) = 0.1, the mean estimate of V(p) was 20.4 when C(gc) and V(c) were dropped from the model and 15.3 when C(gc) = -2.0. When V(p) was ignored, estimates of both C(gc) and V(c) increased in proportion with V(p). Also V(g) increased more with greater V(p). Another unexpected result occurred when pen was considered fixed. Empirical sampling standard errors of estimates of C(gc) and V(c) were decreased generally by factors of 2 to 30. Based on these results, we conclude a high estimate of pen variance may indicate genetic competition effects are important, and ignoring either the pen or competition effects will bias estimates of other components.}, number={1}, journal={Journal of Animal Science}, author={Van Vleck, L. D. and Cassady, J. P.}, year={2005}, pages={68–74} }
 @article{holl_cassady_pomp_johnson_2004, title={A  genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs}, volume={82}, DOI={10.2527/2004.82123421x}, abstractNote={Quantitative trait loci for reproductive traits in a three-generation resource population of a cross between low-indexing pigs from a control line and high-indexing pigs from a line selected 10 generations for increased index of ovulation rate and embryonic survival are reported. Phenotypic data were collected in F2 females for birth weight (BWT, n = 428), weaning weight (WWT, n = 405), age at puberty (AP, n = 295), ovulation rate (OR, n = 423), number of fully formed pigs (FF, n = 370), number of pigs born alive (NBA, n = 370), number of mummified pigs (MUM, n = 370), and number of stillborn pigs (NSB, n = 370). Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers. Sixteen putative QTL (P < 0.10) for reproductive traits were identified in previous analyses of these data with single QTL line-cross models. Data were reanalyzed with multiple QTL models, including imprinting effects. Data also were analyzed with half-sib models. Permutation was used to establish genome-wide significance levels ( = 0.01, 0.05, and 0.10). Thirty-one putative QTL for reproductive traits and two QTL for birth weight were identified (P < 0.10). One Mendelian QTL for FF (P < 0.05), one for NBA (P < 0.05), three for NSB (P < 0.05), three for NN (P < 0.05), seven for AP (P < 0.10), five for MUM (P < 0.10), and one for BWT (P < 0.10) were found. Partial imprinting of QTL affecting OR (P < 0.01), BWT (P < 0.05), and MUM (P < 0.05) was detected. There were four paternally expressed QTL for NN (P < 0.10) and one each for AP (P < 0.05) and MUM (P < 0.10). Maternally expressed QTL affecting NSB (P < 0.10), NN (P < 0.10), and MUM (P < 0.10) were detected. No QTL were detected with half-sib analyses. Multiple QTL models with imprinting effects are more appropriate for analyzing F2 data than single Mendelian QTL line-cross models.}, number={12}, journal={Journal of Animal Science}, author={Holl, J. W. and Cassady, J. P. and Pomp, D. and Johnson, R. K.}, year={2004}, pages={3421–3429} }
 @article{walker_robison_whisnant_cassady_2004, title={Effect of divergent selection for testosterone production on testicular morphology and daily sperm production in boars}, volume={82}, DOI={10.2527/2004.8282259x}, abstractNote={The objective of this study was to characterize correlated responses in testicular morphology and daily sperm production to divergent selection for testosterone production. Duroc boars from high and low lines (HTL and LTL, respectively) divergently selected over 10 generations for testosterone production in response to a GnRH challenge followed by random selection were used. Testicular tissues were sampled from all available males of generation 20 (HTL, n = 46; and LTL, n = 13). Volume densities for Leydig cells, seminiferous tubules, and Sertoli cells were estimated along with sperm production. The HTL boars had greater volume densities of Leydig cells than did LTL (P < 0.01). Volume density of seminiferous tubules tended to differ between lines (P < 0.07), but Sertoli cell volume densities did not differ (P < 0.27). Sperm production traits, adjusted for age, did not differ significantly between lines. Body, testicular, and epididymal weights were recorded for boars from HTL (n = 82) and LTL (n = 44) from generations 20 and 21. After adjustment for BW, average paired testicular weights for HTL and LTL were 417 and 457 g (P < 0.01), respectively. Epididymal weights, adjusted for BW, were heavier for HTL (P < 0.01) than for LTL. To demonstrate that the selection lines still differed for testosterone production, lines were evaluated in generation 21. Endogenous testosterone production of the HTL (n = 54) and LTL (n = 44) testosterone production line averaged 49.0 ng/mL and 27.8 ng/mL (P < 0.01), respectively. Plasma FSH concentrations did not differ between lines (P < 0.30). Selection for testosterone production in response to a GnRH challenge was an effective method of changing testosterone concentrations, testicular size, epididymal weight, and volume density of Leydig cells. However, daily sperm production per gram of testes was unchanged. Based on the results of this study, selection for testosterone production is not recommended as a method of increasing sperm production in pigs.}, number={8}, journal={Journal of Animal Science}, author={Walker, S. and Robison, O. W. and Whisnant, C. S. and Cassady, J. P.}, year={2004}, pages={2259–2263} }
 @article{cassady_robison_johnson_mabry_christian_tokach_miller_goodwin_2004, title={National fork producers council maternal line genetic evaluation: A comparison of growth and carcass traits in terminal progeny}, volume={82}, DOI={10.2527/2004.82123482x}, abstractNote={The objective of this study was to compare growth and carcass traits of 1,252 progeny of six commercially available dam lines included in the National Pork Producers Council Maternal Line Evaluation Project. Lines compared included one maternal line supplied by each of American Diamond Swine Genetics (ADSG), Danbred NA (DB), two lines supplied by Monsanto Choice Genetics (DK and GPK347), Newsham Hybrids (NH), and Landrace x Large White females supplied by the National Swine Registry (NSR). All females were mated to DB, Duroc-Hampshire terminal sires. Traits analyzed were ADG from 56 to 115 kg live weight, days to 115 kg, backfat thickness measured at the 10th rib, carcass length, dressing percent, and 10th-rib LM area. Carcass traits were adjusted to a carcass weight of 85 kg. The statistical model included fixed effects of maternal line, sex, farrowing group, and finishing unit (farm). All two-way interactions among main effects were tested and removed from final models because they were not significant. In addition, because they were not significant, effects of farm and farrowing group were removed from models for carcass length and 10th-rib backfat thickness, and farm was removed from the model for LM area. Least squares means for ADG ranged from 0.74 to 0.79 kg/d. The GPK347 line had lower ADG and greater days to 115 kg than all other lines (P < 0.05). The ADSG (P < 0.05) and NH (P < 0.01) progeny had lower ADG than DK progeny. The DK line had the fewest days to 115 kg (P < 0.05). Progeny for the DB and NH lines had the least 10th-rib backfat, differing from ADSG, DK, and GPK347 (P < 0.05). Pigs from DB females had the greatest dressing percent, differing from ADSG, DK, GPK347, and NH (P < 0.05). The GPK347 had a lower dressing percent than all other lines (P < 0.05). Progeny of DB females had the greatest LM area, differing from ADSG, DK, GPK347, and NSR (P < 0.05). Offspring from ADSG and GPK347 had the smallest LM area; however, GPK347 and NSR did not differ. Differences in carcass length were statistically significant; however, actual differences were small. Economic weights for these traits relative to reproductive traits must be considered in integrated economic analyses to properly compare differences among lines in net economic value for specific markets.}, number={12}, journal={Journal of Animal Science}, author={Cassady, J. P. and Robison, O. W. and Johnson, R. K. and Mabry, J. W. and Christian, L. L. and Tokach, M. D. and Miller, R. K. and Goodwin, R. N.}, year={2004}, pages={3482–3485} }