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Biomedical subjects

J L Noguera

Publications and source records attributed to J L Noguera.

At least 19 recordsLinked to original sources
PubMed2006

Malic enzyme 1 genotype is associated with backfat thickness and meat quality traits in pigs.

Malic enzyme 1 (ME1) is a part of the tricarboxylate shuttle that provides NADPH and acetyl-CoA required in fatty acid biosynthesis. The pig ME1 locus maps on the proximal end of chromosome 1, where a quantitative trait loci (QTL) affecting fat deposition has been previously described. We amplified fragments of 1457 and 1459 bp that corresponded to the complete coding region and the 3'-untranslated region (UTR), respectively, of the pig ME1 gene. The sequences of these two fragments in pigs from three breeds (Landrace, Large White and Piétrain) contained five single nucleotide polymorphisms (SNP) in the 3'-UTR: C1706T, G1762T, A1807C, C1857A and T1880A. Three haplotypes were found in two generations of a selected Landrace population: H1 (C1706 G1762 A1807 C1857 A1880), H2 (C1706 G1762 A1807 C1857 T1880) and H3 (T1706 T1762 C1807 A1857 T1880). Using Bayesian association analyses, significant associations (highest posterior density at 95%) between ME1 genotype and backfat (BF) thickness at 171 days and muscular pH were found in a Landrace population.

Animals↗
PubMed2006

Characterization of the porcine acyl-CoA synthetase long-chain 4 gene and its association with growth and meat quality traits.

Summary Long-chain acyl-CoA synthetase (ACSL) catalyses the formation of long-chain acyl-CoA from fatty acid, ATP and CoA, activating fatty acids for subsequent reactions. Long-chain acyl-CoA synthetase thus plays an essential role in both lipid biosynthesis and fatty acid degradation. The ACSL4 gene was evaluated as a positional candidate gene for the quantitative trait loci (QTL) located between SW2456 and SW1943 on chromosome X. We have sequenced 4906 bp of the pig ACSL4 mRNA. Sequence analysis allowed us to identify 10 polymorphisms located in the 3'-UTR region and to elucidate two ACSL4 haplotypes. Furthermore, a QTL and an association study between polymorphisms of the ACSL4 gene and traits of interest were carried out in an Iberian x Landrace cross. We report QTL that have not been previously identified, and we describe an association of the ACSL4 polymorphisms with growth and percentage of oleic fatty acid. Finally, we have determined allelic frequencies in 140 pigs belonging to the Iberian, Landrace, Large White, Meishan, Pietrain, Duroc, Vietnamese, Peccary and Babirusa populations.

Animals↗
PubMed2006

Polymorphisms of the porcine dopamine beta-hydroxylase gene and their relation to reproduction and piglet survivability in an Iberian x Meishan F2 intercross.

The goals of this study were to sequence and physically map the porcine dopaminebeta-hydroxylase (DBH) gene, as well as to perform an association study between polymorphisms of this gene and the reproductive performance and piglet survivability of F(2) pigs from an Iberian x Meishan cross. The porcine DBH gene was positioned by RH mapping near the telomere of chromosome 1q2.13, close to markers SSC10D08 and SW1301. Sequencing of DBH cDNAs from 10 pigs revealed the existence of six nucleotide polymorphisms, two of which led to non-synonymous amino acid substitutions within exon 3 at positions 463A>G and 616A>G that corresponded to Thr155Ala and Lys206Glu respectively. Three haplotypes segregated in an Iberian x Meishan population: DBH(X) (A(436)-A(616)), DBH(Y) (A(436)-G(616)) and DBH(Z) (G(436)-G(616)). The DBH haplotypes significantly affected rectal temperatures 1 h after birth (P = 0.002) and have a suggestive effect on the time to first colostrum intake (P = 0.019) and on birth weight (P = 0.019).

