BILL E. KUNKLE INTERDISCIPLINARY BEEF SYMPOSIUM: Genetic resistance to the effects of grazing endophyte-infected tall fescue.

Forages are the base source of nutrition for any cow-calf operation. Forage types vary based on soil type and climate. Tall fescue () is the most commonly used cultivated grass for grazing beef cattle in the United States. This cool-season perennial is easily established; is resistant to drought, insects, and nematodes; and has the ability to withstand heavy grazing pressure. Most tall fescue varieties are infected with the endophyte fungus () that is essential for the plant's survival but detrimental to cattle performance. Ergot alkaloids are the generally accepted toxic agents produced by the fescue endophyte. Cattle that consume forages infected with this endophyte can develop fescue foot, fat necrosis, or fescue toxicosis. It is estimated that the beef industry loses over US$500 million annually due to fescue toxicosis through heat stress, reduced weight gain, suppressed appetite, and decreased reproductive performance. Other symptoms include a retained or rough hair coat and increased body temperature, which can be detrimental when animals are located in hot and or humid environments. Different forages and forage systems, feed additives, and animal management strategies have been tested through the years allowing the use of tall fescue in beef production systems while minimizing the adverse effects. An animal genetics approach needs to identify and select animals less susceptible to the ergot alkaloids. Research in this area reports that different cattle within the same herd can respond differently when grazing tall fescue, and evidence exists that breed type may also play a role in genetic tolerance to the negative effects on performance. Some studies have looked at the potential of identifying genetic markers that may assist in the selection of more resistant animals. From these studies, there is evidence that genetic variation does exist for resistance to the ergot alkaloids present when grazing endophyte-infected tall fescue. Forage management coupled with animal genetic selection could allow for more efficient use of tall fescue as a significant forage source in beef cattle systems. These would allow producing more beef per hectare in the United States in response to an increasing population combined with decreasing resources.

Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: II. Genomewide association.

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.

Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: I. Genetic parameter estimation and accuracy of genomic prediction.

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.

Calf birth weight, gestation length, calving ease, and neonatal calf mortality in Holstein, Jersey, and crossbred cows in a pasture system.

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.

Effects of reduced panel, reference origin, and genetic relationship on imputation of genotypes in Hereford cattle.

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.

Using 50 k single nucleotide polymorphisms to elucidate genomic architecture of line 1 hereford cattle.

Hereford is a major beef breed in the USA, and a sub-population, known as Line 1 (L1), was established in 1934 using two paternal half-sib bulls and 50 unrelated females. L1 has since been maintained as a closed population and selected for growth to 1 year of age. Objectives were to characterize the molecular genetic architecture of L1 (n = 240) by comparing a cross-section of L1 with the general US. Hereford population (AHA, n = 311), estimating effects of imposed selection within L1 based on allele frequencies at 50 K SNP loci, and examining loci-specific effects of heterozygosity on the selection criterion. Animals were genotyped using the Illumina BovineSNP50 Beadchip, and SNP were mapped to UMD3.0 assembly of the bovine genome sequence. Average linkage disequilibrium (LD), measured by square of Pearson correlation, of adjacent SNP was 0.36 and 0.16 in L1 and AHA, respectively. Difference in LD between L1 and AHA decreased as SNP spacing increased. Persistence of phase between L1 and AHA decreased from 0.45 to 0.14 as SNP spacing increased from 50 to 5,000 kb. Extended haplotype homozygosity was greater in L1 than in AHA for 95.6% of the SNP. Knowledge of selection applied to L1 facilitated a novel approach to QTL discovery. Minor allele frequency was (FDR < 0.01) affected by cumulative selection differential at 191 out of 25,901 SNP. With the FDR relaxed to 0.05, 13 regions on BTA2, 5, 6, 9, 11, 14, 15, 18, 23, and 26 are co-located with previously identified QTL for growth. After adjustment of postweaning gain phenotypes for fixed effects and direct additive genetic effects, regression of residuals on genome-wide heterozygosity was -235.3 ± 91.6 kg. However, no SNP-specific loci where heterozygotes were significantly superior to the average of homozygotes were revealed (FDR ≥ 0.17). In conclusion, genome-wide SNP genotypes clarified effects of selection and inbreeding within L1 and differences in genomic architecture between the population segment L1 and the AHA population.

