Polymorphisms in the regulatory region of the porcine MYLPF gene are related to meat quality traits in the Large White breed.

The MYLPF gene encodes fast myosin regulatory light chain, and is a positional and functional candidate gene for meat quality. The aim of this study was to identify associations between SNPs in the promoter region of the porcine MYLPF gene and meat quality traits. A total of 22 SNPs were identified in a population of crossbred animals (n=86) and based on minor allele frequency and proximity to the transcription start site, five SNPs were genotyped in purebred; Large White (n=98), Duroc (n=99) and Pietrain (n=98) pigs. No associations were observed in the Pietrain breed, while the Duroc breed was almost monomorphic for all SNPs. In the Large White breed SNP g-1314A>G and linked SNPS g.-871T>G, g.-566T>C, g.-403C>G were associated with ultimate pH and driploss (P<0.05). This study identified associations between MYLPF and meat quality and highlights the importance of considering the genetic background within gene-assisted selection programmes.

Novel variation in the FABP3 promoter and its association with fatness traits in pigs.

This study examines associations between SNPs in the promoter region of the fatty acid binding protein 3 (FABP3) gene and fatness traits in pure bred Large White (n=98), Duroc (n=99) and Pietrain (n=98) populations. In the Large White breed, SNP g.-634 C>A was associated a 27% increase in IMF (%) in the heterozygote (CA) and a 38% increase in the homozygote (CC) relative to the (AA) genotype in the M. semimembranosus (SM) muscle (P=0.02). While the associations observed in this breed were suggestive of significance in both the SM and in the M. longissimus thoracis et lumborum (LTL) (P=0.08), these associations no longer attained significance at thresholds adjusted for multiple testing. In conclusion, SNPs in the FABP3 promoter may contribute to IMF without influencing carcass fatness traits in pigs, however further confirmation of these associations in larger independent populations would be essential before their incorporation into breeding programmes.

An association and haplotype analysis of porcine maternal infanticide: a model for human puerperal psychosis?

An association analysis using the Illumina porcine SNP60 beadchip was performed to identify SNPs significantly associated with porcine maternal infanticide. We previously hypothesised that this was a good animal model for human puerperal psychosis, an extreme form of postnatal mood disorder. Animals were selected from carefully phenotyped unrelated infanticide and control groups (representing extremes of the phenotypic spectrum), from four different lines. Permutation and sliding window analyses and an analysis to see which haplotypes were in linkage disequilibrium (LD) were compared to identify concordant regions. Across all analyses, intervals on SSCs 1, 3, 4, 10, and 13 were constant, contained genes associated with psychiatric or neurological disorders and were significant in multiple lines. The strongest (near GWS) consistent candidate region across all analyses and all breeds was the one located on SSC3 with one peak at 23.4 Mb, syntenic to a candidate region for bipolar disorder and another at 31.9 Mb, syntenic to a candidate region for human puerperal psychosis (16p13). From the haplotype/LD analysis, two regions reached genome wide significance (GWS): the first on SSC4 (KHDRBS3 to FAM135B), which was significant (-logP 5.57) in one Duroc based breed and is syntenic to a region in humans associated with cognition and neurotism; the second on SSC15, which was significant (-log10P 5.68) in two breeds and contained PAX3, which is expressed in the brain.

Mapping QTL in the porcine MHC region affecting fatness and growth traits in a Meishan/Large White composite population.

A number of studies have mapped QTL regulating porcine fatness and growth traits to the region of the major histocompatibility complex (MHC) on porcine chromosome 7 using various experimental crosses. The QTL results from crosses using the Chinese Meishan (MS) (slow growing and fat) are particularly interesting because the MS alleles have been found to be associated with increased growth rate and reduced backfat depth. We investigated these QTL further in a composite population derived previously over eight generations by intercrossing Meishan and the European Large White breeds. Genotype information from 32 markers in a 15cM target region was used in linkage and association analyses. A two-step variance component analysis identified QTL for three growth-related traits, explaining 19 ∼ 24% of the phenotypic variance with a confidence interval of 4 cM in the target region. SNP association analyses found that ss181128966 and ss181128924 within the QTL interval were strongly associated with the growth traits. Only weak signals for an effect on backfat depth were found in the association and linkage analyses, possibly because of past directional selection in the composite population.

Effects of breed, diet and muscle on fat deposition and eating quality in pigs.