Animals↗
PubMed2006

Comparison of genetic models for analysing the effects of a PvuII polymorphism in the oestrogen receptor 1 (ESR1) gene on prolificacy in an Iberian x Meishan pig population.

The effect of a previously reported PvuII polymorphism in oestrogen receptor 1 (ESR1) was analysed in an F(2) population of Iberian x Meishan pigs. We tested three hypotheses: (1) that a causal mutation was fixed in the parental populations, (2) that a causal mutation existed that was in complete linkage disequilibrium with the alleles of the PvuII polymorphism and (3) that a causal mutation existed in linkage disequilibrium within each parental population. The third model was the most plausible based on the available data. ESR1 alleles displayed different patterns of linkage disequilibrium with the causal mutation in each of the parental populations and the PvuII polymorphism was clearly not the causal mutation. As a consequence, the use of the ESR1 mutation for selection must be evaluated for a particular pig population before it is applied.

Alleles↗
PubMed2006

Adipocyte fatty-acid binding protein is closely associated to the porcine FAT1 locus on chromosome 4.

We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene, a strong positional candidate gene for the FAT1 locus in porcine chromosome 4. The most informative polymorphism, an insertion/deletion in intron 1, together with a single nucleotide polymorphism in intron 3, was genotyped in a cross between Iberian and Landrace pigs. After performing QTL, single marker, and haplotype analyses, we showed that there were at least 2 quantitative trait genes in the FAT1 region and that the FABP4 polymorphism was tightly associated to fatness. A comparison of allelic frequencies in a panel of pig breeds suggested that the Del2634C polymorphism was under indirect selection. We also showed that FABP4 is tightly associated to fatness but not growth. Furthermore, a haplotype analysis suggests that there is genetic heterogeneity at the FAT1 locus within the Landrace breed.

Animals↗
PubMed2006

High amino acid variation in the intracellular domain of the pig prolactin receptor (PRLR) and its relation to ovulation rate and piglet survival traits.

Two polymorphisms of the porcine prolactin receptor (PRLR) gene were previously related to litter size by several authors; however, the magnitude and direction of such effects varied depending on the population analyzed. We have sequenced the complete coding region of the porcine PRLR gene and found 6 nonconservative SNP: C1217T (Leu/Pro406), C1283A (Asp/Ala428), G1439A (Lys/Arg480), T1528A (Met/Leu510), G1600A (Gly/Ser534), and G1789A (Gly/Ser597), within exon 10 of the gene, which encodes the entire intracytoplasmic domain of the protein. Eight haplotypes were found and were segregating at different frequencies in 6 porcine breeds. The effects of each individual SNP and haplotype were evaluated in an Iberian x Meishan F2 population using a univariate mixed-inheritance animal model. Significant effects on the number of corpora lutea were found for PRLR haplotypes (P < 0.012), confirming the previously reported associations of PRLR in this process and highlighting the importance of performing analysis of haplotypes rather than of individual SNP. Suggestive effects or tendencies were found for heart rate at birth (P < 0.10), rectal temperature (P < 0.05), and oxygen saturation (P < 0.10) 1 h after birth, and time to first suckle (P < 0.10). We found greater than expected levels of amino acid variability within the intracellular domain of the porcine PRLR, which have been associated with differences in the number of corpus lutea of sows and the preweaning survivability of piglets.

Amino Acid Sequence↗
PubMed2005

Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross.

