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ABSTRACT: BACKGROUND: When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA. RESULTS: This management method, which detects the 'purest' individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. Scenarios involving several introgression events were more efficient than those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period. CONCLUSIONS: Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach.
Genetics Selection Evolution 05/2013; 45(1):13. · 2.88 Impact Factor
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ABSTRACT: Computer simulations were used to investigate the efficiency of management methods for the conservation of a structured population when local adaptation exists. A subdivided population, with subpopulations adapted to different optima for a quantitative trait under stabilizing selection, was managed in order to maintain the highest genetic diversity in a 10-generation period. Two procedures were compared. For the first, minimum coancestry contributions were carried out independently for each subpopulation, and random migration of individuals was accomplished thereafter. For the second, minimum coancestry contributions from individuals were globally implemented, including an optimal migration design. This optimal method can be adjusted to control local inbreeding to different extents. Adaptation to local optima implies a reduction in the efficiency of the management methods because of the effective failure in the established migrations. For strong selection, the optimal design can be very inefficient, even more than the random migration scheme because the intended migrants have usually low fitness in the recipient subpopulations. However, for more realistic moderate or weak selection, the optimal method is more efficient than random migration, especially if inbreeding depression on fitness is also taken into account. It is concluded that the optimal management method can be recommended in conservation programs with local adaptation of subpopulations, but this issue should be accounted for when designing the management strategies.
The Journal of heredity 03/2013; · 2.05 Impact Factor
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ABSTRACT: The heritability of a quantitative trait is a key parameter to quantify the genetic variation present in a population. Although
estimates of heritability require accurate information on the genetic relationship among individuals, pedigree data is generally
lacking in natural populations. Nowadays, the increasing availability of DNA markers is making possible the estimation of
coancestries from neutral molecular information. In 1996, K. Ritland developed an approach to estimate heritability from the
regression of the phenotypic similarity on the marker-based coancestry. We carried out simulations to analyze the accuracy
of the estimates of heritability obtained by this method using information from a variable number of neutral codominant markers.
Because the main application of the estimator is on populations with no family structure, such as natural populations, its
accuracy was tested under this scenario. However, the method was also investigated under other scenarios, in order to test
the influence of different factors (family structure, assortative mating and phenotypic selection) on the precision. Our results
suggest that the main factor causing a directional bias in the estimated heritability is the presence of phenotypic selection,
and that very noisy estimates are obtained in the absence of a familiar structure and for small population sizes. The estimated
heritabilities from marker-based coancestries showed lower accuracy than the estimated heritabilities from genealogical coancestries.
However, a large amount of bias occurred even in the most favourable situation where genealogical coancestries are known.
The results also indicate that the molecular markers are more suitable to infer coancestry than inbreeding.
Conservation Genetics 04/2012; 8(5):1189-1198. · 1.61 Impact Factor
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ABSTRACT: The maintenance of genetically differentiated populations can be important for several reasons (whether for wild species or domestic breeds of economic interest). When those populations are introgressed by foreign individuals, methods to eliminate the exogenous alleles can be implemented to recover the native genetic background. This study used computer simulations to explore the usefulness of several molecular based diagnostic approaches to recover of a native population after suffering an introgression event where some exogenous alleles were admixed for a few generations. To remove the exogenous alleles, different types of molecular markers were used in order to decide which of the available individuals contributed descendants to next generation and their number of offspring. Recovery was most efficient using diagnostic markers (i.e., with private alleles) and least efficient when using alleles present in both native and exogenous populations at different frequencies. The increased inbreeding was a side-effect of the management strategy. Both values (% of native alleles and inbreeding) were largely dependent on the amount of exogenous individuals entering the population and the number of generations of admixture that occurred prior to management.
PLoS ONE 01/2012; 7(11):e49409. · 4.09 Impact Factor
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ABSTRACT: Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new disease pressures. The turbot is one of the most promising European aquaculture species. Furunculosis, caused by the bacterium Aeromonas salmonicida, produces important losses to turbot industry. An appealing solution is to achieve more robust broodstock, which can prevent or diminish the devastating effects of epizooties. Genomics strategies have been developed in turbot to look for candidate genes for resistance to furunculosis and a genetic map with appropriate density to screen for genomic associations has been also constructed. In the present study, a genome scan for QTL affecting resistance and survival to A. salmonicida in four turbot families was carried out. The objectives were to identify consistent QTL using different statistical approaches (linear regression and maximum likelihood) and to locate the tightest associated markers for their application in genetic breeding strategies.
