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Caballero A, Fernández A, Villanueva B, Toro MA. A comparison of marker-based estimators of inbreeding and inbreeding depression. Genet Sel Evol 2022; 54:82. [PMID: 36575379 PMCID: PMC9793638 DOI: 10.1186/s12711-022-00772-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1 and FLH2), VanRaden (FVR1 and FVR2), Yang and colleagues (FYA1 and FYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD). RESULTS If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with FIBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with FIBD is generally obtained by FLH1 and the best estimator of ΔID is FYA2. The estimators FVR2 and FLH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with FIBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (FHOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (FROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (FPED) show a lower correlation with FIBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations. CONCLUSIONS When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with FIBD and provide good estimates of ΔID. When base population allele frequencies are unknown, FLH1 is the marker frequency-based estimator that is most correlated with FIBD, and FYA2 provides the most accurate estimates of ΔID. Estimates from FROH are also very precise in most scenarios. The estimators FVR2 and FLH2 have the poorest performances.
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Affiliation(s)
- Armando Caballero
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310 Vigo, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, Km 7.5, 28040 Madrid, Spain
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, Km 7.5, 28040 Madrid, Spain
| | - Miguel A. Toro
- grid.5690.a0000 0001 2151 2978Departamento de Producción Agraria, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Abstract
The use of genomic information for prediction of future phenotypes or breeding values for the candidates to selection has become a standard over the last decade. However, most procedures for genomic prediction only consider the additive (or substitution) effects associated with polymorphic markers. Nevertheless, the implementation of models that consider nonadditive genetic variation may be interesting because they (1) may increase the ability of prediction, (2) can be used to define mate allocation procedures in plant and animal breeding schemes, and (3) can be used to benefit from nonadditive genetic variation in crossbreeding or purebred breeding schemes. This study reviews the available methods for incorporating nonadditive effects into genomic prediction procedures and their potential applications in predicting future phenotypic performance, mate allocation, and crossbred and purebred selection. Finally, a brief outline of some future research lines is also proposed.
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Affiliation(s)
- Luis Varona
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain.
- Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain.
| | | | - Miguel A Toro
- Dpto. Producción Agraria, ETS Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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Varona L, Legarra A, Toro MA, Vitezica ZG. Correction to: Genomic Prediction Methods Accounting for Nonadditive Genetic Effects. Methods Mol Biol 2022; 2467:C1. [PMID: 35904754 DOI: 10.1007/978-1-0716-2205-6_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Luis Varona
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | | | - Miguel A Toro
- Dpto. Producción Agraria, ETS Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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4
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Lopera TJ, Lujan JA, Zurek E, Zapata W, Hernandez JC, Toro MA, Alzate JF, Taborda NA, Rugeles MT, Aguilar-Jimenez W. A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals. PLoS One 2021; 16:e0260729. [PMID: 34855852 PMCID: PMC8638974 DOI: 10.1371/journal.pone.0260729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
Intestinal microbiota facilitates food breakdown for energy metabolism and influences the immune response, maintaining mucosal homeostasis. Overall, HIV infection is associated with intestinal dysbiosis and immune activation, which has been related to seroconversion in HIV-exposed individuals. However, it is unclear whether microbiota dysbiosis is the cause or the effect of immune alterations and disease progression or if it could modulate the risk of acquiring the HIV infection. We characterize the intestinal microbiota and determine its association with immune regulation in HIV-exposed seronegative individuals (HESN), HIV-infected progressors (HIV+), and healthy control (HC) subjects. For this, feces and blood were collected. The microbiota composition of HESN showed a significantly higher alpha (p = 0.040) and beta diversity (p = 0.006) compared to HC, but no differences were found compared to HIV+. A lower Treg percentage was observed in HESN (1.77%) than HC (2.98%) and HIV+ (4.02%), with enrichment of the genus Butyrivibrio (p = 0.029) being characteristic of this profile. Moreover, we found that Megasphaera (p = 0.017) and Victivallis (p = 0.0029) also are enriched in the microbiota composition in HESN compared to HC and HIV+ subjects. Interestingly, an increase in Succinivibrio and Prevotella, and a reduction in Bacteroides genus, which is typical of HIV-infected individuals, were observed in both HESN and HIV+, compared to HC. Thus, HESNs have a microbiota profile, similar to that observed in HIV+, most likely because HESN are cohabiting with their HIV+ partners.