The leptin receptor gene (LEPR) is a candidate for traits related to growth and body composition, and is located on SSC6 in a region where fatness and meat composition quantitative trait loci (QTL) have previously been detected in several F2 experimental designs. The aims of this work were: (i) to fine map these QTL on a larger sample of animals and generations (F3 and backcross) of an Iberian x Landrace intercross and (ii) to examine the effects of LEPR alleles on body composition traits. Eleven single nucleotide polymorphisms (SNPs) were detected by sequencing LEPR coding regions in Iberian and Landrace pig samples. Three missense polymorphisms were genotyped by pyrosequencing in 33 F0, 70 F1, 418 F2, 86 F3 and 128 individuals coming from the backcross of four F2 males with 24 Landrace females. Thirteen microsatellites and one SNP were also genotyped. Traits analysed were: backfat thickness at different locations (BF(T)), intramuscular fat percentage (IMF(P)), eye muscle area (EM(A)), loin depth (LO(D)), weight of shoulder (SH(W)), weight of ribs (RIB(W)) and weight of belly bacon (BB(W)). Different statistical models were applied in order to evaluate the number and effects of QTL on chromosome 6 and the possible causality of the LEPR gene variants with respect to the QTL. The results support the presence of two QTL on SSC6. One, at position 60-100 cM, affects BF(T) and RIB(W). The other and more significant maps in a narrow region (130-132 cM) and affects BF(T), IMF(P), EM(A), LO(D), SH(W), RIB(W) and BB(W). Results also support the association between LEPR alleles and BF(T) traits. The possible functional implications of the analysed polymorphisms are considered.

Alleles↗
PubMed2005

QTL mapping for teat number in an Iberian-by-Meishan pig intercross.

The aim of this study was to investigate chromosomal regions affecting the number of teats in pigs and possible epistatic interactions between the identified quantitative trait loci (QTL). An experimental F2 cross between Iberian and Chinese Meishan lines was used for this purpose. A genomic scan was conducted with 117 markers covering the 18 porcine autosomes. Linkage analyses were performed by interval mapping using an animal model to estimate QTL and additive polygenic effects. Complementary analyses with models fitting two QTL were also carried out. The results showed three genomewide significant QTL mapping on chromosomes 5, 10 and 12, whose joint action control up to 30% of the phenotypic variance of the trait. Meishan alleles had a positive additive effect on teat number, and a positive-additive x additive-epistatic interaction was detected between QTL on chromosomes 10 and 12.

Animals↗
PubMed2005

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.

Animals↗
PubMed2005

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.

Animals↗
PubMed2005

Effect of the porcine IGF2-intron3-G3072A substitution in an outbred Large White population and in an Iberian x Landrace cross.

The IGF2-intron3-G3072A substitution has been recently described as the causal factor of the imprinted QTL for fat deposition and muscle growth detected within the porcine IGF2 region. The objective of this study was to investigate the IGF2 substitution effect in a Large White outbred population and in an Iberian x Landrace F2 cross. The results showed that the substitution has significant effects on fatness, growth, and shape traits with estimated effects in the expected direction. These results agree with those obtained in the F2 cross, where the IGF2-intron3-G3072A substitution is segregating only in a small family. In addition, a QTL scan has been performed in the F2 population for the traits used in the IGF2 substitution effect validation. Results of this study demonstrated that there are QTL segregating in swine chromosome 2 other than the IGF2 substitution for carcass weight, LM area, and pH measured at 24 h after slaughter. The results confirm the relevance of the IGF2 substitution, but they also show that there are still valuable mutations to be revealed in this chromosome.

Adipose Tissue↗
PubMed2005

Identification of carcass and meat quality quantitative trait loci in a Landrace pig population selected for growth and leanness.

The identification of QTL related to production traits that are relevant for the pig industry has been mostly performed by using divergent crosses. The main objective of the current study was to investigate whether these growth, fatness, and meat quality QTL, previously described in diverse experimental populations, were segregating in a Landrace commercial population selected for litter size, backfat thickness, and growth performance. We have found QTL for carcass weight (posterior P > 0.75), cutlet weight (posterior P > 0.99), weight of ham (posterior P > 0.75), shoulders weight (posterior probability > 0.99), and shear firm-ness (posterior P > 0.99) on pig Chromosome 2. Moreover, QTL with posterior P > 0.75 for fat thickness between the 3rd and 4th ribs (Chromosome 7), rib weights (Chromosome 8), backfat thickness (Chromosomes 8, 9, and 10), and b Minolta color component (Chromosome 7) were identified. These results indicate that commercial purebred populations retain a significant amount of genetic variation, even for traits that have been selected for many generations.

