E.F. Knol

Estimates of genetic parameters for reproduction traits at different parities in Dutch Landrace pigs

Data from Dutch Landrace sows were used to estimate genetic parameters for reproduction traits in the first six parities. Analyses were performed with DFREML using a model with equal design and herd-year-season of first parity as a fixed effect. Estimates of genetic parameters were calculated for different traits and parities using data from 58 194 sows. Heritabilities were found to be low for farrowing after first insemination (FFI), mothering ability (MA) and number of still born piglets (NSB); moderate for number of piglets born in total (NBT) or alive (NBA) and interval from weaning to first insemination (IWI); and high for gestation length (GL) and age at first insemination (AFI). Heritability increased slightly with parity number for NBT and NBA, increased markedly for NSB and MA, and decreased for IWI. Genetic correlations between the same traits measured in different parities were close to unity for parities higher than 2, for all traits. Genetic correlations below 0.70 were found between parity 1 and higher parities, for NBT, NBA, NSB, MA and FFI. Undesirable correlations were found between NBT and NSB (0.53) and NBT and MA (0.49). Indirect selection on MA would be possible using GL (r 5 0.40). IWI was positively correlated with AFI (0.31). It is concluded that selection on litter size, g piglet mortality and also number of litters per year would be worthwhile.

Genetic aspects of piglet survival

Amongst all fully formed piglets at the end of gestation, piglet survival until weaning (PS) is on average 81%. Selection for fast lean growth and increased litter size tends to decrease piglet survivability. Estimated heritabilities for PS and its component traits are generally low, on average around 0.04. Despite this, selection for improved survival is possible since the genetic variance for the trait is substantial. Genetic analyses indicated significant genetic correlations between PS on one side and litter size, gestation length, within-litter variation in birth weight, feed intake, gain, and backfat on the other. Genetic correlation of PS with birth weight, however, was low. Selection on birth weight as an indirect way to improve PS is doubtful. Genetic differences between piglets in survivability will be reflected in differences in body composition rather than in differences in birth weight. Experimental work on litters with high versus low genetic merit for PS, results of various selection experiments and experimental work with Meishan pigs support these findings.

The Contribution of Social Effects to Heritable Variation in Finishing Traits of Domestic Pigs (Sus scrofa)

Social interactions among individuals are ubiquitous both in animals and in plants, and in natural as well as domestic populations. These interactions affect both the direction and the magnitude of responses to selection and are a key factor in evolutionary success of species and in the design of breeding schemes in agriculture. At present, however, very little is known of the contribution of social effects to heritable variance in trait values. Here we present estimates of the direct and social genetic variance in growth rate, feed intake, back fat thickness, and muscle depth in a population of 14,032 domestic pigs with known pedigree. Results show that social effects contribute the vast majority of heritable variance in growth rate and feed intake in this population. Total heritable variance expressed relative to phenotypic variance was 71% for growth rate and 70% for feed intake. These values clearly exceed the usual range of heritability for those traits. Back fat thickness and muscle depth showed no heritable variance due to social effects. Our results suggest that genetic improvement in agriculture can be substantially advanced by redirecting breeding schemes, so as to capture heritable variance due to social effects.

Analysis of stillbirth in different lines of pig

Abstract In order to examine genetic influences on stillbirth in the pig, records of 7817 litters, originating from two purebred dam lines (D1 and D2), one purebred sire line (S), and one two-way cross (D12), were analyzed. For each litter, number of stillbirths, parity of the dam, gestation length (GL), total number of piglets born (TNB), average birth weight of the litter (ABW), variation in birth weight within the litter (VBW) and preweaning mortality rate (PWM) were recorded. After adjustment for ABW, there were no significant line differences in both average birth weight of stillborn and live-born piglets. Number of stillbirths per litter did not differ between lines, neither before nor after adjustment for GL, TNB, ABW and VBW, but was significantly influenced by GL, TNB and ABW, and not by VBW. Number of stillborn piglets per litter increased with decreasing GL, increasing TNB and decreasing ABW. On average, number of stillborn piglets increased between the second and the fifth parity. After adjustment for number of live-born piglets per litter, there was a significant positive relationship between number of stillborn piglets per litter and number of live-born piglets that died before weaning. In conclusion, no line differences in stillbirth were found, but significant line differences in the relation of stillbirth with GL, TNB and ABW indicate a small underlying genetic influence. The positive relationship of number of stillbirths with preweaning mortality of live-borns indicates an overall lower viability of litters in which stillbirths occur.

