Thomas J. Baas

A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition

Genome scans can be employed to identify chromosomal regions and eventually genes (quantitative trait loci or QTL) that control quantitative traits of economic importance. A three-generation resource family was developed by using two Berkshire grand sires and nine Yorkshire grand dams to detect QTL for growth and body composition traits in pigs. A total of 525 F2 progeny were produced from 65 matings. All F2 animals were phenotyped for birth weight, 16-day weight, growth rate, carcass weight, carcass length, back fat thickness, and loin eye area. Animals were genotyped for 125 microsatellite markers covering the genome. Least squares regression interval mapping was used for QTL detection. All carcass traits were adjusted for live weight at slaughter. A total of 16 significant QTL, as determined by a permutation test, were detected at the 5% chromosome-wise level for growth traits on Chromosomes (Chrs) 1, 2, 3, 4, 6, 7, 8, 9, 11, 13, 14, and X, of which two were significant at the 5% genome-wise level and two at the 1% genome-wise level (on Chrs 1, 2, and 4). For composition traits, 20 QTL were significant at the 5% chromosome-wise level (on Chrs 1, 4, 5, 6, 7, 12, 13, 14, 18), of which one was significant at the 5% genome-wise level and three were significant at the 1% genome-wise level (on Chrs 1, 5, and 7). For several QTL the favorable allele originated from the breed with the lower trait mean.

Factors associated with sow stayability in 6 genotypes.

The purpose of this study was to determine the association of production factors with stayability to parity 4 (STAY4) under controlled experimental conditions. Data were from 2,293 female pigs, sampled from 6 genetic lines that were entered into the National Pork Producers Council Maternal Line National Genetic Evaluation Program. Genetic lines evaluated included Newsham (NH), National Swine Registry (NSR), American Diamond Swine Genetics (ADSG), Danbred (DAN), and 2 Dekalb-Monsanto lines (DK44 and GPK347). Stepwise logistic regression was utilized in the analysis of STAY4. All effects were nested within genetic line. Categorical effects in the model were arrival date to the wean-to-finish unit (entry date) and breed-gestation-farrowing facility (farm). Continuous effects in the model were gilt backfat, LM depth, ADG, age at puberty, age at first farrowing, and traits recorded before the last litter of the sow (prefarrow backfat, number born alive, number weaned, litter weaning weight, lactation feed intake, lactation backfat loss, and lactation length). Factors significant for STAY4 included farm, entry date, age at first farrowing, ADG, gilt backfat, and lactation before removal effects, as well as feed intake, number born alive, and lactation length. Age at first farrowing and lactation feed intake affected all genetic lines. Regression coefficients for STAY4 on age at first farrowing were -0.014, -0.022, -0.017, -0.016, -0.011, and -0.021 (all P < 0.05), respectively, for NH, NSR, ADSG, DK44, GPK347, and DAN genetic lines. Regression coefficients for STAY4 on lactation feed intake were 0.043, 0.049, 0.051, 0.061, 0.120, and 0.097 (all P < 0.05), respectively, for NH, NSR, ADSG, DK44, GPK347, and DAN females. Age at puberty, age at first farrowing, and lactation feed intake had the greatest effect on STAY4.

An evaluation of four candidate genes for use in selection programmes aimed at increased intramuscular fat in Duroc swine

A sufficient level of intramuscular fat (IMF) is needed to enhance consumer acceptance of pork products, and is currently receiving greater attention within swine genetic improvement programmes. An examination of previously described and novel genetic variants within candidate genes for IMF deposition was performed to evaluate potential use of genetic markers in marker-assisted selection (MAS). Biological candidate genes implicated to play a role in adipogenesis were investigated within two different lines of purebred Duroc pigs. These included MC4R, FABP3, DLK1, and TCF7L2. Significant variation in IMF within the control line was described by the MC4R genotype and a novel BsrfI single nucleotide polymorphism within the FABP3 gene. Genetic markers for DLK1 and TCF7L2 evaluated in this population are not currently recommended for selection in Duroc swine. Existence of MC4R and FABP3 mutations may be useful markers in MAS aimed at IMF improvement, provided that gene effects are segregating and the presence of an association is detected within the population. However, additional work to confirm the use of the investigated genetic markers in selection programmes is needed.

Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. I. Direct and correlated phenotypic responses to selection.

