New phenotypes for new breeding goals in pigs.

Pig breeders in the past have adopted their breeding goals according to the needs of the producers, processors and consumers and have made remarkable genetic improvements in the traits of interest. However, it is becoming more and more challenging to meet the market needs and expectations of consumers and in general of the citizens. In view of the current and future trends, the breeding goals have to include several additional traits and new phenotypes. These phenotypes include (a) vitality from birth to slaughter, (b) uniformity at different levels of production, (c) robustness, (d) welfare and health and (e) phenotypes to reduce carbon footprint. Advancements in management, genomics, statistical models and other technologies provide opportunities for recording these phenotypes. These new developments also provide opportunities for making effective use of the new phenotypes for faster genetic improvement to meet the newly adapted breeding goals.

Reduced porcine islet isolation yield in the presence of hyperemic islets.

When studying histological characteristics of porcine pancreata in relation to islet isolation, a remarkably high number of hyperemic islets (HIs) was encountered. The abnormalities observed in these HIs ranged from a single dilated vessel to hemorrhages extending into the surrounding exocrine tissue. The aim of the present study was to compare pancreata with and without HI on islet isolation outcomes. This study involved a histological examination of 143 purebred (74 juvenile and 69 adult) and 47 crossbred (only juvenile) porcine pancreata. Islet isolation was performed in 48 purebred adult pigs and in 25 crossbred pigs. Tissue samples were stained with Aldehyde Fuchsine. The presence of HIs was scored semi-quantitatively (HI-, HI+). We observed HIs in 48% of the purebred and in 68% of the crossbred pigs. However, only 3.3±3.1% and 3.1±4.7% of all assessed islets was hyperemic in HI+ pancreata in purebred and crossbred pigs, respectively. In both groups, significantly higher endocrine cell mass was found in the HI+ pancreata (p<0.01). When the higher endocrine cell mass was taken into account, we found significantly lower yields in the HI+ pancreata in both purebred and crossbred pigs (p=0.03 in both groups). The presence of HIs occurs frequently in porcine donor-pancreata and is associated with reduced isolation outcomes.

Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4.

Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.

A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding.

In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (≥90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was ≥5, the number of mismatches was ≤1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.

Breeding replacement gilts for organic pig herds.

In this study, breeding structures and commercial sow lines were evaluated by economic and genetic simulation studies for their suitability to provide the Dutch organic pig sector with replacement gilts. Sow and litter performance from over 2000 crossbred sows from 2006 to 2007 were collected on 11 to 14 Dutch organic pig herds, respectively, and compared with conventional herds. Results showed that organic herds had lower farrowing rates (3.6% to 7.5%), more live born piglets per litter (0.4% to 1.2%) and higher preweaning mortality rates (7% to 13%) compared to conventional herds. These results were used to simulate economic performance of various combinations of breeding structures and sow lines under organic conditions, under the assumption of absence of genotype-environment interactions. Sow and litter performance data under organic conditions (total piglets born/litter, stillborn piglets/litter, mortality until weaning, lactation length, interval weaning-oestrus and sow culling rate) and the costprice calculation for the Dutch organic pig sector were used as input for the economic simulation studies. The expected genetic progress was simulated for three potential breeding structures of the organic sector: organic breeding herds producing F1 gilts (OrgBS), a flower breeding system (FlowerBS) and a two-line rotation breeding system (RotBS). In FlowerBS, an organic purebred sow line is bred, using on-farm gilt replacement. The OrgBS with a Yorkshire × Landrace cross had the highest margin per sow place (€779), followed by RotBS with Yorkshire × Landrace cross (€706) and FlowerBS with Yorkshire sow line (€677). In case that an organic purebred sow population of 5000 sows would be available, FlowerBS gave the highest genetic progress in terms of cost price reduction (€3.72/slaughter pig per generation), followed by RotBS and OrgBS (€3.60/slaughter pig per generation). For FlowerBS, additional costs will be involved for maintaining a dedicated breeding programme. In conclusion, OrgBS using conventional genetics is economically the most viable option for the organic pig sector. However, this structure has clear disadvantages in terms of risks with regard to disease transmission and market demand. FlowerBS using a dedicated purebred organic line will only be cost-effective if sow population size is sufficiently large. RotBS might be a viable alternative, especially in combination with artificial insemination (AI) boars that are ranked according to an organic selection index. Regardless of breeding structure, the Yorkshire sow line gave the highest prolificacy and the highest economic returns on organic herds.