Direct, maternal and nurse sow genetic effects on farrowing-, pre-weaning- and total piglet survival

Abstract Peri- and postnatal survival data, including birth weights and cross-foster information from two line/farm combinations with 33 717 and 29 200 piglets, respectively, were analyzed to find the best genetic model to describe piglet survival. This was done in terms of direct (piglet), maternal and nurse sow genetic effects, maternal to cover uterine quality and nurse sow to cover mothering ability. The two component traits, farrowing and pre-weaning survival and — birth weight, the most important factor for survival — were similarly analyzed. As fixed effects, Year/Season, cross, parity, birth weight in classes of 100 g, litter size as such, and sex were included in the analyses. Models combining the different genetic effects were compared on the basis of the log-likelihood. A maternal/nurse sow model fitted the data best for pre-weaning survival, a direct/maternal model for birth weight, a direct model for farrowing survival in the dam line and a direct/maternal model for farrowing survival in the sire line. Including nurse sow effect in a model for piglet survival as a whole gave erratic results, making it difficult to define an optimal model. Estimated heritabilities for pre-weaning survival, measured on the binary scale, in the dam line were 0.02±0.005 for both maternal and nurse sow effects. Heritabilities for birth weight were, on average for the two lines, 0.04±0.01 for the direct effect and 0.20±0.03 for the maternal effect. In conclusion, selection for increased component traits of piglet survival is possible.

A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6

BackgroundIn many countries, male piglets are castrated shortly after birth because a proportion of un-castrated male pigs produce meat with an unpleasant flavour and odour. Main compounds of boar taint are androstenone and skatole. The aim of this high-density genome-wide association study was to identify single nucleotide polymorphisms (SNPs) associated with androstenone levels in a commercial sire line of pigs. The identification of major genetic effects causing boar taint would accelerate the reduction of boar taint through breeding to finally eliminate the need for castration.ResultsThe Illumina Porcine 60K+SNP Beadchip was genotyped on 987 pigs divergent for androstenone concentration from a commercial Duroc-based sire line. The association analysis with 47,897 SNPs revealed that androstenone levels in fat tissue were significantly affected by 37 SNPs on pig chromosomes SSC1 and SSC6. Among them, the 5 most significant SNPs explained together 13.7% of the genetic variance in androstenone. On SSC6, a larger region of 10 Mb was shown to be associated with androstenone covering several candidate genes potentially involved in the synthesis and metabolism of androgens. Besides known candidate genes, such as cytochrome P450 A19 (CYP2A19), sulfotransferases SULT2A1, and SULT2B1, also new members of the cytochrome P450 CYP2 gene subfamilies and of the hydroxysteroid-dehydrogenases (HSD17B14) were found. In addition, the gene encoding the ß-chain of the luteinizing hormone (LHB) which induces steroid synthesis in the Leydig cells of the testis at onset of puberty maps to this area on SSC6. Interestingly, the gene encoding the α-chain of LH is also located in one of the highly significant areas on SSC1.ConclusionsThis study reveals several areas of the genome at high resolution responsible for variation of androstenone levels in intact boars. Major genetic factors on SSC1 and SSC6 showing moderate to large effects on androstenone concentration were identified in this commercial breeding line of pigs. Known and new candidate genes cluster especially on SSC6. For one of the most significant SNP variants, the difference in the proportion of animals surpassing the threshold of consumer acceptance between the two homozygous genotypes was as much as 15.6%.

Estimation of direct and maternal genetic (co)variances for survival within litters of piglets

Abstract Variation in piglets weaned per sow per year is the main factor explaining differences in income between piglet producers. This parameter is the result of prolificacy of sows and survival rate of piglets. Data on 54500 piglets born between 1988 and 1994 at four nucleus breeding units of a pig breeding organization were used in an analysis of piglet survival. Animals were from two different dam lines. Piglet survival until weaning was considered and management was aimed at weaning at 28 days of age. Variance and covariance components were obtained using mixed models which included direct genetic and maternal genetic effects. In addition, the model included sex, breed, parity and herd-year-season as fixed effect, birth weight as covariable and sow as permanent environmental effect. Bayesian analysis, implemented using Gibbs sampling, was used to estimate the effects and parameters. Heritability of direct and maternal genetic effects was 0.11 (±0.01) and 0.09 (±0.01), respectively, in the full model. Genetic correlation between direct and maternal genetic effects was —0.56 (±0.06). Consequences of excluding maternal genetic effects or permanent environmental effects were studied. Based on the presented results it is concluded that simultaneous selection on maternal and direct genetic merit offers the opportunity to increase piglet survival.