A study was conducted to evaluate the efficacy of selection for intramuscular fat (IMF) in a population of purebred Duroc swine using real-time ultrasound. Forty gilts were purchased from US breeders and randomly mated for 2 generations to boars available in regional boar studs, resulting in a base population of 56 litters. Littermate pairs of gilts from this population were randomly assigned to a select line (SL) or control line (CL) and mated to the same sire to establish genetic ties between lines. At an average BW of 114 kg, a minimum of 4 longitudinal ultrasound images were collected 7 cm off-midline across the 10th to 13th ribs of all pigs for the prediction of IMF (UIMF). At least 1 barrow or gilt was slaughtered from each litter, and carcass data were collected. A sample of the LM from the 10th to 11th rib interface was analyzed for carcass IMF (CIMF). Breeding values for IMF were estimated by fitting a 2-trait (UIMF and CIMF) animal model in MATVEC. In the SL, selection in each subsequent generation was based on EBV for IMF with the top 10 boars and top 75 gilts used to produce the next generation. One boar from each sire family and 50 to 60 gilts representing all sire families were randomly selected to maintain the CL. Through 6 generations of selection, an 88% improvement in IMF has been realized (4.53% in SL vs. 2.41% in CL). Results of this study revealed no significant correlated responses in measures of growth performance. However, 6 generations of selection for IMF have yielded correlated effects of decreased loin muscle area and increased backfat. Additionally, the SL obtained more desirable objective measures of tenderness and sensory evaluations of flavor and off-flavor. Meat quality characteristics of pH, water holding capacity, and percent cooking loss were not significantly affected by selection for IMF. Selection for IMF using real-time ultrasound is effective but may be associated with genetic ramifications for carcass composition traits. Intramuscular fat may be used in purebred Duroc swine breeding programs as an indicator trait for sensory traits that influence consumer acceptance; however, rapid improvement should not be expected when simultaneous improvement in other trait categories is also pursued.

Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. II. Genetic parameters and trends

Design of breeding programs requires knowledge of variance components that exist for traits included in specific breeding goals and the genetic relationships that exist among traits of economic importance. A study was conducted to evaluate direct and correlated genetic responses to selection for intramuscular fat (IMF) and to estimate genetic parameters for economically important traits in Duroc swine. Forty gilts were purchased from US breeders and randomly mated for 2 generations to boars available in regional boar studs to develop a base population of 56 litters. Littermate pairs of gilts from this population were randomly assigned to a select line (SL) or control line (CL) and mated to the same boar to establish genetic ties between lines. In the SL, the top 10 boars and 75 gilts were selected based on IMF EBV obtained from a bivariate animal model that included IMF evaluated on the carcass and IMF predicted via ultrasound. One boar from each sire family and 50 to 60 gilts representing all sire families were randomly selected to maintain the CL. Carcass and ultrasound IMF were both moderately heritable (0.31 and 0.38, respectively). Moderate to high genetic relationships were estimated among carcass backfat and meat quality measures of IMF, Instron tenderness, and objective loin muscle color. Based on estimates obtained in this study, more desirable genetic merit for pH is associated with greater genetic value for loin color, tenderness, and sensory characteristics. Intramuscular fat measures obtained on the carcass and predicted using ultrasound technology were highly correlated (r(g) = 0.86 from a 12-trait analysis; r(g) = 0.90 from a 5-trait analysis). Estimated genetic relationships among IMF measures and other traits evaluated were generally consistent. Intramuscular fat measures were also genetically associated with Instron tenderness and flavor score in a desirable direction. Direct genetic response in IMF measures observed in the SL corresponded to a significant decrease in EBV for carcass loin muscle area (-0.90 cm(2) per generation) and an increase in carcass backfat EBV (0.98 mm per generation). Selection for IMF has led to more desirable EBV for objective tenderness and has had an adverse effect on additive genetic merit for objective loin color.

Effectiveness of transdermal, needle-free injections for reducing pork carcass defects

A needle-free, transdermal injection device was evaluated for effectiveness of vaccine delivery and for injection site lesions in swine. A total of 130 pigs were vaccinated for pseudorabies virus (PRV) and Mycoplasma hyopneumoniae (M. hyopneumoniae). Pigs were divided into three groups; one group served as unvaccinated controls, the second group was vaccinated with conventional hypodermic needles and the third group was vaccinated with a needle-free, airpowered transdermal injection device. Blood samples collected for up to 36 days post-injection showed that both injection methods produced similar serological responses that were significantly greater than for unvaccinated controls. Injection sites, collected at slaughter from each carcass, showed minimal development of lesions and no carcass defects. The results show the needle-free, transdermal injection system to be effective and safe. Elimination of needles will prevent residual needle fragments in carcasses and associated carcass defects that develop from needle-induced injection-site lesions.

Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations

Intramuscular fat (IMF) content is an important trait affecting the quality of pork. Two Duroc populations, one under positive selection for IMF and the other selected for decreased backfat but under stabilizing selection for IMF, were used to identify signatures of selection associated with IMF using 60,000 single-nucleotide polymorphism data. The effects of selection were analyzed between 2 lines or groups representing selected and control animals within each population using a discriminant analysis of principal components and Wright’s fixation index (FST). Moreover, extended haplotype homozygosity-based approaches were used to examine the changes in haplotype frequency due to recent selection. Each statistical method identified 10–20 selection signatures. A few haplotype-based signatures of selection agreed with results from a genome-wide association study (GWAS), while FST measures showed a better agreement with GWAS results. Agreement of marker-trait associations and signatures of selection was limited, and further examination will be necessary to understand the effect of selection on IMF and why some regions identified by GWAS did not appear to respond to the selection practiced. The genes in 21 consensus selection signatures were examined. Several genes with an effect on overall fatness were identified, but further research is needed to assess whether or not some of them could have a specific effect on IMF.

A novel and robust method for testing bimodality and characterizing porcine adipocytes of adipose tissue of 5 purebred lines of pig

ABSTRACT Adipocyte sizes from adipose tissue of mature animals form a bimodal distribution, thus reporting mean cell size is misleading. The objectives of this study were to develop a robust method for testing bimodality of porcine adipocytes, describe the size distribution with an informative metric, and statistically test hypertrophy and appearance of new small adipocytes, possibly resulting from hyperplasia or lipid filling of previously divided fibroblastic cells. Ninety-three percent of adipose samples measured were bimodal (P < 0.0001); therefore, we describe and propose a method of testing hyperplasia or lipid filling of previously divided fibroblastic cells based upon the probability of an adipocyte falling into 2 chosen competing “bins” as adiposity increases. We also conclude that increased adiposity is correlated positively with an adipocyte being found in the minor mode (r = 0.46) and correlated negatively with an adipocyte being found in the major mode (r = −0.22), providing evidence of either hyperplasia or lipid filling of previously divided fibroblastic cells. We additionally conclude that as adiposity increases, the mode of the major distribution of cells occurs at a larger diameter of adipocyte, indicating hypertrophy.

Development of an Objective Feet and Leg Conformation Evaluation Method Using Digital Imagery in Swine

Background: The objectives of this study were to create an objective measurement method of joint angles for knee, hock, front and rear pasterns and a rear stance position in swine using digital imaging technology and to assess the repeatability of the objective measurement process. Methods and Findings: Forty-five multiparous sows (average parity 6.7 ± 2.5; parity range 5 to 14) from two commercial farms (n=21 farm 1 and n=24 farm 2) were used. Sows were moved to a pen where digital images of the profile and rear stance were captured. On average, 5.2 (± 2.6) profile and 2.6 (± 1.0) rear stance high quality images were used per sow. A joint angle measuring system was devised to collect angle measurements on the four feet and leg joints previously mentioned and the rear stance. Joint measurements were analyzed using repeated measure mixed model methods, including farm and parity (as 5, 6, and 7+) as fixed effects. Intraclass correlation coefficients were calculated to evaluate process repeatability. Joint angle measurement repeatability ranged from 0.63 to 0.82. Lowest and highest repeatabilities were observed for the front pastern and hock angle measurements, respectively. No significant farm or parity differences were observed for joint angles measured except for the knee angle between farms (P<0.05) and the hock angle between sows’ parities 5 and 6 and parity 7+ (P<0.05). Conclusions: Feet and leg conformation evaluation using digital images could be successfully used as an objective tool to aide in selection of replacement gilts. This could have a beneficial impact on sow longevity and farm productivity and profitability.

Iodine values of adipose tissue varied among breeds of pigs and were correlated with pork quality

ABSTRACT Our objectives were to investigate fatty acid composition variation amongst adipose tissue sites, breed effects on fat quality, and the relationship of pork fat quality to fresh pork quality. Barrows and gilts (n = 347) of five purebred and one commercial crossbred line were fed commercial swine diets with DDGS inclusion at 30% (as fed) from 31.8 kg body weight until 30-d prior to harvest at 111.4 kg. Immediately after harvest, hot carcass weight was determined, adipose tissue was collected from the back, belly, and jowl, and meat samples were taken from the longissimus muscle for evaluation of pork quality. Iodine values (IV) varied between anatomical site and breed. Jowl fat IV were correlated to back and belly fat IV. Minor but significant correlations were observed between IV and meat quality characteristics. These results support our hypotheses that minor relationships exist between fat and fresh pork quality and that IV vary by anatomical location.