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Affiliation(s)
- Tulio J. Lopera
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jorge A. Lujan
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Eduardo Zurek
- Department of System Engineering, Universidad del Norte, Barranquilla, Colombia
| | - Wildeman Zapata
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Juan C. Hernandez
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Miguel A. Toro
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
- Facultad de Medicina, Grupo de Parasitología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Natalia A. Taborda
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Ciencias de la Salud, Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T. Rugeles
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
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Mäki‐Tanila A, Toro MA, Frankham R. Obituary: Richard C. Lewontin 1929‐2021. J Anim Breed Genet 2021. [DOI: 10.1111/jbg.12657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Asko Mäki‐Tanila
- University of Helsinki Helsinki Finland
- Universidad Politécnica de Madrid Madrid Spain
- Macquarie University Sydney NSW Australia
| | - Miguel A. Toro
- University of Helsinki Helsinki Finland
- Universidad Politécnica de Madrid Madrid Spain
- Macquarie University Sydney NSW Australia
| | - Richard Frankham
- University of Helsinki Helsinki Finland
- Universidad Politécnica de Madrid Madrid Spain
- Macquarie University Sydney NSW Australia
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Villanueva B, Fernández A, Saura M, Caballero A, Fernández J, Morales-González E, Toro MA, Pong-Wong R. The value of genomic relationship matrices to estimate levels of inbreeding. Genet Sel Evol 2021; 53:42. [PMID: 33933002 PMCID: PMC8088726 DOI: 10.1186/s12711-021-00635-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. RESULTS Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. CONCLUSIONS Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.
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Affiliation(s)
- Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Bioquímica, Genética E Inmunología, Campus de Vigo, 36310 Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | | | - Miguel A. Toro
- Departamento de Producción Agraria, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Ricardo Pong-Wong
- Genetics and Genomics, The Roslin Institute and the R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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7
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de Lucio H, Toro MA, Camarasa M, Velázquez S, Gago F, Jiménez‐Ruiz A. Pseudoirreversible slow-binding inhibition of trypanothione reductase by a protein-protein interaction disruptor. Br J Pharmacol 2020; 177:5163-5176. [PMID: 32888319 PMCID: PMC7588817 DOI: 10.1111/bph.15250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/02/2020] [Accepted: 08/20/2020] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND AND PURPOSE Peptide P4 was described as a dimerization disruptor of trypanothione reductase (TryR), a homodimeric enzyme essential for survival of trypanosomatids. Determination of the true inhibitory constant (Ki ) for P4 was not achieved because reaction rates continuously decreased with time, even when substrate concentration was kept constant. The aim of this study was to find a suitable kinetic model that could allow characterization of the complex pattern of TryR inhibition caused by P4. EXPERIMENTAL APPROACH After showing the slow-binding and pseudoirreversible activity of P4 against Leishmania infantum trypanothione reductase (Li-TryR), analysis of the curvatures of the reaction progress curves at different inhibitor concentrations allowed us to define the apparent inhibitory constants (Kiapp ) at five different substrate concentrations. Analysis of the changes in Kiapp values allowed precise definition of the type of inhibition. KEY RESULTS Li-TryR inhibition by P4 requires two sequential steps that involve rapid generation of a reversible enzyme-inhibitor complex followed by a pseudoirreversible slow inactivation of the enzyme. Recovery of enzyme activity after inhibitor dissociation is barely detectable. P4 is a non-competitive pseudoirreversible inhibitor of Li- TryR that displays an overall inhibition constant (Ki* ) smaller than 0.02 μM. CONCLUSION AND IMPLICATIONS Li-TryRdimer disruption by peptide P4 is a pseudoirreversible time-dependent process which is non-competitive with respect to the oxidized trypanothione (TS2 ) substrate. Therefore, unlike reversible Li-TryR competitive inhibitors, enzyme inhibition by P4 is not affected by the TS2 accumulation observed during oxidant processes such as the oxidative burst in host macrophages.
