First-degree relationships and genotyping errors deciphered by a high-density SNP array in a Duroc × Iberian pig cross.

BACKGROUND: Two individuals with a first-degree relationship share about 50 percent of their alleles. Parent-offspring relationships cannot be homozygous for alternative alleles (genetic exclusion). METHODS: Applying the concept of genetic exclusion to HD arrays typed in animals for experimental purposes or genomic selection allows estimation of the rate of rejection of first-degree relationships as the rate at which two individuals typed for a large number of Single Nucleotide Polymorphisms (SNPs) do not share at least one allele. An Expectation-Maximization algorithm is applied to estimate parentage. In addition, genotyping errors are estimated in true parent-offspring relationships. Samples from nine candidate Duroc sires and 55 Iberian dams producing 214 Duroc × Iberian barrows were typed for the HD porcine Affymetrix array. RESULTS: We were able to establish paternity and maternity of 75 and 85 piglets, respectively. Rate of rejection in true parent-offspring relationships was estimated as 0.000735. This is a lower bound of the genotyping error since rate of rejection depends on allele frequencies. After accounting for allele frequencies, our estimate of the genotyping error is 0.6%. A total of 7,744 SNPs were rejected in five or more true parent-offspring relationships facilitating identification of "problematic" SNPs with inconsistent inheritance in multiple parent-offspring relationships. CONCLUSIONS: This study shows that animal experiments and routine genotyping in genomic selection allow to establish or to verify first-degree relationships as well as to estimate genotyping errors for each batch of animals or experiment.

The relationship between feed intake behaviour with intramuscular fat, cholesterol and fatty acid composition in pork.

The aim of this study was to investigate the phenotypic relationship between feed intake (FI) characteristics with intramuscular fat, cholesterol and fatty acid composition in pork. Data were available on 202 Duroc barrows. Intramuscular fatness was positively correlated with a higher percentage of saturated (SFA) and monounsaturated fatty acids (MUFA), a lower percentage of polyunsaturated (PUFA), omega-3 (ω3) and omega-6 (ω6) fatty acids, and a lower ω6/ω3 and P:S ratio (p < 0.05). Faster growth resulted in a higher level of SFA and a lower level of ω3 fatty acids (p < 0.05). Increased FI, residual feed intake (RFI) and feed intake time (TIME) and a decreased feed intake frequency (FREQ) resulted in an increase in MUFA, a decrease in PUFA, ω3 and ω6 fatty acids and a lower P:S ratio (p < 0.05). In addition, increased FI and RFI and a decreased FREQ resulted in an increase in SFA (p < 0.05). Most of the correlations were a result of a concomitant relationship with intramuscular fatness and disappeared after correction for that trait. Serum total, high-density lipoprotein and low-density lipoprotein cholesterol levels were positively correlated with SFA and MUFA, and negatively with PUFA, omega-3 and omega-6 fatty acids, and the P:S ratio (p < 0.05). These results have implications for programmes aimed at improving meat quality through selection.

Gene expression in Sinclair swine with malignant melanoma.

Sinclair swine develop an aggressive form of melanoma, which, in many cases, spontaneously regresses after a complete metastatic phase. We used Affymetrix GeneChip® Porcine Genome Arrays consisting of 24 123 probe sets to compare gene expression in white blood cells (WBCs) and various tissues including the liver, lungs, inguinal lymph nodes and spleen harvested from a Sinclair piglet afflicted by melanoma at birth and exhibiting metastatic lesions at weaning (6 weeks) with those from a full-sibling piglet that showed no incidence of melanoma at birth and weaning. The highest number (3489; ∼14%) of significantly upregulated transcripts (fold change in gene expression ≥2.0 and t-test P-value ≤0.05) was observed in the liver, while the spleen exhibited the lowest number of upregulated transcripts (528; ∼2%). Among significantly downregulated genes, the highest numbers were observed in the inguinal lymph nodes (3651; ∼15%) and the least in WBCs (730; ∼3%). Differentially expressed transcripts included genes involved in melanoma pathogenesis including SILV, TYR and RAB28. SILV was over-expressed 784-, 430- and 164-fold, while TYR was over-expressed 138-, 81- and 28-fold in the liver, lungs and inguinal lymph nodes, respectively. Quantitative real-time RT-PCR (qRT-PCR) confirmed the microarray data of 12 selected differentially expressed sequences. These results suggest that significant changes in gene expression occur during metastasis of malignant melanoma in the Sinclair swine model. In addition, qRT-PCR analysis of the above 12 differentially expressed sequences was carried out on liver samples collected from 22 pigs (12 of which had melanoma during the first 6 weeks of life), and an ANOVA test contrasting absolute RNA expression between pigs with regressing, progressing and without tumors was significant for TYR, TACSTD1, MATP, GPNMB and CYP4A22, with P-values of 0.034, 0.015, 0.007, 0.050 and 0.022, respectively.

