Correction to: A bivariate genomic model with additive, dominance and inbreeding depression effects for sire line and three-way crossbred pigs.

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A bivariate genomic model with additive, dominance and inbreeding depression effects for sire line and three-way crossbred pigs.

BACKGROUND: Crossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content, whereas maternal lines are also bred for reproduction and longevity traits, and the resulting three-way crossbred pigs are used for production of meat. The most important genetic basis for heterosis is dominance effects, e.g. removal of inbreeding depression. The aims of this study were to (1) present a modification of a previously developed model with additive, dominance and inbreeding depression genetic effects for analysis of data from a purebred sire line and three-way crossbred pigs; (2) based on this model, present equations for additive genetic variances, additive genetic covariance, and estimated breeding values (EBV) with associated accuracies for purebred and crossbred performances; (3) use the model to analyse four production traits, i.e. ultra-sound recorded backfat thickness (BF), conformation score (CONF), average daily gain (ADG), and feed conversion ratio (FCR), recorded on Danbred Duroc and Danbred Duroc-Landrace-Yorkshire crossbred pigs reared in the same environment; and (4) obtain estimates of genetic parameters, additive genetic correlations between purebred and crossbred performances, and EBV with associated accuracies for purebred and crossbred performances for this data set. RESULTS: Additive genetic correlations (with associated standard errors) between purebred and crossbred performances were equal to 0.96 (0.07), 0.83 (0.16), 0.75 (0.17), and 0.87 (0.18) for BF, CONF, ADG, and FCR, respectively. For BF, ADG, and FCR, the additive genetic variance was smaller for purebred performance than for crossbred performance, but for CONF the reverse was observed. EBV on Duroc boars were more accurate for purebred performance than for crossbred performance for BF, CONF and FCR, but not for ADG. CONCLUSIONS: Methodological developments led to equations for genetic (co)variances and EBV with associated accuracies for purebred and crossbred performances in a three-way crossbreeding system. As illustrated by the data analysis, these equations may be useful for implementation of genomic selection in this system.

Analysis of the genetics of boar taint reveals both single SNPs and regional effects.

BACKGROUND: Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk of boar taint. There is evidence for genetic variation in the predisposition to boar taint.A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred Danish Landrace boars with high levels of skatole in fat (>0.3 µg/g), were each matched with a litter mate with low levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on 938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For androstenone, a 'regional heritability approach' combining information from multiple SNPs was used to estimate the genetic variation attributable to individual autosomes. RESULTS: A highly significant association was found between variation in skatole levels and SNPs within the CYP2E1 gene on chromosome 14 (SSC14), which encodes an enzyme involved in degradation of skatole. Nominal significance was found for effects on skatole associated with 4 other SNPs including a region of SSC6 reported previously. Genome-wide significance was found for an association between SNPs on SSC5 and androstenone levels and nominal significance for associations with SNPs on SSC13 and SSC17. The regional analyses confirmed large effects on SSC5 for androstenone and suggest that SSC5 explains 23% of the genetic variation in androstenone. The autosomal heritability analyses also suggest that there is a large effect associated with androstenone on SSC2, not detected using GWAS. CONCLUSIONS: Significant SNP associations were found for skatole on SSC14 and for androstenone on SSC5 in Landrace pigs. The study agrees with evidence that the CYP2E1 gene has effects on skatole breakdown in the liver. Autosomal heritability estimates can uncover clusters of smaller genetic effects that individually do not exceed the threshold for GWAS significance.

Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds.

BACKGROUND: Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. RESULTS: Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL), 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 µg/g). In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. CONCLUSIONS: Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.

Duroc boars have lower progeny mortality and lower fertility than Pietrain boars.