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Affiliation(s)
- Héctor de Lucio
- Área de Bioquímica y Biología Molecular, Departamento de Biología de SistemasUniversidad de AlcaláAlcalá de Henares, MadridSpain
| | - Miguel A. Toro
- Centro Nacional de Secuenciación Genómica—CNSGUniversidad de AntioquiaMedellinAntioquiaColombia
| | - María‐José Camarasa
- Departamento de Biomiméticos para el descubrimiento de FármacosInstituto de Química Médica (IQM‐CSIC)MadridSpain
| | - Sonsoles Velázquez
- Departamento de Biomiméticos para el descubrimiento de FármacosInstituto de Química Médica (IQM‐CSIC)MadridSpain
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada Al IQM‐CSICUniversidad de AlcaláAlcalá de Henares, MadridSpain
| | - Antonio Jiménez‐Ruiz
- Área de Bioquímica y Biología Molecular, Departamento de Biología de SistemasUniversidad de AlcaláAlcalá de Henares, MadridSpain
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Toro MA, Villanueva B, Fernández J. The concept of effective population size loses its meaning in the context of optimal management of diversity using molecular markers. J Anim Breed Genet 2019; 137:345-355. [PMID: 31713272 DOI: 10.1111/jbg.12455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/03/2019] [Accepted: 10/11/2019] [Indexed: 11/28/2022]
Abstract
Effective population size is a key parameter in conservation genetics. In the management of conservation programs using pedigree information, there is a consensus that the optimal method for maximizing effective population size is to calculate the contribution of each potential parent (the number of offspring that each individual leaves to the next generation) by minimizing the global pedigree-based coancestry between potential parents weighted by their contributions. When using molecular data, the optimal method for managing genetic diversity will remain the same but now the molecular coancestry calculated from markers will replace the pedigree-based coancestry. However, in this situation, the concept of effective population size loses its meaning because with optimal molecular management, genetic diversity increases in early generations and therefore effective population size takes negative values. Furthermore, in the long term, the molecular effective population size does not attain an asymptotic value but it shows an unpredictable behaviour.
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Affiliation(s)
- Miguel A Toro
- Departamento de Producción Agraria, Universidad Politécnica de Madrid, Madrid, Spain
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9
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Affiliation(s)
- M A Toro
- Universidad Politécnica de Madrid, Madrid, Spain
| | - A Mäki-Tanila
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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10
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Abstract
In the last decade, genomic selection has become a standard in the genetic evaluation of livestock populations. However, most procedures for the implementation of genomic selection only consider the additive effects associated with SNP (Single Nucleotide Polymorphism) markers used to calculate the prediction of the breeding values of candidates for selection. Nevertheless, the availability of estimates of non-additive effects is of interest because: (i) they contribute to an increase in the accuracy of the prediction of breeding values and the genetic response; (ii) they allow the definition of mate allocation procedures between candidates for selection; and (iii) they can be used to enhance non-additive genetic variation through the definition of appropriate crossbreeding or purebred breeding schemes. This study presents a review of methods for the incorporation of non-additive genetic effects into genomic selection procedures and their potential applications in the prediction of future performance, mate allocation, crossbreeding, and purebred selection. The work concludes with a brief outline of some ideas for future lines of that may help the standard inclusion of non-additive effects in genomic selection.
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Affiliation(s)
- Luis Varona
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | - Andres Legarra
- Génétique Physiologie et Systèmes d'Elevage (GenPhySE), Institut National de la Recherche Agronomique de Toulouse, Castanet-Tolosan, France
| | - Miguel A Toro
- Departamento Producción Agraria, ETS Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Zulma G Vitezica
- Génétique Physiologie et Systèmes d'Elevage (GenPhySE), Université de Toulouse, Castanet-Tolosan, France
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11
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Toro MA, Saura M, Fernandez J, Villanueva B. Accuracy of genomic within-family selection in aquaculture breeding programmes. J Anim Breed Genet 2017; 134:256-263. [PMID: 28508478 DOI: 10.1111/jbg.12272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/07/2017] [Indexed: 01/27/2023]
Abstract
In aquaculture breeding programmes, selection within families cannot be applied for traits that cannot be recorded on the candidates (e.g., disease resistance or fillet quality). However, this problem can be overcome if genomic evaluation is used. Within-family genomic evaluation has been proposed for these programmes as large family sizes are available and substantial levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers even in populations in global linkage equilibrium. Here, we compare by computer simulation: (i) within-family and population-wide LD; and (ii) the accuracy of within-family genomic selection when genomic evaluations are carried out either at the population level or within families. The population simulated was composed by a varying number of families of full-sibs (half for training and half for testing). The results indicate that, to practice within-family selection, performing the genomic evaluation separately for each family using only molecular information from the family could be recommended for populations either in linkage equilibrium or with a low level of disequilibrium.