Adaptability of pregnant Merino ewes to the cold desert climate in Nevada.

Grazing ability is difficult to record in animals under free-ranging conditions without sophisticated methods. Alternatively, grazing ability may be indirectly inferred from changes in BW and production characteristics during the grazing period. The present study investigated the effect of grazing on resource-limited rangelands on BW, wool characteristics, and offspring weaning weights in nine hundred five 5/8, 7/8, and fullblood Merino ewes of 2 to 7 yr of age during a grazing period of approximately 2.5 mo (between January and March). A total of 469 ewes gave birth to a single lamb, 248 to twin lambs, and 188 did not give birth. Body weights were measured and wool samples taken before and after the ewes were allowed to graze freely on the rangelands; absolute change in BW and change in BW as a percentage of initial BW were estimated. On average, grazing on resource-poor rangelands resulted in BW loss, a reduction in fiber diameter and its CV, and increased staple length. Animals with finer wool at the start of the grazing period lost phenotypically (r = -0.07, P < 0.05) and genetically (r = -0.23, P < 0.05) less BW during the grazing period and had a greater probability to carry 1 lamb (or 2) to term (P < 0.05). Animals that lost less BW produced more greasy fleece (r = 0.09, P < 0.01). Body weight change did not significantly influence offspring weaning weights. Change in BW was moderately heritable at h(2) = 0.29; fiber diameter was strongly heritable at h(2) = 0.51. Animals with the least inclusion of Merino genetics lost more BW (P < 0.01) during the grazing period and had a more uniform fiber diameter (P < 0.05) but shorter staples (P < 0.05) and less fleece (P < 0.0001) than animals with a greater level of Merino genetics. Our results indicate that animals with finer wool appeared to be better adapted to the cold Nevada desert. Thus, selection for finer wool may positively influence adaptability to resource-limited cold climate conditions; alternatively, BW change may be selected for directly. Because nutritional deficiencies during pregnancy can have adverse consequences for the offspring, indirect selection for grazing ability would foremost result in healthier ewes that can produce lambs and wool without compromising their welfare.

Role of selection and inbreeding on the incidence of cutaneous malignant melanoma in Sinclair swine.

This paper reports the quantitative analysis of the historical database of a herd of Sinclair swine affected by cutaneous malignant melanoma. The herd was under partial and non-systematic selection for melanoma susceptibility (animals having at least one tumour during the first 6 weeks of life). Weighted selection differentials for the number of tumours at birth and the number of tumours at 6 weeks were generally positive and between -0.43 and 4.76 tumours for the number of tumours at 6 weeks. Estimates of the heritability for number of tumours at birth and at 6 weeks using 1934 animals were 0.27 (+/-0.03) and 0.25 (+/-0.03), respectively. The estimate of the genetic correlation between these two traits was 0.95 (+/-0.03). Genetic trends were positive for the number of tumours at birth and at 6 weeks. In spite of positive selection differentials and a moderate heritability, there was a negative phenotypic trend in the number of tumours. Natural selection might be acting in a direction opposite to artificial selection in the Sinclair herd. The slopes of the regression of the number of tumours at birth, at 6 weeks, and melanoma susceptibility on individual inbreeding coefficients were non-significant, indicating no evidence of dominance. The number of live-born pigs was lower in litters from parents susceptible to the disease (p < 0.01).

The value of DNA paternity identification in beef cattle: examples from Nevada's free-range ranches.