A study in 192 entire male pigs examined the effects of breed, diet and muscle on growth, fatness, sensory traits and fatty acid composition. There were four breeds: two modern breeds, Duroc and Large White and two traditional breeds, Berkshire and Tamworth. The diets differed in energy:protein ratio, being conventional (C) and low protein (LP) diets, respectively. Muscles investigated were the `white' longissimus dorsi (LD) and the `red' psoas major (PS). Breed influenced growth rate and fatness, the modern breeds being faster-growing with leaner carcasses. However, the concentrations of neutral lipid fatty acids and marbling fat (neutral lipid+phosopholipid fatty acids) were higher in Berkshire and Duroc, in both LD and PS. Relationships between marbling fat and P2 fat thickness showed clear breed effects, with Duroc having high marbling fat at low P2 and Tamworth low marbling fat at high P2. Breed effects on sensory scores given by the trained taste panel to griddled LD and PS steaks were relatively small. Breed affected the fatty acid composition of intramuscular neutral lipid, with high % values for the saturated fatty acids, 14:0 and 16:0 in Berkshire and Tamworth (fat carcasses) and high values for polyunsaturated fatty acids in Duroc and Large White (lean carcasses). Duroc had particularly high concentrations of the long-chain polyunsaturated fatty acids, 20:5n-3 and 22:6n-3 in phospholipid of both muscles. Diet influenced growth rate and fatness, the LP diet slowing growth and producing fatter meat, more so in the two modern breeds, and particularly in intramuscular rather than subcutaneous fat. This diet produced more tender and juicy meat, although pork flavour and flavour liking were reduced. The PS muscle had higher tenderness, juiciness, pork flavour, flavour liking and overall liking scores than LD. The concentration of phospholipid fatty acids was higher in PS than LD but neutral lipid fatty acid content and marbling fat were higher in LD.

Identification of quantitative trait loci for production traits in commercial pig populations.

The aim of this study was to investigate methods for detecting QTL in outbred commercial pig populations. Several QTL for back fat and growth rate, previously detected in experimental resource populations, were examined for segregation in 10 different populations. Two hundred trait-by-population-by-chromosome tests were performed, resulting in 20 tests being significant at the 5% level. In addition, 53 QTL tests for 11 meat quality traits were declared significant, using a subset of the populations. These results show that a considerable amount of phenotypic variance observed in these populations can be explained by major alleles segregating at several of the loci described. Thus, despite a relatively strong selection pressure for growth and back fat traits in these populations, these alleles have not yet reached fixation. The approaches used here demonstrate that it is possible to verify segregation of QTL in commercial populations by limited genotyping of a selection of informative animals. Such verified QTL may be directly exploited in marker-assisted selection (MAS) programs in commercial populations and their molecular basis may be revealed by positional candidate cloning.

X/XY/XYY mosaicism as a cause of subfertility in boars: a single case study.

Sex chromosome abnormalities are common in mammals and humans and are often associated with subfertility. In this study a boar with normal sperm parameters was indicated to have reduced prolificacy from figures obtained for return rate, farrowing rate and total number of piglets born. G-banded cytogenetic analysis of peripheral blood identified an abnormal mosaic sex chromosome constitution 39,XYY[74]/38,XY[23]/37,X[3]. Cytogenetic analysis of fibroblasts confirmed this mosaic karyotype with similar percentages of cell lines observed 39,XYY[76]/38,XY[19]/37,X[5]. External genitalia revealed a poorly developed scrotum with the right testicle being smaller than the left. To the best of our knowledge this is the first time that this chromosome constitution has been reported in the pig. It is of particular interest that this karyotype is associated with reduced boar fertility, which could lead to potential economic losses if such a boar were selected for breeding purposes.

Relationships of myosin heavy chain fibre types to meat quality traits in traditional and modern pigs.

Porcine skeletal muscle fibres were molecularly classified, using in situ hybridisation and immunocytochemistry, into four types, according to the isoform of myosin heavy chain (MyHC) that was present in each fibre (MyHC slow/I, MyHC 2a, MyHC 2x and MyHC 2b). The relationship between MyHC fibre types and meat quality traits between two phenotypically divergent muscles [longissimus dorsi (LD) and psoas], and between the same muscles of different breeds (traditional Berkshire and Tamworth, and modern Duroc-based and Large White-based) were examined. We found that the greater abundance of fast oxidative-glycolytic MyHC 2a and 2x fibres in the psoas was associated with superior meat quality traits, and that the greater presence of fast glycolytic MyHC 2b fibres in the LD could account for less favourable quality traits, both in terms of pH, drip loss, grain, colour, yield force and work done. Although significant correlations were found between specific fibre types and quality traits, within either the psoas or LD muscle of some breeds, no consistent correlation was found across both muscles and all breeds. This finding was in line with the view that a given fibre type could have considerable differences in phenotype between breeds, and between muscles. The observed inverse compositional and functional-meat quality relationship between MyHC 2b and 2x fibres, and MyHC 2b and 2a fibres could form a basis of fibre type manipulation to improve meat quality.

Effect of the estrogen receptor locus on reproduction and production traits in four commercial pig lines.

