Kenneth J. Stalder

Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs

Background The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs. Methodology/Principal Findings Using Illuminas PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages. Conclusions/Significance This study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection.

A whole-genome association study for pig reproductive traits

A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.

Whole-genome association analyses for lifetime reproductive traits in the pig.

Profits for commercial pork producers vary in part because of sow productivity or sow productive life (SPL) and replacement costs. During the last decade, culling rates of sows have increased to more than 50% in the United States. Both SPL and culling rates are influenced by genetic and nongenetic factors. A whole-genome association study was conducted for pig lifetime reproductive traits, including lifetime total number born (LTNB), lifetime number born alive (LNBA), removal parity, and the ratio between lifetime nonproductive days and herd life. The proportion of phenotypic variance explained by markers was 0.15 for LTNB and LNBA, 0.12 for removal parity, and 0.06 for the ratio between lifetime nonproductive days and herd life. Several informative QTL regions (e.g., 14 QTL regions for LTNB) and genes within the regions (e.g., SLC22A18 on SSC2 for LTNB) were associated with lifetime reproductive traits in this study. Genes associated with LTNB and LNBA were similar, reflecting the high genetic correlation (0.99 ± 0.003) between these traits. Functional annotation revealed that many genes at the associated regions are expressed in reproductive tissues. For instance, the SLC22A18 gene on SSC2 associated with LTNB has been shown to be expressed in the placenta of mice. Many of the QTL regions showing associations coincided with previously identified QTL for fat deposition. This reinforces the role of fat regulation for lifetime reproductive traits. Overall, this whole-genome association study provides a list of genomic locations and markers associated with pig lifetime reproductive traits that could be considered for SPL in future studies.

Factors associated with fatigued, injured, and dead pig frequency during transport and lairage at a commercial abattoir

The objective of this study was to identify environmental and management factors that are associated with the frequency of fatigued, injured, and dead pigs on arrival and in resting pens during lairage at a commercial Midwest abattoir. The terms transport losses or total losses refer to pigs that die or become nonambulatory at any stage of the marketing process. In this study, fatigued, injured, and dead pigs were summed into a variable termed total losses. Relative humidity (%), temperature ( degrees C), wind speed (m/s), and dew point ( degrees C) data were collected on 12,333 trailer loads of pigs. Week, sort from barn (first or third pig removal from barn), farm, normal vs. split load type (from 1 or multiple barns), load crew, driver, trailer, and wind direction were used as fixed effects in the model for the analysis of losses per load using generalized mixed models for Poisson distributions. Seven temperature-humidity indices (THI) were calculated and compared as model covariates. Load time per pig, trailer density (pigs per trailer x average BW/trailer space; kg/m(2)), wait time before unloading at the abattoir, and wind speed were used as model covariates. The log of the number of hogs per trailer was used to standardize the response variable. The linear covariate density accounted for the greatest portion of variance (based on F-value) followed by the fixed effect sort from barn, the fixed effect load type (pigs from 1 or multiple barns within a farm), load time per pig linear covariate, and THI. Pigs transported to the abattoir from June through July experienced fewer losses (P < 0.001) when compared with pigs that were transported from November through December. Keeping other factors constant, the log of total losses (%) per load increased by 0.0102x + 0.000541x(2) per unit of THI and 0.0191 kg/m(2) of density. Similarly, of 9 farms, the poorest-performing farm in regards to total loss percentage experienced 0.93% more losses per load when compared with the farm with the least loss percentage. This study demonstrates that multiple environment and management factors influence the incidence of market hog transport losses.

Large-scale association study for structural soundness and leg locomotion traits in the pig.

BackgroundIdentification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.MethodsIn this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenoms MassARRAY system.ResultsBased on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 and VDBP were very highly significantly (P < 0.001) associated with body conformation traits. The genes ALOX5, BMP8, CALCR, OPG, OXTR and WNT16 were very highly significantly (P < 0.001) associated with FL structures, and APOE, CALCR, COL1A2, GNRHR, IHH, MTHFR and WNT16 were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between CALCR and COL1A2 on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits.ConclusionThe present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.

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.

Associations between two gene markers and indicator traits affecting fresh and dry-cured ham processing quality.