The feasibility and economic value of DNA paternity identification were investigated and illustrated using Nevada beef cattle operations. A panel of 15 microsatellites was genotyped in 2,196 animals from 8 ranches with a total of 31,571 genotypes. Probabilities of exclusion for each marker within ranch and across ranches were computed. Joint probabilities of exclusion for the 15 microsatellites were also determined, resulting in values over 0.99 for any individual ranch and across ranches. Dropping 1 or 2 microsatellites with the lowest probabilities of exclusion resulted in joint probabilities greater than 0.99 and with marginal reduction compared with the probabilities with 15 microsatellites. Formulas for benefit-cost analysis for a DNA paternity identification program in beef cattle were derived. Genotyping 15 microsatellites with 20 calves per sire resulted in benefits of $1.71 and $2.44 per dollar invested at bull culling rates of 0.20 and 0.30, respectively. The breakpoints for the program to be profitable occurred when the ratio of the price of 1 kg of calf liveweight over the cost of genotyping 1 microsatellite was greater than 1.1 for a bull culling rate of 0.30. Benefit-cost analysis was also derived under incomplete DNA paternity identification using a lower number of DNA markers than necessary to achieve joint probabilities of exclusion of 0.99. Approximately a 20% increase in the benefit-cost ratio was achieved using 10 vs. 12 microsatellites with incomplete paternity identification. The greater the number of bulls in the operation, the lower the benefit-cost ratio of the paternity testing program. Low probabilities of exclusion and a high number of bulls in the beef operation reduced the benefit-cost ratio dramatically. The DNA paternity identification programs are feasible and may be profitable for free-range beef cattle operations.

Modeling inheritance of malignant melanoma with DNA markers in Sinclair swine.

Cutaneous malignant melanoma in Sinclair swine is a hereditary disease that develops in utero or during the first 6 weeks of life. In many cases, the tumors regress and piglets survive the disease. Two different sets of gene(s) might be involved in the disease: tumor initiator (suppressor) locus or loci and loci affecting the aggressiveness of the disease (number and stage of tumors). We develop maximum-likelihood methods for interval mapping for both types of loci. The experimental design consisted of a boar mated to tumor-bearing sows with recording of tumor status and number of tumors in the 6 weeks of life of the offspring. The model to search for the tumor initiator locus (with alleles T and t) was tested by computer simulation. Estimates of penetrances (Psi(TT) and Psi(Tt) for genotypes TT and Tt, respectively) were accurate even for small family sizes. Statistical power was >99% for a family size of 70 with Psi(TT) = 1 and Psi(Tt) = 0. The models to test for number of tumors incorporated genotype information for the tumor initiator locus. All models were tested with data from a single boar family of 72 piglets over swine chromosomes 6 and 8 (SSC6 and SSC8). No tumor evidence for initiator loci was found associated with these chromosomes. However, association of a QTL affecting number of tumors at birth near microsatellite SW1953 on SSC8 was chromosomewise significant (P<0.0124).

Behaviour influences cholesterol plasma levels in a pig model.

Little is known about the relationship between feed intake behaviour and cholesterol levels in humans. This can be attributed to the fact that feed intake behaviour in humans is difficult to assess. The relationships between feed intake, feed efficiency and feed intake behaviour, and cholesterol and triglyceride levels were investigated at an average age of 187 days, in a pig model consisting of 202 Duroc barrows. Feed intake and feed intake behaviour were recorded individually and daily by means of an electronic identification system. Animals with high levels of total cholesterol also had high levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides. Animals with high levels of HDL also had high levels of LDL and triglycerides, and animals with high levels of LDL also had high levels of triglycerides. Animals with higher BW, higher backfat thickness, higher BW gain, higher gain of backfat deposition, higher feed intake, higher residual feed intake (RFI) and higher feed intake rate had higher levels of total, HDL and LDL plasma cholesterol. Results indicate that the relationship between feed intake and cholesterol levels is a long-term relationship, while the relationship between RFI and cholesterol levels is more of a short-term nature. The relationship between intake rate and cholesterol plasma levels disappeared after correction for the amount of feed consumed. Results indicate that feed intake independent of metabolic BW, growth and fatness, i.e. 'RFI', was positively correlated with cholesterol plasma levels. This suggests that eating food over and above the maintenance and growth requirements constitutes a health risk independent of the level of fatness.

Feeding time and feeding rate and its relationship with feed intake, feed efficiency, growth rate, and rate of fat deposition in growing Duroc barrows.

