Economic evaluation of progeny-testing and genomic selection schemes for small-sized nucleus dairy cattle breeding programs in developing countries.

In developing countries minimal and erratic performance and pedigree recording impede implementation of large-sized breeding programs. Small-sized nucleus programs offer an alternative but rely on their economic performance for their viability. We investigated the economic performance of 2 alternative small-sized dairy nucleus programs [i.e., progeny testing (PT) and genomic selection (GS)] over a 20-yr investment period. The nucleus was made up of 453 male and 360 female animals distributed in 8 non-overlapping age classes. Each year 10 active sires and 100 elite dams were selected. Populations of commercial recorded cows (CRC) of sizes 12,592 and 25,184 were used to produce test daughters in PT or to create a reference population in GS, respectively. Economic performance was defined as gross margins, calculated as discounted revenues minus discounted costs following a single generation of selection. Revenues were calculated as cumulative discounted expressions (CDE, kg) × 0.32 (€/kg of milk) × 100,000 (size commercial population). Genetic superiorities, deterministically simulated using pseudo-BLUP index and CDE, were determined using gene flow. Costs were for one generation of selection. Results show that GS schemes had higher cumulated genetic gain in the commercial cow population and higher gross margins compared with PT schemes. Gross margins were between 3.2- and 5.2-fold higher for GS, depending on size of the CRC population. The increase in gross margin was mostly due to a decreased generation interval and lower running costs in GS schemes. In PT schemes many bulls are culled before selection. We therefore also compared 2 schemes in which semen was stored instead of keeping live bulls. As expected, semen storage resulted in an increase in gross margins in PT schemes, but gross margins remained lower than those of GS schemes. We conclude that implementation of small-sized GS breeding schemes can be economically viable for developing countries.

Genotype by environment interaction for milk production traits between organic and conventional dairy cattle production in The Netherlands.

Estimates of genetic parameters for organic dairy farming have not been published previously, and neither is information available on the magnitude of genotype by environment interaction (GxE) between organic and conventional farming. However, organic farming is growing worldwide and basic information about genetic parameters is needed for future breeding strategies for organic dairy farming. The goal of this study was to estimate heritabilities of milk production traits under organic farming conditions and to estimate the magnitude of GxE between organic and conventional dairy farming. For this purpose, production records of first-parity Holstein heifers were used. Heritabilities of milk, fat and protein yield, and somatic cell score (SCS) were higher under organic farming conditions. For percentages of fat and protein, heritabilities of organic and conventional production were very similar. Genetic correlations between preorganic and organic, and organic and conventional milk production were 0.79 and 0.80, respectively. For fat yield, these correlations were 0.86 and 0.88, and for protein yield, these were 0.78 and 0.71, respectively. Our findings indicate that moderate GxE was present for yield traits. For percentage of fat and protein and SCS, genetic correlations between organic and conventional and preorganic production were close to unity, indicating that there was no GxE for these traits.

A whole-genome scan for quantitative trait loci affecting teat number in pigs.

A whole-genome scan was conducted using 132 microsatellite markers to identify chromosomal regions that have an effect on teat number. For this purpose, an experimental cross between Chinese Meishan pigs and five commercial Dutch pig lines was used. Linkage analyses were performed using interval mapping by regression under line cross models including a test for imprinting effects. The whole-genome scan revealed highly significant evidence for three quantitative trait loci (QTL) affecting teat number, of which two were imprinted. Paternally expressed (i.e., maternally imprinted) QTL were found on chromosomes 2 and 12. A Mendelian expressed QTL was found on chromosome 10. The estimated additive effects showed that, for the QTL on chromosomes 10 and 12, the Meishan allele had a positive effect on teat number, but, for the QTL on chromosome 2, the Meishan allele had a negative effect on teat number. This study shows that imprinting may play an important role in the expression of teat number.

Detection and characterization of quantitative trait loci for meat quality traits in pigs.

In an experimental cross between Meishan and Dutch Large White and Landrace lines, 785 F2 animals with carcass information and their parents were typed for molecular markers covering the entire porcine genome. Linkage was studied between these markers and eight meat quality traits. Quantitative trait locus analyses were performed using interval mapping by regression under two genetic models: 1) the line-cross approach, where the founder lines were assumed to be fixed for different QTL alleles and 2) a half-sib model where a unique allele substitution effect was fitted within each of the 38 half-sib families. The line-cross approach included tests for genomic imprinting and sex-specific QTL effects. In total, three genome-wide significant and 26 suggestive QTL were detected. The significant QTL on chromosomes 3, 4, and 13, affecting meat color, were only detected under the half-sib model. Failure of the line-cross approach to detect the meat color QTL suggests that the founder lines have similar allele frequencies for these QTL. This study provides information on new QTL affecting meat quality traits. It also shows the benefit of analyzing experimental data under different genetic and statistical models.