The study objective was to evaluate the effects of mutations in two genes, PRKAG3 and CAST, on fresh and dry-cured processing characteristics. Processing and curing followed normal commercial procedures. A 100 g sample of the semimembranosus was excised and frozen for later DNA harvest. Genotypes for CAST, and PRKAG3 were determined after DNA extraction from the frozen samples. The PRKAG3 marker had no affect on dry-cured ham processing characteristics. The CAST gene marker was a significant source (P<0.05) of variation for cured ham moisture content and tended to be a significant source (P<0.10) for yield, ham weight loss, salt content and Minolta color change. The data demonstrate that the CAST 11 genotype is associated with greater processing yields. Alternatively, selection or sorting for the CAST 22 genotype should produce cured hams that exhibit more efficient moisture loss and, as a result, require less processing time and contain greater salt content.

Validation of a lameness model in sows using physiological and mechanical measurements

The objective of this study was to develop a validated, transient, chemically induced lameness model in sows using subjective and objective lameness detection tools. Experiment 1 determined an effective joint injection technique based on volume and placement of dye using feet collected from 9 finisher pigs and 10 multiparity cull sow carcasses. Experiment 2 confirmed the injection technique in live animals and produced a transient clinical lameness in 4 anesthetized sows injected with amphotericin B (15 mg/mL) in the distal interphalangeal joints of the claw. Clinical lameness was assessed by a categorical lameness scoring system, and a postmortem visual confirmation of joint injection technique was obtained. In Exp. 3, 6 sows were injected with 0, 10, or 15 mg/mL amphotericin B in either the left or right hind foot and were monitored until clinical resolution. Treated sows demonstrated elevated clinical lameness scores. These changes resolved by 7 d after lameness induction. Control sows injected with sterile saline developed a clinical lameness score of 0.5, which resolved 72 h post injection. In Exp. 4, 36 sows were injected with 10 mg/mL amphotericin B in 1 of 4 injection sites (left front claws, right front claws, left rear claws, and right rear claws). All injected sows exhibited a decrease in maximum pressure, stance time, and number of sensors activated on the GaitFour (P < 0.05) sensor system. A static force plate also demonstrated a decrease in weight (kg) being placed on the injected foot when all feet were injected (P ≤ 0.05). Injection of amphotericin B induced a predictable acute lameness that resolved spontaneously and is an effective method to model lameness in sows.

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.

Genetic associations for gilt growth, compositional, and structural soundness traits with sow longevity and lifetime reproductive performance

The objective of this study was to estimate genetic associations for gilt growth, compositional, and structural soundness with sow longevity and lifetime reproduction. Performance and pedigree information from 1,447 commercial females from 2 genetic lines were included in the data analyzed. Growth was expressed as days to 113.5 kg BW (DAYS) and compositional traits included loin muscle area (LMA), 10th rib backfat (BF10), and last rib backfat (LRF). Structural soundness traits included body structure traits [length (BL), depth (BD), width (BWD), rib shape (BRS), top line (BTL), and hip structure (BHS)], leg structure traits [front legs: legs turned (FLT), buck knees (FBK), pastern posture (FPP), foot size (FFS), and uneven toes (FUT); rear legs: legs turned (RLT), leg posture (RLP), pastern posture (RPP), foot size (RFS), and uneven toes (RUT)], and overall leg action (OLA). Lifetime (LT) and removal parity (RP) were considered as longevity traits whereas lifetime reproductive traits included lifetime total number born (LNB), lifetime number born alive (LBA), number born alive per lifetime day (LBA/LT), and percentage productive days from total herd days (PD%). Genetic parameters were estimated with linear animal models using the average information REML algorithm. Second, to account for censored longevity and lifetime reproduction records, genetic parameters were estimated using Markov Chain Monte Carlo and Gibbs sampling methods. Similar estimates were obtained across the analysis methods. Heritability estimates for growth and compositional traits ranged from 0.50 to 0.70 and for structural soundness traits from 0.07 to 0.31. Longevity and lifetime reproductive trait heritability estimates ranged from 0.14 to 0.17 when REML was used. Unfavorable genetic correlations were obtained for DAYS with LT, RP, LNB, LBA, and PD% and for LRF with PD%. However, LMA was favorably associated with LT, RP, and LNB. Moderate to high correlations were obtained for BL and BRS with all longevity and lifetime reproductive traits. Correlations of BWD with LT and RP were moderate. Associations for leg soundness traits with longevity and lifetime reproductive traits were mainly low and nonsignificant (P ≥ 0.10). However, RLP was moderately correlated with LBA/LT and PD%. Current results indicate that selection for fewer DAYS has an antagonistic effect on lifetime performance. Furthermore, great BL, flat BRS, narrow BWD, and upright RLP seem detrimental to sow longevity and lifetime reproduction.