Progress of farrowing and early postnatal pig behavior in relation to genetic merit for pig survival.

The objective of this study was to investigate whether pigs with different genetic merit for survival differed in birth weight, progress of farrowing, early postnatal behavior, or rectal temperature within 24 h after birth. On a nucleus farm in Rio Verde, Brazil, information was collected on 280 pigs, originating from 25 litters with known estimated breeding values for pig survival (EBVps). Litters were selected in such a way that a continuous range of EBVps with a maximum genetic contrast was achieved. Birth weight was recorded for all pigs. Indicators for progress of farrowing were birth intervals and duration of farrowing. Behavioral indicators of pig vitality were time until first upright standing (FUS), time until first udder contact (FUC), time until first teat in mouth (FTM), and time until first colostrum uptake (FCU). Rectal temperature was measured within 24 h after birth. Farrowing survival and early postnatal survival (within 3 d after farrowing) were registered. Farrowing survival and early postnatal survival both increased with increasing EBVps (farrowing survival: P = 0.007; early postnatal survival: P = 0.027). Birth weight decreased with increasing EBVps (P = 0.01). Birth intervals tended to increase with increasing EBVps (P = 0.10) and duration of farrowing was not related to EBVps. Time until first teat in mouth increased with increasing EBVps (P = 0.05), but the other behavioral indicators of pig vitality were not related to EBVps. Rectal temperature within 24 h after birth was not related to EBVps. Pigs with a higher genetic merit for survival have a lower birth weight but nevertheless have an increased farrowing survival and early postnatal survival. Their increased survival cannot be explained by differences in progress of farrowing, early postnatal behavior, or rectal temperature within 24 h after birth.

Genetic parameters and predicted selection results for maternal traits related to lactation efficiency in sows

The increased productivity of sows increases the risk of a more pronounced negative energy balance during lactation. One possibility to prevent this is to increase the lactation efficiency (LE) genetically and thereby increase milk output for a given feed intake and mobilization of body tissue. The benefits of selection for LE depend on its heritability and the relationships with other traits of interest. The objectives of this study were to estimate genetic parameters for LE, its underlying traits, and to predict the consequences of current selection strategies in dam lines. Data from 4 farms were available to estimate genetic parameters. Heritabilities were estimated by using a univariate repeatability model, and genetic correlations were estimated bivariately. Selection index theory was used to predict the genetic progress by 3 alternative breeding programs: 1) a breeding program that aimed at balanced progress in the total number of piglets born, piglet mortality, and percent prolonged interval from weaning to estrus; 2) extension of this breeding goal with LE; and 3) a breeding goal that included only one selection criterion, litter weight gain, to demonstrate the effect of indirect selection for milk production. The heritability for LE was low (0.12). Body fat mass (0.52) and BW (0.45) of sows at the beginning of lactation showed the greatest heritabilities. Protein mass at the beginning of lactation, protein loss, weight loss, and ad libitum feed intake during lactation showed moderate heritabilities (0.39, 0.21, 0.20, and 0.30, respectively). Low to moderate heritabilities were found for litter weight at birth, within-litter SD in the birth weight of piglets, litter weight gain, fat loss, and restricted feed intake during lactation (0.19, 0.09, 0.18, 0.05, and 0.14, respectively). Within-litter SD in the weaning weight of piglets showed no genetic variability. It was predicted that a breeding goal for dam lines with an emphasis on the total number of piglets born, piglet mortality, and percent prolonged interval from weaning to estrus would not dramatically change BW or body composition at the beginning of lactation, or mobilization of body tissue and feed intake during lactation. Inclusion of LE in the breeding goal will improve stayability, as defined by the first-litter survival of sows and LE itself, without negative consequences for other economically important traits. Nevertheless, it might be worthwhile to design a breeding goal in which LE increases and feed intake remains unchanged.

Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values.

The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.