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Affiliation(s)
- M A Toro
- Departamento de Producción Agraria, Universidad Politécnica de Madrid, Madrid, Spain
| | - M Saura
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
| | - J Fernandez
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
| | - B Villanueva
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
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de Lucio H, Gamo AM, Ruiz-Santaquiteria M, de Castro S, Sánchez-Murcia PA, Toro MA, Gutiérrez KJ, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Improved proteolytic stability and potent activity against Leishmania infantum trypanothione reductase of α/β-peptide foldamers conjugated to cell-penetrating peptides. Eur J Med Chem 2017; 140:615-623. [DOI: 10.1016/j.ejmech.2017.09.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/30/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023]
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Lopez-Suarez C, Toro MA, Garcia C. GENETIC HETEROGENEITY INCREASES VIABILITY IN COMPETING GROUPS OF DROSOPHILA HYDEI. Evolution 2017; 47:977-981. [PMID: 28567895 DOI: 10.1111/j.1558-5646.1993.tb01253.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/1992] [Accepted: 11/10/1992] [Indexed: 11/28/2022]
Affiliation(s)
- Cristina Lopez-Suarez
- Area de Xenética, Departamento de Bioloxía Fundamental, Facultade de Bioloxía, Santiago de Compostela, Galicia, Spain
| | - Miguel A Toro
- Departamento de Producción Animal, CIT-INIA, Carretera de la Coruña, Km 7 s/n, Madrid, Spain
| | - Carlos Garcia
- Area de Xenética, Departamento de Bioloxía Fundamental, Facultade de Bioloxía, Santiago de Compostela, Galicia, Spain
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González-Recio O, Toro MA, Bach A. Response: Commentary: Past, present and future of epigenetics applied to livestock breeding. Front Genet 2016; 7:101. [PMID: 27377318 PMCID: PMC4894893 DOI: 10.3389/fgene.2016.00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Affiliation(s)
- Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- *Correspondence: Oscar González-Recio
| | - Miguel A. Toro
- Departamento de Produccion Animal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de MadridMadrid, Spain
| | - Alex Bach
- Department of Ruminant Production, Institució Catalana de Recerca i Estudis Avançats – Institut de Recerca i Tecnologia AgroalimentàriesCaldes de Montbui, Spain
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Abstract
This article reviews the concept of Lamarckian inheritance and the use of the term epigenetics in the field of animal genetics. Epigenetics was first coined by Conrad Hal Waddington (1905–1975), who derived the term from the Aristotelian word epigenesis. There exists some controversy around the word epigenetics and its broad definition. It includes any modification of the expression of genes due to factors other than mutation in the DNA sequence. This involves DNA methylation, post-translational modification of histones, but also linked to regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. There is little evidence of the existence of transgenerational epigenetic inheritance in mammals, which may commonly be confounded with environmental forces acting simultaneously on an individual, her developing fetus and the germ cell lines of the latter, although it could have an important role in the cellular energetic status of cells. Finally, we review some of the scarce literature on the use of epigenetics in animal breeding programs.
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Affiliation(s)
- Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid Spain
| | - Miguel A Toro
- Departamento de Producción Animal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid Madrid, Spain
| | - Alex Bach
- Department of Ruminant Production, Institució Catalana de Recerca i Estudis Avançats - Institut de Recerca i Tecnologia Agroalimentàries, Caldes de Montbui Spain
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16
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Sánchez-Murcia PA, Ruiz-Santaquiteria M, Toro MA, de Lucio H, Jiménez MÁ, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Comparison of hydrocarbon-and lactam-bridged cyclic peptides as dimerization inhibitors of Leishmania infantum trypanothione reductase. RSC Adv 2015. [DOI: 10.1039/c5ra06853c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Helical peptides stabilizedviaall-hydrocarbon or lactam side-chain bridging were investigated as disruptors ofLeishmania infantumtrypanothione reductase.