Significant QTL for resistance were identified by the linear regression method in three linkage groups (LGs 4, 6 and 9) and for survival in two LGs (6 and 9). The maximum likelihood methodology identified QTL in three LGs (5, 6 and 9) for both traits. Significant association between disease traits and genotypes was detected for several markers, some of them explaining up to 17% of the phenotypic variance. We also identified candidate genes located in the detected QTL using data from previously mapped markers.
Several regions controlling resistance to A. salmonicida in turbot have been detected. The observed concordance between different statistical methods at particular linkage groups gives consistency to our results. The detected associated markers could be useful for genetic breeding strategies. A finer mapping will be necessary at the detected QTL intervals to narrow associations and around the closely associated markers to look for candidate genes through comparative genomics or positional cloning strategies. The identification of associated variants at specific genes will be essential, together with the QTL associations detected in this study, for future marker assisted selection programs.
BMC Genomics 11/2011; 12:541. · 4.07 Impact Factor
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ABSTRACT: The turbot (Scophthalmus maximus) is a highly appreciated European aquaculture species. Growth related traits constitute the main goal of the ongoing genetic breeding programs of this species. The recent construction of a consensus linkage map in this species has allowed the selection of a panel of 100 homogeneously distributed markers covering the 26 linkage groups (LG) suitable for QTL search. In this study we addressed the detection of QTL with effect on body weight, length and Fulton's condition factor.
Eight families from two genetic breeding programs comprising 814 individuals were used to search for growth related QTL using the panel of microsatellites available for QTL screening. Two different approaches, maximum likelihood and regression interval mapping, were used in order to search for QTL. Up to eleven significant QTL were detected with both methods in at least one family: four for weight on LGs 5, 14, 15 and 16; five for length on LGs 5, 6, 12, 14 and 15; and two for Fulton's condition factor on LGs 3 and 16. In these LGs an association analysis was performed to ascertain the microsatellite marker with the highest apparent effect on the trait, in order to test the possibility of using them for marker assisted selection.
The use of regression interval mapping and maximum likelihood methods for QTL detection provided consistent results in many cases, although the high variation observed for traits mean among families made it difficult to evaluate QTL effects. Finer mapping of detected QTL, looking for tightly linked markers to the causative mutation, and comparative genomics are suggested to deepen in the analysis of QTL in turbot so they can be applied in marker assisted selection programs.
BMC Genomics 09/2011; 12:473. · 4.07 Impact Factor
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Paulino Martínez,
Carmen Bouza,
Miguel Hermida, Jesús Fernández,
Miguel Angel Toro,
Manuel Vera,
Belén Pardo,
Adrián Millán,
Carlos Fernández,
Román Vilas,
Ana Viñas,
Laura Sánchez,
Alicia Felip,
Francesc Piferrer,
Isabel Ferreiro,
Santiago Cabaleiro
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ABSTRACT: Sex determination in fish is a labile character in evolutionary terms. The sex-determining (SD) master gene can differ even between closely related fish species. This group is an interesting model for studying the evolution of the SD region and the gonadal differentiation pathway. The turbot (Scophthalmus maximus) is a flatfish of great commercial value, where a strong sexual dimorphism exists for growth rate. Following a QTL and marker association approach in five families and a natural population, we identified the main SD region of turbot at the proximal end of linkage group (LG) 5, close to the SmaUSC-E30 marker. The refined map of this region suggested that this marker would be 2.6 cM and 1.4 Mb from the putative SD gene. This region appeared mostly undifferentiated between males and females, and no relevant recombination frequency differences were detected between sexes. Comparative genomics of LG5 marker sequences against five model species showed no similarity of this chromosome to the sex chromosomes of medaka, stickleback, and fugu, but suggested a similarity to a sex-associated QTL from Oreochromis spp. The segregation analysis of the closest markers to the SD region demonstrated a ZW/ZZ model of sex determination in turbot. A small proportion of families did not fit perfectly with this model, which suggests that other minor genetic and/or environmental factors are involved in sex determination in this species.
