Timo Serenius

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.

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.

Effect of polymorphisms in candidate genes on reproduction traits in Finnish pig populations.

Reproduction traits play an important role in economically viable piglet production and are closely related to the quality and length of the productive life of the sow. A increased removal rate of young sows is undesirable not only because of the associated financial penalties incurred, but also because of ethical concerns. Candidate genes and gene pathways have been identified for fertility in model species, and recent studies have provided evidence that polymorphisms within these genes are associated with reproduction traits in American Yorkshire/Large White and Landrace populations. In this study we evaluated the impact of single polymorphisms (n = 7) in 7 candidate genes on reproductive efficiency in Finnish Yorkshire (n = 280) and Landrace (n = 271) populations: IGFBP1, IGFBP2, IGFBP3, IGFBP5, CPTIA (carnitine O-palmitoyltransferase I), COX2 (PG-endoperoxide synthase 2, also known as cyclooxygenase-2), and SLC22A5 [organic cation/carnitine transporter 2 (solute carrier family member I), OCTN2]. In the Finnish Yorkshire population, only 4 of the analyzed markers were polymorphic. Significant effects on farrowing time were detected from the Yorkshire data, with polymorphisms within the genes CPT1A [a (allele substitution effect of allele A) = 2.97 d for age at first farrowing)], IGFBP3 (a = 0.54 d for farrowing interval of parities >1), and IGFBP5 (a = 3.22, 1.27, and 0.85 d for age at first farrowing and farrowing interval in the first and later parities, respectively). For the Landrace population, 6 markers were polymorphic, and significant effects were detected for traits affecting litter size. The polymorphism within the COX2 gene had an additive effect of 0.3 piglets for litter size in parities >1, and the IGFBP1 gene had an additive effect of 0.21, 0.26, and 0.11 piglets for litter size in the first parity, parities >1, and stillborn in parities >1, respectively. The additive effect of the SNP within the IGFBP2 gene was 0.16, 0.09, and 0.09 piglets for litter size in parities >1 and stillborn in the first and later parities, respectively. Finally, the IGFBP5 gene had an additive effect of 0.18, 0.07, and 0.07 piglets for litter size in the first parity, stillborn in parities >1, and mortality between farrowing and weaning in the first parity, respectively. These results support the suitability of the candidate gene approach for identification of markers to improve the reproductive performance of sows and to provide potential markers for marker-assisted selection.

Phenotypic correlations among quality traits of fresh and dry-cured hams.

In this study, fresh and processing quality traits were collected on a total of 312 Country Hams. Phenotypic correlations between traits were estimated and numerous values were significantly different (P<0.05) from zero. Yield was significantly correlated with several fresh pork quality traits measured on the fresh hams, including subjective color (0.34) and lipid percentage (0.32). Some meat color traits were significantly correlated, including associations between the color scores taken on the fresh and cured hams. Correlations between fresh pork quality traits were also determined, with results showing significant correlations between ultimate pH and other pork quality traits. The results indicate that yield can be maximized if hams with good fresh pork quality parameters are used for curing. The correlations estimates are helpful for understanding of the biological mechanisms behind the production of dry-cured hams and can potentially be used to improve the efficiency of the dry-cured ham production chain.

Genetic parameters for growth, body composition, and structural soundness traits in commercial gilts

The objective of this study was to estimate genetic parameters for growth, body composition, and structural soundness traits in commercial gilt lines. The data included 1,449 gilts: 462 females from a grandparent maternal line and 987 from a parent maternal line. Growth was expressed as number of days to a constant 113.5 kg BW (DAYS) and compositional traits included loin muscle area (LMA), 10th rib backfat (BF10), and last rib backfat (LRF). Subjective structural soundness evaluation was completed using a 9-point scale and included: body length (BL), body depth (BD), body width (BWD), rib shape (BRS), top line (BTL), and hip structure (BHS); 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). Genetic parameters were estimated with multivariate linear animal models, using the average information REML algorithm. Heritability estimates for growth and body composition traits ranged from 0.50 to 0.70, for body structure traits from 0.15 to 0.31, for leg structure traits from 0.07 to 0.31, and the estimate for OLA was 0.12. Several moderate to high genetic correlations were obtained among body structure traits, whereas correlations among leg structure traits were mainly low and nonsignificant. A strong correlation was found between FPP and OLA (P < 0.001); more upright FPP coincided with inferior OLA. Furthermore, FBK and FFS appeared to be favorably associated with OLA (0.05 < P < 0.10). Body structure trait correlations among each other and with leg soundness traits were primarily favorable. Correlations indicated that great BL and high BTL coincided with each other and deterioration of other structural soundness traits. Although genetic correlations obtained for DAYS and backfat measurements with structural soundness traits had an unfavorable trend, they were mainly low to moderate (i.e., simultaneous genetic improvement would be possible, including adversely associated traits). Due to greater heritabilities, faster genetic change could be expected for compositional and body structure traits than leg structure traits. Because of the genetic relationship among the trait groups, using information across traits when making selection decisions could result in genetic improvement among leg soundness traits.

SNP Discovery in Genes Affecting Leg Health Traits in Pigs

Sow reproductive life is influenced by lameness issues. It has been reported that up to 44 percent of sows have locomotive problems. To date, few genome scans or association studies have been conducted to look at genes controlling lameness and other gait traits. In addition to health problems associated with leg and bone disorders, the pig has been suggested to be a good model for human bone disorders. Hence, the present study examined 134 porcine genes affecting skeletal development, mineral metabolism and other candidate genes for single nucleotide polymorphism (SNP) discovery. Atotal of over 370 SNPs have been identified to date and are being mapped. These SNPs are also being investigated for their associations with gait and locomotion problems in approximately 2,000 commercial pigs scored for various leg and locomotion traits. The association analysis of 22 genes revealed that the genes CALCR, HDBP CALCA, MTHFR, OXTR, IHH, ANKH, LRCH1 and OPN were significantly associated with leg and body conformation traits which affect the health and productivity of pigs.

Characterization of Lesions in U.S. Cull Sows

Physical and reproductive conditions of 3,158 cull sows from 2 U.S. Midwestern harvest facilities were assessed. Body condition, feet, shoulders, teeth, lungs, and reproductive tracts were visually evaluated for gross lesions at harvest. Based on the observations of this study, body condition score (BCS) was associated with several abnormal conditions of sows. Foot-related lesions (overgrown toes, foot pad lesions) represented the most frequently documented lesions. Temporal associations of the interactions between lesions and BCS are unknown. Even though causal relations were not established by this study, the strong associations observed suggest that sows who do not respond to increased feeding with improved BCS could reasonably be expected to have additional lesions that may impact performance and welfare. On-farm management practices may be related to 1 or more lesions (including foot lesions) that had a high prevalence in this study. Farm management practices and nonhuman animal welfare could not be evaluated with this study so no extrapolation can be given to the type of animal housing or the antemortem behavior of these sows.