Adipose Tissue↗
PubMed2005

Bayesian analysis of quantitative trait loci for boar taint in a Landrace outbred population.

The genetic basis of the main components of boar taint was investigated in intact male pigs in a commercial population. We analyzed fat androsten-one and skatole concentrations from 217 males of an outbred Landrace population. Records were normalized using a logarithm transformation and tested for normality using a Wilk-Shapiro test. Bayesian analysis was then used to map QTL in 10 candidate regions previously selected on chromosomes 1, 2, 3, 4, 6, 7, 8, 9, 10, and 13. The criterion for QTL detection was the Bayes factor (BF) between polygenic models with and without QTL effects. Both traits had considerable genetic determination, with posterior means of total heritabilities ranging from 0.59 to 0.73 for androstenone and from 0.74 to 0.89 for skatole. Positive evidence for a fat skatole QTL was detected on SSC6 (BF = 5.16); however, no QTL for androstenone were found in any of the 10 chromosomal regions analyzed. With the detection of a QTL for the fat skatole concentration segregating in this population, marker-assisted selection or even gene-assisted selection could be used once the causal mutation of the QTL was identified.

Adipose Tissue↗
PubMed2005

Bayes factor analysis for the genetic background of physiological and vitality variables of F2 Iberian x Meishan newborn piglets.

The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 min later), birth weight, interval between birth and first teats contact, and interval between birth and first colostrum intake. The available numbers of data ranged from 288 (heart rate at 60 min) to 839 records (birth weight) from F(2) Iberian x Meishan newborn pigs. We compared a model with zero heritability (nonheritable) with the one where the additive genetic background was included. The BF was used to discriminate between both candidate models. Very strong evidence of genetic background was detected for heart rate 60 min after birth (BF = 48.90), and strong evidence was detected for rectal temperature at birth (BF = 13.82). Posterior modes (means) of heritabilities were 0.29 (0.32) and 0.40 (0.39), respectively. In addition, substantial evidence of absence of genetic background was detected for arterial oxygen saturation at birth.

Animals↗
PubMed2005

Polymorphism of the pig 2,4-dienoyl CoA reductase 1 gene (DECR1) and its association with carcass and meat quality traits.

We characterized the nearly complete coding sequence of the pig 2,4-dienoyl CoA reductase 1 (DECR1) gene, which encodes an enzyme involved in the beta-oxidation of polyunsaturated fatty enoyl-CoA esters and maps on a linoleic QTL located on Chromosome 4. Sequencing of a 937-bp fragment encompassing exons 2 and 10 revealed the existence of two missense SNP at exon 2 (C181 --> G181) and exon 5 (C458 -->G458). These two SNP are associated with Val (C) --> Leu (G) and Ser (C) --> Thr (G) conservative AA replacements at positions 61 and 153 of the DECR1 protein, respectively. Moreover, DECR1 genotyping in a representative sample of 184 pigs from the Large White, Pietrain, Iberian, Duroc, and Landrace breeds demonstrated the existence of disequilibrium linkage between these two SNP (Haplotype 1: C181C458; Haplotype 2: G181G458). An association analysis between DECR1 genotype and growth, carcass, and meat quality traits in a highly selected Landrace population (n = 470) revealed differences among genotypes for isocitrate dehydrogenase activity (highest posterior density [HPD] of 90%), longissimus thoracis pH (HPD of 95%), lightness (HPD of 90 to 95%), and redness (HPD of 95%). Because these associations were not consistently found in the three available genotype comparisons, we believe that exon 2 and 5 polymorphisms at the DECR1 gene might be in linkage disequilibrium with the true causal mutation influencing isocitrate dehydrogenase activity and muscle color and pH.

Animals↗
PubMed2004

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.

Animals↗
PubMed2004

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.

Adaptation, Physiological↗