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. Using 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. 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.

Intramuscular fat (IMF) and ultimate pH (pHu) influence tenderness, but their roles have not been conclusively determined. Length of storage also affects tenderness and may interact with IMF and pHu. We evaluated the effects of pHu, IMF, and storage time on the tenderness of pork longissimus muscle and determined whether the contribution of the various factors was dependent on genetic line. To obtain variation in IMF, Berkshire (B), Duroc (D) and Hampshire (H) boars were crossed with Yorkshire-Landrace sows. In four trials, a total of 176 pigs were used. To obtain a range in pHu, half of the pigs were deprived of feed before slaughter. Warner-Bratzler shear force (WBS) of each loin was assessed after 2, 7, and 14 d of storage at 0 to 2°C. Warner-Bratzler shear force decreased (P < 0.05) from 4.89 kg at d 2 to 4.16 kg at d 7 to 3.52 kg at d 14. The H pork (n = 62) had a lower (P < 0.05) WBS than the other pork at d 2. After 7 d of storage, this difference had disappeared. Based on glycolytic potential, 30 of the H pigs were carriers of the Rendement Napole (RN) gene. When these pigs were excluded from the analysis, there was no difference in tenderness or tenderization of H, D, and B pork. The correlation between IMF and WBS was −0.11 at d 2, −0.21 at d 7, and −0.19 at d 14. In D pork, the relationship between IMF and WBS was linear, and IMF accounted for 47% of the differences in WBS. In H and B pork, the relationship between IMF and WBS was not significant. For each cross, the relationship between pHu and WBS was different; in D pork it was quadratic, in H pork WBS increased linearly, and in B pork there was no significant relationship between WBS and pHu. The 30 kDa/actin ratio, a measure of myofibrillar degradation, increased (P < 0.05) during storage. Differences in 30 kDa/actin ratio did not explain differences in pork tenderness or tenderization. Further research on determinants and mechanisms of pork tenderness and pork tenderization is needed before production of consistently tender pork will be possible.

The objective of this study was to estimate direct and indirect selection potential for length of productive life and lifetime prolificacy in Finnish Large White and Landrace swine populations. To study the direct selection potential, the heritabilities of these traits were estimated. The genetic correlations of length of productive life and lifetime prolificacy with prolificacy traits and overall leg conformation were estimated to evaluate whether selection for these traits could indirectly improve measures of sow longevity. In addition, correlations between length of productive life, lifetime prolificacy, ADG, and backfat thickness were estimated. Records were used from Finnish purebred Landrace (n = 26,744) and Large White (n = 24,007) sows born on operations that perform on-farm production tests on all females. Heritabilities were estimated using both a survival analysis procedure and a linear model. Due to computational limitations, correlations were estimated with the linear model only. Estimated length of productive life heritabilities obtained from linear model analyses were less (0.05 to 0.10) than those obtained from survival analyses (0.16 to 0.19). This may be indicative of the superiority of survival analysis compared with linear model analysis methods when evaluating longevity or similar types of data. All the prolificacy traits were genetically correlated with length of productive life and lifetime prolificacy, and the correlations were greater than 0.13. These results indicate that selection for increased number of piglets weaned in the first litter and for short first farrowing interval is beneficial for sow longevity and also for sow's lifetime prolificacy. The genetic correlations between length of productive life and leg conformation score also were favorable (0.32 in Landrace and 0.17 in Large White). The heritability estimates indicate that survival analysis is likely the most appropriate method of evaluating longevity traits in swine. Because of computational problems, simultaneous analysis of linear traits and longevity is not currently possible. More research is needed to develop methods for multiple linear and survival trait analyses.

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. Copyright © 2007. . Copyright 2007 Journal of Animal Science

A study was conducted to evaluate differences in meat and eating quality traits between purebred Duroc pigs sired by boars currently available and pigs sired by boars from the mid 1980s. Two lines were developed by randomly allocating littermate and half-sib pairs of females to matings by current time period (CTP) or old time period (OTP) boars. Matings by CTP boars were made using fresh semen, and matings by OTP boars were via frozen semen. All available barrows and randomly selected gilts were sent to a commercial abattoir and used for meat and eating quality evaluation. A total of 178 pigs from 23 CTP sires and 99 pigs from 15 OTP sires, across 2 replications and at a mean live weight of 109 kg, were slaughtered and analyzed. Chemical intramuscular fat percentage was determined by lab analysis of a slice from the LM at the 10th rib. Additional meat and eating quality traits measured on the LM were Minolta reflectance and Hunter L color (24 h); pH (24 h and 7 d); water-holding capacity; subjective visual scores for color, marbling, and firmness (48 h); Instron tenderness; cooking loss; and trained sensory panel evaluations (7 d). Time period differences were assessed by use of a mixed model that included fixed effects of sire time period, replication, sex, contemporary group, and the interaction of sex × time period. The random effect of dam and the random effect of sire nested within time period were also included. Loins from pigs sired by OTP boars had greater intramuscular fat (3.48 vs. 3.09%) and visual marbling scores (3.54 vs. 3.07), required less Instron force (5.31 vs. 5.98 kg) to compress, and had darker visual color scores (4.09 vs. 3.87) compared with loins from pigs sired by CTP boars (P < 0.05). No differences were observed between time periods for Minolta reflectance, Hunter L (24 h), water-holding capacity, pH (24 h and 7 d), or subjective firmness scores. Trained sensory evaluations revealed more pork flavor and less off-flavor (P < 0.05) for OTP-sired pigs; however, no differences in tenderness score, juiciness score, chewiness score, or cooking loss were found between lines. Long-term selection response in carcass composition has been at the expense of meat and eating quality traits.