Because feed is the major cost to pork production, management practices and breeding strategies are aimed at optimizing feed intake. Knowledge about the shape of feed intake and feeding behavior curves may be of interest for optimization of lean meat production. This study investigated trends based on daily measurements of feeding behavior in 200 Duroc barrows, originating from 5 sires and 200 dams, during growth. Daily values were examined between 88 and 188 d of age. Furthermore, phenotypic correlations between feeding length and feeding rate, and feeding frequency, feed intake, residual feed intake, growth rate, and rate of fat deposition were investigated for a period between 95 and 175 d of age. No differences were observed between sires for parameter estimates of a curvilinear function fitted to data on feeding length as a function of age, but the effect of sire was significant (P < 0.01) for values at individual ages up to 132 d of age. Feeding rate (feed ingested for each minute spent eating) increased in a linear fashion with age (average R(2) = 0.80) and differently so for different sires (P < 0.05 for the intercept and P < 0.01 for the regression coefficient). Because the increase in BW is linear over this time period (average R(2) = 0.99), the results suggest that feeding rate increased with increased BW and is related to the physical capacity for feed intake. Results indicate that pigs that ate faster also ate more (r = 0.29, P < 0.001), grew faster (r = 0.40, P < 0.001), and grew fatter (r = 0.28, P < 0.001), but had no greater or lower residual feed intake (r = -0.01). The linear regression slope of feeding rate on age seemed inherent to the individual and was correlated with feed intake but not with residual feed intake. Feeding length may be selected for in order to regulate absolute feed intake at different stages of growth.

The relationship between residual feed intake and feed intake behavior in group-housed Duroc barrows.

Because feed is the major input in pork production, conversion of feed into lean tissue at minimum costs has been a focus for improvement. Several researchers have proposed using residual feed intake (RFI) rather than feed conversion ratio (FCR) for genetic improvement of feed efficiency. Little is known about the variation in RFI in pigs. As several studies suggest a greater RFI is related to greater animal activity levels, the current study investigated the phenotypic relationship between RFI and feed intake (FI) behavior of 104 group-housed growing Duroc barrows allowed ad libitum access to feed. Feed intake, BW gain, feeding time (TIME), feeding frequency (VISITS), RFI, and FCR were calculated for 5 periods of 14, 23, 28, 21, or 23 d in length (periods 1 through 5, respectively) on animals that were between 73 to 95 d of age at the start of the testing period. Barrows that grew faster consumed more feed (P < 0.001), and barrows that consumed more feed were fatter (P < 0.01). There were no correlations between VISITS and TIME, between VISITS and FI, or between VISITS and RFI. Barrows that spent more time at the feeder, however, consumed more feed (P < 0.05) and had greater RFI in periods 1, 3, and 5 (P < 0.05). As expected, FI and FCR were highly correlated with RFI (P < 0.001). These results suggest that a greater FI rather than greater feed intake activity resulted in greater RFI values.

A simulation study on the detection of causal mutations from F2 experiments.

A simulation study has been performed to evaluate the power and the rate of false positives for the detection of causal mutations under two different models of analysis. We used an F2 design generated from an F0 population of five sires of line 1 and 40 dams of line 2 to produce an F1 population of 10 sires and 80 dams. Two different locations of the causal mutation and several frequencies of the mutations in the parental populations were considered. The first model included only the genetic configuration of the mutation, while the second model also included the probability of line origin given the neutral markers. Both models performed well when the mutation at the candidate gene was the causal mutation, although a greater power was obtained using the first model, because of its relative simplicity compared to the second one. However, when the candidate gene mutation was a neutral mutation, the second model presented a lower rate of false positives than the first. Moreover, in some cases the second model allowed distinction between the neutral and the causal mutation. The F2 design has a great power to detect quantitative trait loci provided by linkage disequilibrium, but also makes it difficult to discriminate between causal and neutral mutations. Therefore a high percentage of false positives can be expected. The limitations of F2 designs for discriminating between neutral and causal mutations are discussed.

The value of prior information for detection of QTL affecting longitudinal traits: an example using Von Bertalanffy growth function.

A Bayesian procedure is presented for detecting quantitative trait loci (QTL) affecting longitudinal traits. The statistical model assumes a QTL affecting the prior distribution of the parameters of a given production function, under a hierarchical Bayesian scheme. Marginal posterior distributions for the effects associated with the QTL are calculated using Markov chain Monte Carlo methods. Furthermore, the Bayesian analysis allows the use of some available relevant information that can improve the detection of the QTL substantially. To illustrate the procedure, an example of QTL detection using the Von Bertalanffy growth function is presented with a F2 pig population bred from Iberian boars and Landrace sows. Animals of the F2 population were genotyped for seven markers in chromosome 2 (SSC2). Two prior distributions for the mean effect of the parameters related with birth and adult weight were compared. On the one hand, vague prior distributions were used, and, on the other, there were assumed univariate Gaussian distributions that ensure biologically meaningful adult and birth weights on the posterior growth curves. Results from the second prior distribution supported the presence of QTL, by showing that individuals with both alleles of Iberian origin had lower rates of maturation. On the contrary, when vague priors were used, the procedure was not able to detect QTL.

