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.

BackgroundThe 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 FindingsUsing Illumina's 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/SignificanceThis 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.

The objective of this project was to determine the contribution of lipid content to textural and sensory properties of fresh pork within defined pH classifications. Pigs (n = 1,535; from 248 sires and 836 dams) from the 1991, 1992, and 1994 National Barrow Show Sire Progeny Test were used in this study. The test included purebred Berkshire (107), Chester White (113), Duroc (249), Hampshire (220), Landrace (165), Poland China (101), Spotted (181), and Yorkshire (399) barrows (901) and gilts (634). Diets were uniform across breeds within test. The halothane (Hal 1843) genotype (1346 NN and 189 Nn) was determined. Pigs were slaughtered at 105 kg of BW, and samples of the LM were obtained from each carcass at the 10th rib. Star probe, sensory traits, and lipid content were determined on the LM from each pig. A pH classification of LM was assigned as follows: class A, >5.95, n = 186; class B, ≥5.80 to 5.95, n = 236; class C, ≥5.65 to 5.80, n = 467; class D, ≥5.50 to 5.65, n = 441; class E, <5.50, n = 205. Data were analyzed using a mixed linear model including pH classification, test, sex, halothane genotype, breed, and breed × sex interaction as fixed effects, with sire and dam within breed included as random effects. Correlations were determined within pH class. Lipid content was a significant source of variation for models predicting star probe values in class C and D and for chewiness in class B, C, and D. Increasing lipid content tended to increase sensory tenderness in pH class D. Sensory tenderness was not affected by lipid content in pH class A, B, or E. Lipid content was not a significant source of variation for juiciness scores within any pH class. Intramuscular lipid is correlated with sensory texture traits primarily in classes C and D. Within class C and D, correlations indicate that increasing lipid content is associated with high sensory tenderness, low sensory chewiness, and low star probe values. It is concluded that lipid content is a small source of variation in texture and tenderness of pork loin with pH between 5.80 and 5.50, but not at a greater or lesser pH. KeywordsFood Science and Human Nutrition, fatty acid, lipid, pH, pork quality, sensory, tenderness

The objective of this study was to estimate the effects of breed, sex, and halothane genotype on fatty acid composition and several fatty acid indices of lipid extracted from porcine LM. Purebred Yorkshire (n = 436), Duroc (n = 353), Hampshire (n = 218), Spotted (n = 187), Chester White (n = 173), Poland China (n = 124), Berkshire (n = 256), and Landrace (n = 187) pigs (n = 1,934; 1,128 barrows and 806 gilts) from 1991, 1992, 1994, and 2001 National Barrow Show Sire Progeny Tests were used. Pigs were classified as the HAL-1843 normal (NN) genotype (n = 1,718) or the HAL-1843 carrier (Nn) genotype (n = 216). For statistical analysis, a mixed model was used that included fixed effects of breed, sex, halothane genotype, test, slaughter date, interaction of breed × sex, and random effects of sire and dam within breed. Breed significantly affected the concentration of individual fatty acids, total lipid content, and the values of several fatty acid indices of LM. Duroc pigs had the greatest (P< 0.01) content of total SFA. Total MUFA concentration in Poland China pigs was greater (P < 0.05) than in all other breeds except the Spotted (P> 0.05). The concentrations of total PUFA were greater (P < 0.01) in Hampshire, Landrace, and Yorkshire pigs compared with those of other breeds. Significant sex differences for individual fatty acids were detected. Compared with gilts, barrows had greater (P < 0.01) concentrations of SFA and MUFA but lower (P < 0.01) total PUFA. Halothane genotype was a significant source of variation for the percentages of some fatty acids. Pigs with the carrier (Nn) genotype had lower concentrations of SFA (P < 0.05) and MUFA (P < 0.01) but a greater concentration of PUFA (P < 0.01) compared with NN pigs. There were significant negative correlations between total lipid content and individual PUFA and significant positive correlations between lipid concentration and most individual SFA and MUFA. In conclusion, the results suggest that breed and sex are important sources of variation for fatty acid composition of LM. KeywordsBiochemistry Biophysics and Molecular Biology, breed, fatty acid, halothane genotype, longissimus muscle, pig, sex

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.