In pig production, Pietrain and Duroc lines are often used as terminal sire lines to produce crossbred slaughter pigs. The objective of this study was to identify the differences in paternal fertility and mortality during the suckling period of crossbred progeny from Pietrain and Duroc terminal sire lines. In total, 87 purebred Duroc boars and 68 purebred Pietrain boars were used as terminal sires to produce 1,823 crossbred Duroc litters (D-litters) and 1,705 crossbred Pietrain litters (P-litters) in two production herds. The sows were crosses between DanBred Landrace and Yorkshire (F1). All boars were kept at the same artificial insemination (AI) station, and all semen doses were produced in the same laboratory. The experiment was balanced according to herd, boars, and time, with approximately 13 sows from each herd mated to each boar within each breed. The results showed higher fertility expressed as litter size at birth in P-litters compared with D-litters led to 0.5 higher total number born (TNB) for P-litters (P = 0.0076). However, piglet mortality including number of stillborn piglets was lower in D-litters compared with P-litters (P < 0.0001), and 5 d after farrowing, the average litter size in P-litters ranged 0.4 below the litter size in D-litters (P < 0.027). At 21 d after birth, mean litter size in P- and D-litters were 14.5 and 14.9 piglets per litter, respectively (P < 0.015). This indicated that Pietrain progenies were weaker than Duroc progenies, and it was concluded that use of Duroc boars as the terminal sire line led to lower piglet mortality. In the two herds, the mean piglet mortality rate including still born piglets ranged from 19.5% to 23.6% and from 17.6% to 19.1% in P- and D-litters, respectively.

Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II: meat quality traits.

BACKGROUND: Meat quality traits are important in pig breeding programs, but they are difficult to include in a traditional selection program. Marker assisted selection (MAS) of meat quality traits is therefore of interest in breeding programs and a Quantitative Trait Locus (QTL) analysis is the key to identifying markers that can be used in MAS. In this study, Landrace and Hampshire intercross and backcross families were used to investigate meat quality traits. Hampshire pigs are commonly used as the sire line in commercial pig breeding. This is the first time a pedigree including Hampshire pigs has been used for a QTL analysis of meat quality traits. RESULTS: In total, we analyzed 39 meat quality traits and identified eight genome-wide significant QTL peaks in four regions: one on chromosome 3, two on chromosome 6 and one on chromosome 16. At least two of the QTLs do not appear to have been detected in previous studies. On chromosome 6 we identified QTLs for water content in M. longissimus dorsi (LD), drip loss in LD and post mortem pH decline in LD. On chromosomes 3 and 16 we identified previously undetected QTLs for protein content in LD and for freezing and cooking loss respectively. CONCLUSION: We identified at least two new meat quality trait QTLs at the genome-wide significance level. We detected two QTLs on chromosome 6 that possibly coincide with QTLs detected in other studies. We were also able to exclude the C1843T mutation in the ryanodine receptor (RYR1) as a causative mutation for one of the chromosome 6 QTLs in this cross.

A second mutant allele (V199I) at the PRKAG3 (RN) locus- I. Effect on technological meat quality of pork loin.

The effect of three alleles (RN(-), rn(+) and a second mutant allele V199I, denoted rn*) at the PRKAG3 (RN) locus on such meat quality traits as pH, internal reflectance (FOP), Warner-Bratzler shear force, water-holding capacity and cooking loss were studied. M. longissimus dorsi (LD) from a total of 334 crossbreed pigs, entire males and females, Hampshire (H) and Finnish Landrace (L) of three combinations H × LH, LH × H and LH × LH, were used. The PRKAG3 alleles were identified with a DNA test and all possible RN genotypes, RN(-)/RN(-) (23%), RN(-)/rn(+) (24%), RN(-)/rn* (33%), rn(+)/rn(+) (8%), rn(+)/rn* (9%) and rn*/rn* (2%), were found. Water, intramuscular fat, protein and glycogen contents were determined. All the three alleles at the RN locus affected the studied technological meat quality traits of pork loin, except for the internal reflectance 24 h post mortem and the shear force. The RN(-) allele was dominant over the other two alleles, rn(+) and rn*, in LD with regard to ultimate pH, water-holding capacity and cooking loss, giving lower ultimate pH and water-holding capacity and higher cooking loss. The rn* allele affected ultimate pH in LD of non-carriers of the RN(-) allele, giving higher ultimate pH. The RN(-) allele was also dominant over the other two alleles in residual glycogen content in entire male pigs, but not in female pigs, where the rn* allele had a glycogen-lowering effect. The water content was higher and the protein content lower in LD of all RN(-)/- animals compared with the other genotypes, while no significant differences were found with regard to IMF content. Water-holding capacity, cooking loss and shear force were higher in LD of entire males compared with females.