Sow line differences in heat stress tolerance expressed in reproductive performance traits.

The objectives of this study were 1) to investigate if there were differences in the relation between temperature and reproductive performance traits in 2 different sow lines, a Yorkshire line producing mainly in temperate climates and a Large White line producing mainly in warm climates, and 2) to determine the upper critical temperature (UCT) for the reproductive performance of these 2 lines. Sows are exposed to heat stress when temperature exceeds the UCT of the thermo-neutral zone. Data included 32,631 observations on reproductive performance from 11,935 sows on 20 farms in Spain, collected from 2003 to 2005. Sows belonged to 2 different purebred sow lines, named D (Yorkshire sow line, producing mainly in temperate climates) and I (Large White sow line, producing mainly in warm climates). Only first insemination records per parity were used and were combined with the maximum outside temperature at day of insemination. Upper critical temperatures were studied for 3 reproduction traits: farrowing rate (0 or 1), litter size (range from 1 to 25), and total number of piglets born per first insemination (combination of farrowing rate and litter size, range from 0 to 25). Data were corrected for fixed effects, which included parity, service sire, and an interaction between farm and year. Corrected data were used as observations in the models to study the effect of outside temperature on reproductive performance. Two models were compared for goodness of fit: a linear regression model and a plateau-linear model with the plateau representing the thermo-neutral zone and a linear decrease above that zone. Farrowing rate of I-line sows was not affected by temperature. For litter size and total number born per first insemination of I-line sows no UCT could be estimated. These traits were linearly affected by temperature. For all 3 reproduction traits of the D-line the best model was the plateau-linear model; the UCT for the D-line sows was estimated to be 19.2 degrees C for farrowing rate, 21.7 degrees C for litter size, and 19.6 degrees C for total number born per first insemination. The decrease in reproductive performance of I-line sows with increasing outside temperature was less than in D-line sows. From this study it can be concluded that there are differences in heat stress tolerance between sow lines as measured by the differences in reproductive performance. These differences are an indication of genetic differences in heat stress tolerance in sow lines.

Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition.

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.

Perspective of NIRS measurements early post mortem for prediction of pork quality.

The potential of near-infrared spectroscopy (NIRS) measurements early post mortem was investigated to predict ultimate drip loss, colour, tenderness and intra-muscular fat of pork. Three locations (M. longissimus thoracis, M. longissimus lumborum and M. semimembranosus) in 102 pig carcasses were tested at the end of the slaughter line. A priori variation in pork quality was introduced using an experimental design covering: genotype, lairage time, pre-slaughter handling and day of slaughter. At 1 h post mortem a diode array VIS/NIR instrument (Zeiss MCS 511/522, 380-1700 nm) equipped with a surface fibre optic probe was used and at 1 day post mortem ultimate pH, drip loss, colour and shear force was measured on similar locations. Results indicated that it was possible to predict intra-muscular fat content (correlation (R(2) of 0.35 with multiple linear regression), standard error of prediction (SEP)=3.6 g/kg), but the configuration has to be refined for on-line application (bigger aperture). For drip loss no correlation was achieved with the PLS method. Even extremes (low drip loss (<2.5%) or high drip loss (>4.5%)) in drip loss were not discriminated. Predicting drip loss with NIRS early post mortem is not successful, although NIRS in the slaughter line has potential as a fast predictor of intra-muscular fat. Possibilities for using the NIRS technique to get to know more about muscle metabolism and post mortem changes are promising.