Genetics 09/2009; 183(4):1443-52. · 4.01 Impact Factor
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ABSTRACT: The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strategies differed in the type of information used to compute global coancestries, the number and type of evaluated individuals, and the system of mating. Genealogical information proved to be very useful (at least for 10 generations of management) to arrange individuals' contributions via the minimization of global coancestry. In fact, the level of expected heterozygosity after 10 generations yielded by this strategy was 88-100% of the maximum possible improvement obtained if the genotype for all loci was known. Marker information was of very limited value if used alone. The amount and degree of polymorphism of markers to be used to compute molecular coancestry had to be high to mimic the performance of the strategy relying on pedigree, especially in the short term (for example, >10 markers per chromosome with 10 alleles each were needed if only the parents' genotype was available). When both sources of information are combined to calculate the coancestry conditional on markers, clear increases in effective population size (Ne) were found, but observed diversity levels (either gene or allelic diversity) in the early generations were quite similar to the ones obtained with pedigree alone. The advantage of including molecular information is greater when information is available on a greater number of individuals (offspring and parents vs. parents only). However, for realistic situations (i.e., large genomes) the benefits of using information on offspring are small. The same conclusions were reached when comparing the use of the different types of information (genealogical or/and molecular) to perform minimum coancestry matings.
Genetics 08/2005; 170(3):1313-21. · 4.01 Impact Factor
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ABSTRACT: Parasitological examination of European otter originating from Extremadura, Spain revealed the presence of a new isosporan species. Ocysts of Isospora lutrae n. sp. are spherical to subspherical, 31.2 (27.5–32) 29.6 (28–31) m and have a smooth wall c. 1m thick. Sporocysts are ellipsoidal, 18.2 (17–19) 14.4 (14–16) m and lack Stieda and substieda bodies. A spherical sporocyst residuum is present, consisting of granules scattered among the sporozoites. Sporozoites are spindle-shaped, 12.4 2.5m and have anterior and posterior refractile bodies. Based on its unique morphologic structure and host, I.lutrae is considered to be new.
Systematic Parasitology 08/2000; 47(1):59-63. · 1.25 Impact Factor
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ABSTRACT: Clustering techniques for the generation of fuzzy models have been used and have shown promising results in many applications
involving complex data. This chapter proposes a new incremental clustering technique to improve the discovery of local structures
in the obtained fuzzy models. This clustering method is evaluated on two data sets and the results are compared with the results
of other clustering methods. The proposed clustering approach is applied for nonlinear Takagi–Sugeno (TS) fuzzy modeling.
This incremental clustering procedure that generates clusters that are used to form the fuzzy rule antecedent part in online
mode is used as a first stage of the learning process.
01/1970: pages 163-178;
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ABSTRACT: Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, half-sibs and unrelated) if there is a previous knowledge of the population structure. Transformations are usually based on arbitrary thresholds, but the possibility of correcting the coancestry estimates via explicit pedigree reconstruction methods has been suggested. Using molecular data for ten highly polymorphic microsatellite loci on a population of turbot (Scophthalmus maximus) with a known genealogy, the behaviour of four pairwise marker-based coancestry estimators and the molecular coancestry has been evaluated. The population consisted on 138 families with 4 full-sib individuals each and one family with 8 full-sib individuals (up to 15 half-sib families were also present due to the sharing of parents between some of the full-sibs families). Our results suggested that transforming the pairwise estimators and the molecular coancestry to family relationships through the establishment of thresholds performs slightly better than the explicit pedigree reconstruction method, when accuracy is measured in a pairwise basis. However, if joint relationships between more than two individuals were tested at a time, the threshold methods led to a high percentage of incongruous triads of full-sib individuals, with Mendelian incompatibilities appearing in congruous full-sib families (more than 70% and 60% in our study, respectively). The explicit pedigree reconstruction approach, due to its nature, is free from such problems. Therefore, the pedigree reconstruction approach seems to be a valuable tool to provide a congruent and compatible pedigree when the pairwise marker-based coancestry matrices or the molecular coancestry need to be transformed.
Aquaculture.