A second mutant allele (V199I) at the PRKAG3 (RN) locus-II. Effect on colour characteristics of pork loin.

Three alleles at the PRKAG3 (RN) locus that influence the glycogen content of pork were found to be segregating in Hampshire×Landrace crossbred pigs, RN(-), rn(+) as well as second mutant allele V 199I (here denoted rn*). The effect of these three alleles on ultimate pH, pigment content, internal reflectance (FOP), surface colour measured by tristimulus colorimetry (L*, a*, b*) and fractions of deoxymyoglobin (Mb), oxymyoglobin (MbO(2)) and metmyoglobin (MetMb) of pork loin was studied. Moreover, the effect of sex, entire male versus female pigs, on these traits was also analysed. The three PRKAG3 alleles affected ultimate pH, internal reflectance, colour and distribution of myoglobin derivatives of pork loin, while the pigment content was not influenced. Ultimate pH values of loins from the three genotypes were found to be in the order RN(-)/- genotypes rn(+)/rn(+) genotype=rn(+)/rn* genotype=rn*/rn* genotype. The RN(-) allele was dominant resulting in higher redness (a* value) and yellowness (b* value), while the rn* allele tended to result in lower redness and yellowness compared with the rn* allele. The RN(-) allele was dominant over the rn* allele in lightness (L* value) giving a lighter colour. Surface colour differences were mainly explained by differences in the distribution of the myoglobin derivatives. Finally, surface lightness was higher and pigment content, redness and fraction of MbO(2) lower in loin from entire males compared with females.

The influence of RN genotype, including the new V199I allele, on the eating quality of pork loin.

The eating quality of M. longissimus dorsi (LD) from RN(-) homozygotes, RN(-) heterozygotes and RN(-) non-carriers was investigated in a Swedish Hampshire×Finnish Landrace pig population. The recently identified new allele (V199I, here denoted rn*) at the RN locus was also detected among the pigs selected and included in the sensory evaluation. The number of animals varied from 10 to 15 in the five genotype groups; RN(-)/RN(-), RN(-)/rn+, RN(-)/rn*, rn+/rn+ and rn+/rn* (in total 59 pigs). In addition, one pig was determined to be rn*/rn* but was excluded from the analysis. The three genotypes in which the RN(-) allele was represented (RN(-)/RN(-), RN(-)/rn+ and RN(-)/rn*) had higher glycogen and lower protein contents as well as lower ultimate pH (measured 48 h post-mortem) in LD than the non-carriers (rn+/rn+ and rn+rn*). Of the sensory parameters evaluated (tenderness, chewing time, chewing residual, juiciness, meat flavour and acidity), the five RN genotypes only affected acidity significantly; the RN(-) allele contributing to a more acid taste in LD. The influence of the rn* allele resembled that of rn+ on the sensory parameters. When the material was divided into three groups (homozygous, heterozygous and non-carriers of the RN(-) allele) the juiciness was found to be significantly influenced by RN genotype, and LD from animals that were homozygous and heterozygous with respect to the RN(-) allele exhibited a higher juiciness than LD from non-carriers. The RN(-) allele also tended to contribute to greater tenderness, which was significantly higher in LD from heterozygous carriers than from non-carriers of the RN(-) allele. A more rapid decline in pH (measured as pH at 45 min and 3 h post-mortem) contributed to a greater tenderness in LD (according to a trained panel and Warner-Bratzler shear force). In addition to the RN genotype, the decline in pH was influenced by carcass weight, which varied between 71 and 97 kg, and by stunning procedure, which changed during the course of the study from individual to group stunning with CO(2). The individual stunning procedure contributed to a lower pH in the initial post-mortem phase (pH(45)), whereas a higher carcass weight and the RN(-) allele lowered the pH in the mid-post-mortem region (pH(3h) and pH(24h)), significantly (P⩽0.05). The pH continued to decline after 24 h post-mortem and the ultimate pH was not reached until 48 h post-mortem. The cooking loss, juiciness and acidity were related to the specific characteristics of the RN(-) carriers, such as higher glycogen content, lower protein content and lower ultimate pH (pH(48h)).