Viability of Iberian x Meishan F2 newborn pigs. I. Analysis of physiological and vitality variables.

Eight physiological and vitality variables related to the first minutes of the life of Iberian x Meishan F2 piglets were analyzed. Variables included rectal temperature, arterial oxygen saturation, heart rate (all were monitored at birth and 60 min later), time to reach the udder, and time to the first colostrum intake. Litter effect within boar, a random source of variation, influenced all variables, whereas the random boar effect was not significant for heart rate and arterial oxygen saturation at birth and the time to reach the udder. Birth weight influenced rectal temperature at birth (P < 0.01) and 60 min later (P < 0.001), arterial oxygen saturation 1 h after birth (P < 0.05), heart rate 1 h after birth (P < 0.001), time to reach the udder (P < 0.05), and time to the first suckle (P < 0.01), whereas viability score influenced rectal temperatures (at birth and 60 min later; P < 0.001), and time to reach the udder (P < 0.001) and to suckle (P < 0.001). Finally, the order of birth showed significant effects for rectal temperature 1 h after birth (P < 0.001) and time to first colostrum intake (P < 0.001). Correlation coefficients between physiological variables were generally low, with the exception of the ones for rectal temperature 1 h after birth and arterial oxygen saturation 1 h after birth (0.38; P < 0.001), and for rectal temperature at birth and rectal temperature 1 h after birth (0.34; P < 0.001). Times to reach the udder and to suckle were highly correlated (0.67; P < 0.001) and also were moderately and negatively correlated with rectal temperature 1 h after birth (-0.36 and -0.38 respectively; P < 0.001). Heart rates at birth and 1 h later, as well as arterial oxygen saturation at birth and 1 h later, were not correlated, showing that the values at birth do not necessarily provide information about the physiological status of the pig 1 h after birth. The recording of physiological variables, birth weight, and viability score may be useful to identify weak piglets quickly and to establish palliative measures.

Derivation of a Bayes factor to distinguish between linked or pleiotropic quantitative trait loci.

A simple procedure to calculate the Bayes factor between linked and pleiotropic QTL models is presented. The Bayes factor is calculated from the marginal prior and posterior densities of the locations of the QTL under a linkage and a pleiotropy model. The procedure is computed with a Gibbs sampler, and it can be easily applied to any model including the location of the QTL as a variable. The procedure was compared with a multivariate least-squares method. The proposed procedure showed better results in terms of power of detection of linkage when low information is available. As information increases, the performance of both procedures becomes similar. An example using data provided by an Iberian by Landrace pig intercross is presented. The results showed that three different QTL segregate in SSC6: a pleiotropic QTL affects myristic, palmitic, and eicosadienoic fatty acids; another pleiotropic QTL affects palmitoleic, stearic, and vaccenic fatty acids; and a third QTL affects the percentage of linoleic acid. In the example, the Bayes factor approach was more powerful than the multivariate least-squares approach.

Reallocation of body resources in lactating mice highly selected for litter size.

The present study investigated differences in the allocation patterns of body stores in lactating female mice from a line selected for high litter size at birth (S-line, average litter size of 20) and dams from a nonselected control line (C-line, average litter size of 10). Body weight, litter size, litter weight, and absolute and relative lipid and protein mass were measured at peak lactation (2 wk in lactation) and at weaning (3 wk in lactation). Body size in S-line females has been increased as a correlated effect of selection for high litter size at birth, allowing for larger litters and higher absolute milk production. However, these dams produce larger litters relative to their own body weight. At peak lactation, lipid and protein percentage did not differ between lines. At weaning, S-line females had a higher protein percentage (P < 0.001) and lower lipid percentage (P < 0.05) than C-line females. Apparently, S-line females produce more offspring but at a greater cost to their own metabolism. This process was insufficient to supply the offspring with adequate resources, resulting in reduced (P < 0.0001) pup development and increased (P < 0.0001) preweaning mortality rates.