Genome-wide scan for body composition in pigs reveals important role of imprinting.

The role of imprinting in body composition was investigated in an experimental cross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genome scan revealed significant evidence for five quantitative trait loci (QTL) affecting body composition, of which four were imprinted. Imprinting was tested with a statistical model that separated the expression of paternally and maternally inherited alleles. For back fat thickness, a paternally expressed QTL was found on Sus scrofa chromosome 2 (SSC2), and a Mendelian-expressed QTL was found on SSC7. In the same region of SSC7, a maternally expressed QTL affecting muscle depth was found. Chromosome 6 harbored a maternally expressed QTL on the short arm and a paternally expressed QTL on the long arm, both affecting intramuscular fat content. The individual QTL explained from 2% up to 10% of the phenotypic variance. The known homologies to human and mouse did not reveal positional candidate genes. This study demonstrates that testing for imprinting should become a standard procedure to unravel the genetic control of multifactorial traits.

Evaluation of genetic, common-litter, and within-litter effects on preweaning mortality in a birth cohort of puppies.

OBJECTIVE: To determine relative impact of genetic, common-litter, and within-litter factors on puppy mortality. ANIMALS: 2,622 Boxer puppies of 413 litters born during a 14-month period. PROCEDURE: For each puppy, pedigree was determined, and litter in which it was born was registered. Overall mortality and mortality per specific cause of death were analyzed by use of a model that included an additive genetic effect, common-litter effect, within-litter effect, and regression of mortality on inbreeding coefficient. Relative importance of the effects was determined from estimates of the variance in mortality explained by each factor. RESULTS: 22% of the puppies died before reaching 7 weeks old. Stillbirth was the most frequent cause of death, followed by infection. Most observed differences were attributable to within-litter factors, which explained 67% of the variance in death attributable to infection and < or = 96% of the variance in death attributable to asphyxia. Common-litter factors were more important than additive genetic factors. Variance attributed to common-litter factors ranged from 2% for cheiloschisis, palatoschisis, or cheilopalatoschisis to 30% for death attributable to infection, and variance attributed to additive genetic factors ranged from 0% for asphyxia to 14% for euthanatized because of white color. Inbreeding coefficient had a significant effect on death attributable to infection, which increased 0.26% for each percentage increase of inbreeding. CONCLUSIONS AND CLINICAL RELEVANCE: Additive genetic factors have less impact on preweaning mortality than common-litter factors, which in turn have less impact than within-litter factors. Mortality attributable to infection increases significantly with increases in inbreeding.

Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa).

In an experimental cross between Meishan and Dutch Large White and Landrace lines, 619 F(2) animals and their parents were typed for molecular markers covering the entire porcine genome. Associations were studied between these markers and two fatness traits: intramuscular fat content and backfat thickness. Association analyses were performed using interval mapping by regression under two genetic models: (1) an outbred line-cross model where the founder lines were assumed to be fixed for different QTL alleles; and (2) a half-sib model where a unique allele substitution effect was fitted within each of the 19 half-sib families. Both approaches revealed for backfat thickness a highly significant QTL on chromosome 7 and suggestive evidence for a QTL at chromosome 2. Furthermore, suggestive QTL affecting backfat thickness were detected on chromosomes 1 and 6 under the line-cross model. For intramuscular fat content the line-cross approach showed suggestive evidence for QTL on chromosomes 2, 4, and 6, whereas the half-sib analysis showed suggestive linkage for chromosomes 4 and 7. The nature of the QTL effects and assumptions underlying both models could explain discrepancies between the findings under the two models. It is concluded that both approaches can complement each other in the analysis of data from outbred line crosses.

Discounted expressions of traits in broiler breeding programs.

