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M Pérez-Enciso

Publications and source records attributed to M Pérez-Enciso.

At least 19 recordsLinked to original sources
PubMed2006

Multiple association analysis via simulated annealing (MASSA).

SUMMARY: Genome-wide association studies are now technically feasible and likely to become a fundamental tool in unraveling the ultimate genetic basis of complex traits. However, new statistical and computational methods need to be developed to extract the maximum information in a realistic computing time. Here we propose a new method for multiple association analysis via simulated annealing that allows for epistasis and any number of markers. It consists of finding the model with lowest Bayesian information criterion using simulated annealing. The data are described by means of a mixed model and new alternative models are proposed using a set of rules, e.g. new sites can be added (or deleted), or new epistatic interactions can be included between existing genetic factors. The method is illustrated with simulated and real data. AVAILABILITY: An executable version of the program (MASSA) running under the Linux OS is freely available, together with documentation, at http://www.icrea.es/pag.asp?id=Miguel.Perez.

Algorithms↗
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

Characterization of the porcine FABP5 gene and its association with the FAT1 QTL in an Iberian by Landrace cross.

We have characterized and mapped the porcine fatty acid binding protein 5, epidermal (FABP5) gene. According to linkage and RH mapping, this gene is located close to the FABP4 (fatty acid binding protein 4, adipocyte) gene on swine chromosome 4. We resequenced 4.7 kb of the FABP5 gene in the parental population of an Iberian x Landrace cross (IBMAP), identifying seven SNPs arranged in two distinct FABP5 haplotypes. QTL and association analyses in the IBMAP population showed that this gene is strongly associated with fat deposition. QTL and haplotype analysis revealed that both FABP4 and FABP5 (clustered in mammals) are major candidate genes for the FAT1 QTL; the most likely position for the FAT1 QTL is between these two genes. Finally, our results suggest the presence of more than one QTL affecting fatness traits on porcine chromosome 4.

Animals↗
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↗
PubMed2005

Atlas: a java-based tool for managing genotypes.

With the exponential increase in genotyping capability, it is fundamental to check data consistency and improve genotype management. Atlas is a Java-based application for managing genotypes that also provides a series of tools useful in traceability, parentage testing, and identification, as well as pedigree and marker visualization.

Computational Biology↗
PubMed2005

Large-scale, multibreed, multitrait analyses of quantitative trait loci experiments: the case of porcine X chromosome.

A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10(-43)), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < 10(-15)) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks.

Adipose Tissue↗
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↗
PubMed2004

Qxpak: a versatile mixed model application for genetical genomics and QTL analyses.

MOTIVATION: Current methodology and software for quantitative trait loci (QTL) analyses do not use all available information and are inadequate to deal with the huge amount of QTL analyses to be needed in forecoming genetical genomics' studies. RESULTS: We show that a mixed model statistical framework provides a very flexible tool for QTL modeling in a variety of populations, be it a cross between inbred lines, a within population study, or experiments involving a mixture of populations or crosses. The software allows multitrait and multiQTL analyses, inclusion of infinitesimal genetic value and a batch multitrait option suitable for genetical genomics studies. It also allows massive association studies between single nucleotide polymorphisms and the trait(s) of interest. AVAILABILITY: A software (Qxpak), together with a manual and example files, is freely available for research purposes. So far, the compiled program is available for linux systems, the windows version will follow soon. See http://www.icrea.es/pag.asp?id=Miguel.Perez

Algorithms↗
PubMed2002

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects.

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.

Adipose Tissue↗
PubMed2002

Quantitative trait locus mapping for meat quality traits in an Iberian x Landrace F2 pig population.