A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations.

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.

Phenotypic and genetic correlations between gilt estrus, puberty, growth, composition, and structural conformation traits with first-litter reproductive measures.

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.

Estimates of variance components for genetic correlations among swine estrus traits.

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.

Genetic relationships among pig behavior, growth, backfat, and loin muscle area.

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.

Evidence of phenotypic relationships among behavioral characteristics of individual pigs and performance.

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.

Characterization of a line of pigs previously selected for increased litter size for RBP4 and follistatin.

The objective of this study was to determine if selection response for increased litter size in pigs could be partially attributed to three type 1 marker loci coding for genes known to affect litter size: oestrogen receptor (ESR), retinol-binding protein 4 (RBP4) and follistatin (FS). In the high litter size line (LS), pigs from the largest litters, based on number of pigs born alive (NBA), were retained to parent the next generation. A randomly selected control line (LC) was maintained. Gilts were reared in litters of 10 pigs or less to minimize maternal effects. Pigs were measured at generations 10-12. Additional traits scored were number of fully formed pigs (NFF) and number of mummified fetuses (MUM). Breeding values for NFF and NBA were greater (p < 0.05) in LS than LC in generations 11 and 12, but no significant line differences were found for MUM. The A allele of the ESR locus was fixed in both lines. After adjustment for effects of genetic drift, frequency of the two alleles segregating for the FS and RBP4 loci did not differ significantly between lines. No significant additive or dominance effects of the FS markers were detected for NFF, NBA and MUM in either LS or LC. Response to selection for increased litter size could not be attributed to effects at the ESR, RBP4 or FS loci.

Refinement of quantitative trait loci on bovine chromosome 18 affecting health and reproduction in US Holsteins.

Selection for increased milk yield is associated with decreased fertility in US Holsteins. Previously, a putative quantitative trait locus (QTL) on chromosome 18 affecting daughter pregnancy rate (DPR) was identified in one family. Our aim was to determine the validity of the QTL using additional markers and an extended pedigree. Twelve markers were genotyped in 940 descendants of the original sire in which the QTL was identified. Analysis of the extended pedigree detected significant and suggestive QTL for DPR, productive life and somatic cell score. Further analysis is underway to refine the QTL region so that positional candidate genes can be identified.

Correlated responses in growth, carcass, and meat quality traits to divergent selection for testosterone production in pigs.

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.

Conjugated linoleic acid evokes de-lipidation through the regulation of genes controlling lipid metabolism in adipose and liver tissue.

Conjugated linoleic acid (CLA) is a unique lipid that elicits dramatic reductions in adiposity in several animal models when included at < or = 1% of the diet. Despite a flurry of investigations, the precise mechanisms by which conjugated linoleic acid elicits its dramatic effects in adipose tissue and liver are still largely unknown. In vivo and in vitro analyses of physiological modifications imparted by conjugated linoleic acid on protein and gene expression suggest that conjugated linoleic acid exerts its de-lipidating effects by modulating energy expenditure, apoptosis, fatty acid oxidation, lipolysis, stromal vascular cell differentiation and lipogenesis. The purpose of this review shall be to examine the recent advances and insights into conjugated linoleic acid's effects on obesity and lipid metabolism, specifically focused on changes in gene expression and physiology of liver and adipose tissue.

Unexpected estimates of variance components with a true model containing genetic competition effects.

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.

A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs.

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.

National Pork Producers Council Maternal Line Genetic Evaluation: a comparison of growth and carcass traits in terminal progeny.

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.

Effect of divergent selection for testosterone production on testicular morphology and daily sperm production in boars.

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.