The commercially grown broiler usually is a crossbred from specialized purebred sire and dam lines. The position of a purebred line in the crossbreeding system influences its genetic contribution to expression of productive and reproductive performance at different stages of the production column and, thus, influences the breeding goal for a given line. In broiler breeding, cumulative discounted expressions (CDE) should be considered to define breeding goals for multi-trait selection. In the present study, a systematic design for the application of discounted gene flow methodology to derive CDE for production and reproduction traits in broiler breeding was developed. Factors considered as influencing the magnitude of CDE were: crossbreeding system (two-way, three-way, and four-way cross), selection scheme (with and without progeny testing and intensity of selection), selection path, trait (production at commercial stage and reproduction at either nucleus or multiplier stage), interest rate, and time horizon for evaluation. Performance data from a commercial breeding stock were applied in the analysis. Results indicated that levels of CDE were significantly affected by all factors studied. The more that pure lines were included in the crossbreeding system, the lower the CDE for a particular selection path. However, the summation of all selection paths did not differ much among crossbreeding systems. Progeny testing decreased CDE by increasing generation intervals. The CDE for reproduction traits were higher than those for production traits mainly as a result of earlier expression of the reproduction traits.

Economic values in broiler breeding.

The objectives of this study were to derive economic values in broiler breeding and to determine their relationship with production circumstances. Economic values were derived using a deterministic economic model based on profit equations with a fixed amount of broiler meat output of the production system. Nonintegrated and the integrated broiler production systems were studied. The difference between these originates from different definitions of cost components and scaling aspects. For each stage of an nonintegrated system, the model calculated the profit margin; for an integrated system, (total) cost prices per unit of product at each stage were calculated. The Dutch broiler performance data and prices were input into the model as the representative situation. For all traits, in the nonintegrated system, economic values were derived, expressed as Dutch guilders (Dfl) per unit of product, where the unit of product depends on the stage of the production system and equals an egg for the multiplier breeder, a day-old chick for the hatchery, and a marketable broiler for the commercial grower and processor. Resulting levels of economic values were illustrated by showing underlying cost or profit changes in the production system. For the integrated system, economic values were expressed as Dfl x marketable broiler(-1) x unit(-1). Economic values of traits in the integrated system were also derived for situations where technical parameters or prices of productive factors were changed (20% increase or decrease). A general conclusion from these sensitivity analyses is that the economic values are sensitive to production levels, product prices and feed prices; there are both linear and nonlinear relationships between economic values and production circumstances.

Genetics of the interval from weaning to estrus in first-litter sows: correlated responses.

The objective of this study was to evaluate relationships between rebreeding performance and growth performance (n = 3,777 gilts) and rebreeding performance and reproductive performance (n = 2,242 sows). Our data were from a selection experiment for shorter intervals from weaning to estrus after the first parity (IWE), involving Dutch Landrace pigs, in which a selection line and a control line without selection were maintained for eight generations. Relationships were evaluated before and after transforming IWE to normal interval (NI; IWE < or = 7 d), prolonged interval (PI; IWE > 7 d), and incidence of a prolonged interval (INC). Heritabilities of NI, PI, and INC were .18, .17, and .27. Within-line phenotypic and genetic trends in growth and reproductive performance were not different from zero and did not diverge as a correlated response to the selection applied. Phenotypic correlations between IWE, NI, or PI and growth or reproductive performance were low and ranged from -.14 to .11. Genetic correlations were higher, and, for the majority of traits, the genetic correlations with NI and PI had a different sign. Phenotypic and genetic contrasts between sows with NI and sows with PI different from zero indicated that INC may increase as a correlated response to selection for reproductive performance. Analyses using untransformed IWE or data from populations selected for rebreeding performance may underestimate the correlated response in IWE due to selection on economically important traits.

Segregation analyses for presence of major genes affecting growth, backfat, and litter size in Dutch Meishan crossbreds.

Presence of major genes was investigated for two growth traits, backfat thickness, and two litter size traits in the F1 and F2 population of a cross between Meishan and European "White" pig lines. Segregation analyses were performed in a Bayesian setting, estimating the contribution of background polygenes and the contribution of a possible major gene to the expression of the traits considered. In a first analysis, F1 and F2 crossbred data were evaluated; different error variances were fitted for F1 and F2 observations. In the first analysis, significant contributions of major-gene variance were found for the two growth traits, backfat thickness, and litter size at first parity. In a second analysis, F2 data were evaluated to determine whether biases were introduced in the joint analysis of F1 and F2 data. In the second analysis, no major genes were found for growth traits. Major genes affecting backfat and litter size at first parity were confirmed. The gene identified to affect backfat is a dominant gene; the homozygous recessive genotype has approximately 6 mm of additional backfat. The gene identified to affect litter size at first parity also is a dominant gene; the homozygous recessive genotype produces five to six fewer pigs per litter.