An experimental F2 cross between Iberian and Landrace pig strains was performed to map quantitative trait loci (QTL) for diverse productive traits. Here we report results for meat quality traits from 369 F2 animals with records for pH 24 h postmortem (pH 24 h), muscle color Minolta measurements L* (lightness), a* (redness), and b* (yellowness), H* (hue angle), C* (chroma), intramuscular fat (IMF) and haematin pigment content measured in the longissimus thoracis. Pigs were genotyped for 92 markers covering the 18 porcine autosomes (SSC). Results of the genome scan show evidence for QTL for IMF (SSC6; F = 27.16), pH 24 h (SSC3; F = 7.73), haematin pigments (SSC4 and SSC7; F = 8.68 and 9.47 respectively) and Minolta color measurements L* (SSC4 and SSC7; F =16.42 and 7.17 respectively), and a* (SSC4 and SSC8; F = 8.05 and 7.36 respectively). No QTL were observed for the color measurements b*, H*, and C*. Alternative models fitting epistasis between QTL were also tested, but detected epistatic interactions were not significant at a genome-wise level. In this work we identify genomic regions related with meat quality traits. Improvement by traditional selection methods is complicated, and finer mapping would be required for their application in introgression programs.

Animals↗
PubMed2001

Quantitative trait locus analysis in crosses between outbred lines with dominance and inbreeding.

We provide a theoretical framework for quantitative trait locus (QTL) analysis of a crossed population where parental lines may be outbred and dominance as well as inbreeding are allowed for. It can be applied to any pedigree. A biallelic QTL is assumed, and the QTL allele frequencies can be different in each breed. The genetic covariance between any two individuals is expressed as a nonlinear function of the probability of up to 15 possible identity modes and of the additive and dominance effects, together with the allelic frequencies in each of the two parental breeds. The probabilities of each identity mode are obtained at the desired genome positions using a Monte Carlo Markov chain method. Unbiased estimates of the actual genetic parameters are recovered in a simulated F(2) cross and in a six-generation complex pedigree under a variety of genetic models (allele fixed or segregating in the parental populations and additive or dominance action). Results from analyzing an F(2) cross between Meishan and Large White pigs are also presented.

Alleles↗
PubMed2000

Quantitative trait loci mapping in F(2) crosses between outbred lines.

We develop a mixed-model approach for QTL analysis in crosses between outbred lines that allows for QTL segregation within lines as well as for differences in mean QTL effects between lines. We also propose a method called "segment mapping" that is based in partitioning the genome in a series of segments. The expected change in mean according to percentage of breed origin, together with the genetic variance associated with each segment, is estimated using maximum likelihood. The method also allows the estimation of differences in additive variances between the parental lines. Completely fixed random and mixed models together with segment mapping are compared via simulation. The segment mapping and mixed-model behaviors are similar to those of classical methods, either the fixed or random models, under simple genetic models (a single QTL with alternative alleles fixed in each line), whereas they provide less biased estimates and have higher power than fixed or random models in more complex situations, i.e., when the QTL are segregating within the parental lines. The segment mapping approach is particularly useful to determining which chromosome regions are likely to contain QTL when these are linked.

Chromosome Mapping↗
PubMed2000

A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross.

Three Iberian boars were bred to 31 Landrace sows to produce 79 F1 pigs. Six F1 boars were mated to 73 F1 sows. The F2 progeny from 33 full-sib families (250 individuals) were genotyped for seven microsatellites spanning the length of chromosome 4. Least squares procedures for interval mapping were used to detect quantitative trait loci (QTL). A permutation test was used to establish nominal significance levels associated with QTL effects, and resulting probability levels were corrected to a genomewide basis. Observed QTL effects were (genomewide significance, position of maximum significance in centimorgans): percentage of linoleic acid in subcutaneous adipose tissue (< 0.01, 81); backfat thickness (< 0.01, 83); backfat weight (< 0.01, 80); longissimus muscle area (0.02, 83); live weight (0.19, 88); and percentage of oleic acid in subcutaneous adipose tissue (0.25, 81). Gene action was primarily additive. The Iberian genotypes were fatter, slower growing, and had lower linoleic and higher oleic acid contents than Landrace genotypes. The interval from 80 to 83 cM contains the FAT1 and A-FABP loci that have been shown previously to affect fat deposition in pigs. This is the first report of a QTL affecting fatty acid composition of subcutaneous adipose tissue in pigs and provides a guide for the metabolic pathways affected by candidate genes described in this region of chromosome 4.

Adipose Tissue↗