We investigated the effect of the estrogen receptor (ESR) gene on growth and reproductive traits in four Large White-based commercial pig lines. A total of 9,015 litter records from 4,262 sows genotyped at the ESR locus were analyzed to determine whether ESR influenced total number born (TNB) or number born alive (NBA). Teat number (TN), test ADG, ADFI, feed:gain ratio (F/G), and ultrasonic backfat (BF) were also analyzed to determine effects of ESR. The TNB and NBA were increased per favorable allele of ESR (P < .01) with additive effects of .42 (.31) and .39 (.31) pigs/litter in the first parity (later parities), respectively. Dominance effects were near zero in parity one, but they were .16 and .14 pigs for TNB and NBA, respectively, in later parities (P < .05). A favorable additive pleiotropic effect was detected for BF (P < .001; -.11 mm per copy of the favorable litter size allele). There were no detectable effects on ADG or F/G (P > .10), although ADF was reduced 18 g/d per copy of the favorable litter size allele (P < .05). Average TN was 13.1 for pigs carrying the favorable litter size allele vs 13.2 for noncarriers (P < .05). Marker-assisted selection using ESR is warranted to increase litter size in the Large White-based lines considered here and will be of considerable economic value to pork producers.

The estrogen receptor locus is associated with a major gene influencing litter size in pigs.

Identification of individual major genes affecting quantitative traits in livestock species has been limited to date. By using a candidate gene approach and a divergent breed cross involving the Chinese Meishan pig, we have shown that a specific allele of the estrogen receptor (ER) locus is associated with increased litter size. Female pigs from synthetic lines with a 50% Meishan background that were homozygous for this beneficial allele produced 2.3 more pigs in first parities and 1.5 more pigs averaged over all parities than females from the same synthetic lines and homozygous for the undesirable allele. This beneficial ER allele was also found in pigs with Large White breed ancestory. Analysis of females with Large White breed background showed an advantage for females homozygous for the beneficial allele as compared to females homozygous for the other allele of more than 1 total pig born. Analyses of growth performance test records detected no significant unfavorable associations of the beneficial allele with growth and developmental traits. Mapping of the ER gene demonstrated that the closest known genes or markers were 3 centimorgans from ER. To our knowledge, one of these, superoxide dismutase gene (SOD2), was mapped for the first time in the pig. Analysis of ER and these linked markers indicated that ER is the best predictor of litter size differences. Introgression of the beneficial allele into commercial pig breeding lines, in which the allele was not present, and marker-assisted selection for the beneficial allele in lines with Meishan and Large White background have begun.

Genetic and environmental trends for litter size in swine.

Best linear unbiased predictors (BLUP) of breeding values for additive direct and additive maternal genetic effects were estimated from 3,944 purebred Yorkshire and Landrace first-parity litters recorded on the Quebec Record of Performance Sow Productivity Program and born between 1977 and 1987. Breeding values for gilts, dams, and sires were estimated using an individual animal model for measures of litter size of total number born (NOBN), number born alive (NOBA), and number weaned (NOWN). Environmental trends were estimated from average herd-year solutions, and genetic trends were estimated by regression of estimated breeding value on year of birth. Environmental trends were positive for all traits in both breeds but were significant only for NOWN in Landrace (.051 +/- .021 pigs/yr). Genetic trends were very small but were mainly negative for direct breeding value and combined direct and maternal breeding value. Significant estimates of genetic trends (P less than .05) were observed only within the Yorkshire breed, and these ranged from -.012 +/- .004 to .004 +/- .002 pigs/yr.

Estimation of direct and maternal genetic variance for litter size in Canadian Yorkshire and Landrace swine using an animal model.

Estimates of additive direct heritability (h2a) for traits such as litter size may be biased by maternal effects. The size of these effects was estimated using a derivative-free restricted maximum likelihood procedure under an animal model. First-parity records from Yorkshire (Y) and Landrace (L) gilts were obtained from the Quebec Record of Performance sow productivity program for 21,127 litters born between 1977 and 1987. Direct (sigma 2a) and maternal (sigma 2m) additive genetic variances, their covariance (sigma am) and error variance (sigma 2e) were estimated for total numbers born (NOBN), born alive (NOBA) and weaned (NOWN). Analysis of purebred Y and crossbred litters indicated that estimates of sigma 2a were of similar magnitude for all traits, with h2a ranging from .06 to .13. Except for L litters, estimates of sigma 2m were relatively low for NOBN and NOBA, and increased in size for NOWN, with h2m ranging from 0 to .08. Also, estimates of sigma am were negative, except for NOBN and NOBA with crossbred litters, and became increasingly negative for NOWN. Results from purebred L litters indicated there was a stronger negative correlation between direct and maternal genetic effects for NOBN and NOBA than for NOWN.

Estimation of additive maternal and cytoplasmic genetic variances in animal models.

Two pathways for maternal genetic effects to act on production traits are additive maternal and cytoplasmic. Estimation of these variances have generally assumed that the correct maternal pathway is known. A method is described that allows simultaneous estimation of additive maternal and cytoplasmic genetic variances as well as additive direct genetic variances and error variances using an animal model. Data were simulated assuming an additive maternal model, cytoplasmic model, or both. The method was tested by analyzing the data under the true or incorrect maternal model using REML with an animal model that accounted for additive genetic relationships. Additive direct, additive maternal, cytoplasmic, and error variances were correctly partitioned when estimated under the true model. However, when additive maternal or cytoplasmic genetic effects were ignored in the model used for analysis, estimates of additive direct variance were significantly inflated. Also, under an additive maternal genetic model, a small cytoplasmic variance was estimated although none was present in the data.