Bayesian statistical analyses for presence of single genes affecting meat quality traits in a crossed pig population.

Presence of single genes affecting meat quality traits was investigated in F2 individuals of a cross between Chinese Meishan and Western pig lines using phenotypic measurements on 11 traits. A Bayesian approach was used for inference about a mixed model of inheritance, postulating effects of polygenic background genes, action of a biallelic autosomal single gene and various nongenetic effects. Cooking loss, drip loss, two pH measurements, intramuscular fat, shearforce and back-fat thickness were traits found to be likely influenced by a single gene. In all cases, a recessive allele was found, which likely originates from the Meishan breed and is absent in the Western founder lines. By studying associations between genotypes assigned-to individuals based on phenotypic measurements for various traits, it was concluded that cooking loss, two pH measurements and possibly backfat thickness are influenced by one gene, and that a second gene influences intramuscular fat and possibly shearforce and drip loss. Statistical findings were supported by demonstrating marked differences in variances of families of fathers inferred as carriers and those inferred as noncarriers. It is concluded that further molecular genetic research effort to map single genes affecting these traits based on the same experimental data has a high probability of success.

Genetics of the interval from weaning to estrus in first-litter sows: distribution of data, direct response of selection, and heritability.

A selection experiment with a selection and a control line maintained for eight generations was set up to study efficacy of selection for a short interval from weaning to estrus after weaning the first litter and to estimate genetic variation in the Dutch Landrace population. Intervals were recorded without truncation (i.e., intervals up to 234 d were observed). A mating scheme with 10 mating groups was used to avoid inbreeding. Distribution of intervals from weaning to estrus was described by a mixture of a normal and an exponential distribution. Between lines, both underlying distributions were similar, but the contribution to the total distribution was different. From generation 4 onward, intervals were significantly shorter in the selection line than in the control line. Variances within lines, generations, and mating groups varied to a large extent. Response per unit selection differential was calculated for original data and three sets of transformed data, both with and without correction for unequal subclass numbers. Standardized responses were more precise and linear, when data were log-transformed, and when corrected for unequal subclass numbers. The assumed best estimate of the realized heritability was .17. The heritability in the foundation population was estimated at .36 +/- .05, using an animal model including all genetic relationships in the data. It was concluded that genetic selection decreases the average interval from weaning to estrus by reducing the number of sows with a record in the exponential part of the distribution.

[Possibilities of selection for high disease resistance in swine based on immunological indicators]. / Mogelijkheden van selectie op verhoogde ziekteweerstand bij varkens op basis van immunologische kengetallen.

Disease resistance results from different processes which partly are immunological in nature. Immunological processes can be subdivided into innate (non-specific) resistance (phagocytosis) and acquired resistance. The latter can be subdivided in cellular and humoral immunity. These three compartments of the immune system do not act independently but are complementary. Parameters for each of the compartments have a genetic basis, and expression is affected by many genes, some of which are known. Experimental results suggest that especially aspects of innate disease resistance (the killing capacity of phagocytes) are negatively correlated with humoral immune response. Comparison of pig breeds supports this idea. On the other hand selection experiments show that simultaneous improvement of various aspects of the immune system is possible. Consequently, selection programmes should utilize index selection including parameters of all three compartments. Research in mice and various farm animal species studied genetic aspects of immune parameters. Little attention has been paid to the relationships between immune responsiveness and resistance to specific infections. To support the implementation of selection programmes for disease resistance in pigs, further experiments using e.g. mice as a model and the design of simulation models are useful.

Economic values of optimum traits: the example of meat quality in pigs.

In this paper a method is outlined to derive marginal-income functions and to calculate economic values for traits with an intermediate optimum such as meat-quality traits. A normal distribution of the quality trait was assumed, but the method can be used for other distributions as well. The parameters necessary to use this method are distribution of the quality trait, population mean and the standard deviation of the quality trait, optimum range, and price differences between products within and outside the optimum range. Especially, the optimum range for the quality trait and the price differences to be used have to be derived from consumer and processing research. Some alternative methods that can be used for selection on quality traits, such as restricted selection index, desired-gains index, and indices based on a quadratic aggregate genotype, are discussed.