A genome-wide association study for gestation length in swine.

Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska-Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1-GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.

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.

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.

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.

Identification of genetic markers for productive life in commercial sows.

Escalating replacement rates and production costs warrant attention on sow productive life (SPL). Increasing average SPL by one-tenth of 1 parity would result in an annual revenue increase of over $15 million in the United States. Research in model organisms has revealed conserved genes and gene pathways that lead to longer lifespan. The most prominent gene pathways are those involved in growth, most notably genes in the IGF pathway that serve to mimic the response of caloric restriction. The objective of this research was to test the hypothesis that these well conserved genes and gene pathways could also play a role in SPL, even though the productive life of sows is both a measure of longevity and their reproductive performance. Preliminary research on 3 distinct populations of over 2,000 animals suggested that several genes were associated with components of SPL. Genetic markers were then analyzed against the corresponding records of the sows for reproductive and longevity traits using a validation population of 2,000 commercial females. Right censored data were used to test associations of genetic markers with survival to defined time points. Three distinct models of survival analysis were implemented using nonparametric estimates of the survival distribution in a sequential order, using a parametric accelerated failure time model with a Weibull distribution of the error term, and a Cox proportional hazards model, which is a semiparametric model that uses an unspecified baseline hazard function. The genetic markers CCR7 and CPT1A were significantly associated (P < 0.05) with survival using the nonparametric model and tended (P < 0.1) toward significance using the parametric and semiparametric models with significantly different effects (P < 0.05) between some genotype classes. Genetic markers for MBL2, IGFBP3, and WARS2 also tended (P < 0.1) toward significance for survival traits, but were not consistent. Mixed model analyses were used to determine the associations of these genetic markers with reproductive traits. The genetic markers for IGFBP1, MBL2, CPT1A, CCR7, SLC22A5, and ACE were significantly (P < 0.05) associated with at least 1 reproductive trait. These results show that molecular markers should be considered for use in marker-assisted selection to improve SPL.

Cracking the genomic piggy bank: identifying secrets of the pig genome.

Though researchers are uncovering valuable information about the pig genome at unprecedented speed, the porcine genome community is barely scratching the surface as to understanding interactions of the biological code. The pig genetic linkage map has nearly 5,000 loci comprised of genes, microsatellites, and amplified fragment length polymorphism markers. Likewise, the physical map is becoming denser with nearly 6,000 markers. The long awaited sequencing efforts are providing multidimensional benefits with sequence available for comparative genomics and identifying single nucleotide polymorphisms for use in linkage and trait association studies. Scientists are using exotic and commercial breeds for quantitative trait loci scans. Additionally, candidate gene studies continue to identify chromosomal regions or genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve said traits. Researchers are utilizing novel tools including pig microarrays along with advanced bioinformatics to identify new candidate genes, understand gene function, and piece together gene networks involved in important biological processes. Advances in pig genomics and implications to the pork industry as well as human health are reviewed.