Reproduction results and offspring performance after non-surgical embryo transfer in pigs.

Increased interest in transfer of valuable genetic material around the world with minimal health risks has stimulated the development of non-surgical embryo transfer (nsET) technologies in pigs. Experimental evidence shows that nsET without sedation of the recipients is now feasible. The goal of this study, therefore, was to evaluate a method of nsET under commercial conditions. The experiment included 135 donor gilts and 45 multiparous recipient sows. Ovulation was induced in both donors and recipients, and nsET was performed using the Swinlet catheter. Donor gilts averaged 16.5 (7-45) corpora lutea, but this depended on age of the donor (P < 0.05). An average of 10.1 transferable blastocysts was recovered per donor, and the recovery rate was 84%. For 44 nsET, 14 recipients (31%) came into estrous before Day 23 after ovulation, 7 recipients (16%) came into estrous between Days 23 and 30, 3 recipients (6.8%) came into estrous between Days 39 and 48, 2 recipients (4.5%) had a late abortion. Finally, 18 of 44 recipients (41%) resulted in successful births, with an average liter size of 7.2 +/- 2.8. Birth weight of nsET piglets were 0.2 kg more than control piglets, but depended on litter size ((P < 0.05). The sex-ratio was not different from 50%. No anatomical abnormalities were observed in the offspring of nsET. Of the recipients that did not become pregnant from nsET, 91% became pregnant after insemination in the next estrous. Gilts born from nsET gave on average 12.4 +/- 3.0 total born piglets in their first pregnancy. In conclusion, the nsET procedure used in this study can be applied in practice without the need for special facilities, such as surgical and anesthesia equipment.

[Risk factors of contamination of pig farms in the Netherlands with pig diseases and agents thereof: a review of the literature]. / Risicofactoren voor insleep van varkensziekten/-ziekteverwekkers op varkensbedrijven in Nederland: een literatuuroverzicht.

Part of the project 'Clean pigs' an extensive study of literature was made of the risk factors related to the introduction of pathogenic micro-organisms in pigfarms in the Netherlands. On the basis of this study of literature and in close cooperation with the experts of the steering group of the project 'Clean pigs' a number of risk factors relevant for the Dutch pig farming were estimated. The impact of these risk factors on the introduction of the most important pig diseases/-agents in Dutch pig farming was quantified for three different levels of preventive measures. It is shown that many risks can be reduced or even be neglected by the biosecurity measures already applied on pig farms. For most diseases, including list A and B diseases of the OIE list, introduction of new animals is regarded as the main risk factor, but this risk can be reduced in several ways. Besides this, aerogenic transmission and introduction by rodents and pet animals need the most attention. Through specific actions and measures several important risk factors can be diminished or even eliminated.

[Improved pig health with farm management systems. Project 'Beautiful stream of pigs' 21]. / Gezondheidsverbetering in de varkenshouderij door toepassing van bedrijfssystemen. Project 'Schone varkensstromen' 21.

As part of the project 'Clean pigs', an inventory was made of the different pig farm management systems described in the literature. These systems were evaluated for their potential use in improving animal health, focusing on the pathogens important in the Netherlands. The most promising systems for the control and/or eradication of pig pathogens in the Netherlands can be divided into two groups (with decreasing effect): I. Eradication from an existing positive population. The best systems for this are Embryo Transplantation (ET), Specific-Pathogen Free pigs (SPF), Piglet Snatching and Segregated Weaning (SW). II. Strategic veterinary and breeding strategies. The best systems for this are Freeze infection, test and removal, Test and removal, Vaccination, Medical elimination, Strategic medication and Genetic resistance. Farm systems can be a big help when trying to improve animal health, but the 'biosecurity' measures on the farm are at least of equal importance.