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Affiliation(s)
| | | | - Miguel A. Toro
- Departamento de Biología de Sistemas
- Universidad de Alcalá
- Madrid
- Spain
| | - Héctor de Lucio
- Departamento de Biología de Sistemas
- Universidad de Alcalá
- Madrid
- Spain
| | | | - Federico Gago
- Departamento de Ciencias Biomédicas
- Unidad Asociada al CSIC
- Universidad de Alcalá
- Madrid
- Spain
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Rodríguez-Ramilo ST, De La Herrán R, Ruiz-Rejón C, Hermida M, Fernández C, Pereiro P, Figueras A, Bouza C, Toro MA, Martínez P, Fernández J. Identification of quantitative trait loci associated with resistance to viral haemorrhagic septicaemia (VHS) in turbot (Scophthalmus maximus ): a comparison between bacterium, parasite and virus diseases. Mar Biotechnol (NY) 2014; 16:265-276. [PMID: 24078233 DOI: 10.1007/s10126-013-9544-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/12/2013] [Indexed: 06/02/2023]
Abstract
One of the main objectives of genetic breeding programs in turbot industry is to reduce disease-related mortality. In the present study, a genome scan to detect quantitative trait loci (QTL) affecting resistance and survival to viral haemorrhagic septicaemia (VHS) was carried out. Three full-sib families with approximately 90 individuals each were genotyped and evaluated by linear regression and maximum likelihood approaches. In addition, a comparison between QTL detected for resistance and survival time to other important bacterial and parasite diseases affecting turbot (furunculosis and scuticociliatosis) was also carried out. Finally, the relationship between QTL affecting resistance/survival time to the virus and growth-related QTL was also evaluated. Several genomic regions controlling resistance and survival time to VHS were detected. Also significant associations between the evaluated traits and genotypes at particular markers were identified, explaining up to 14 % of the phenotypic variance. Several genomic regions controlling general and specific resistance to different diseases in turbot were detected. A preliminary gene mining approach identified candidate genes related to general or specific immunity. This information will be valuable to develop marker-assisted selection programs and to discover candidate genes related to disease resistance to improve turbot production.
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Abstract
In humans, cultural transmission occurs usually by cumulative inheritance, generating complex adaptive behavioral features. Cumulative culture requires key psychological processes (fundamentally imitation and teaching) that are absent or impoverished in non-human primates. In this paper we analyze the role that teaching has played in human cumulative cultural evolution. We assume that a system of cumulative culture generates increasingly adaptive behaviors, that are also more complex and difficult to imitate. Our thesis is that, as cultural traits become more complex, cumulative cultural transmission requires teaching to ensure accurate transmission from one generation to the next. In an increasingly complex cultural environment, we consider that individuals commit errors in imitation. We develop a model of cumulative cultural evolution in a changing environment and show that these errors hamper the process of cultural accumulation. We also show that a system of teaching between parents and offspring that increases the fidelity of imitation unblocks the accumulation and becomes adaptive whenever the gain in fitness compensates the cost of teaching.
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Affiliation(s)
- Laureano Castro
- Centro Asociado de Madrid, UNED, Centro Andrés Manjón, C/Francos Rodríguez 77, 28039 Madrid, Spain.
| | - Miguel A Toro
- Departamento de Producción Animal, ETS Ingenieros Agrónomos, UPM, Ciudad Universitaria, 28040 Madrid, Spain.
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García-Cortés LA, Legarra A, Toro MA. The coefficient of dominance is not (always) estimable with biallelic markers. J Anim Breed Genet 2014; 131:97-104. [PMID: 24397385 DOI: 10.1111/jbg.12076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/29/2013] [Indexed: 11/29/2022]
Abstract
The genetic relationship among individuals at one locus is characterized by nine coefficients of identity. The coefficients of inbreeding, coancestry and dominance (or fraternity) are just linear functions of them. Here, it is shown how they can be estimated using biallelic and triallelic markers using the method of moments, and comparisons are made with other methods based on molecular coancestry or molecular covariance. It is concluded that in the general case of dominance and inbreeding with biallelic markers, only the coefficients of inbreeding and coancestry can be estimated, but neither the single coefficients of identity nor the coefficient of dominance can be estimated. More than two alleles are required for a full estimation as illustrated with the triallelic situation.
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Saura M, Fernández A, Rodríguez MC, Toro MA, Barragán C, Fernández AI, Villanueva B. Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs. PLoS One 2013; 8:e78314. [PMID: 24205195 PMCID: PMC3814548 DOI: 10.1371/journal.pone.0078314] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/11/2013] [Indexed: 01/19/2023] Open
Abstract
Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.
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Affiliation(s)
- María Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - M. Carmen Rodríguez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Miguel A. Toro
- Departamento de Producción Animal, Escuela Técnica Superior de Ingenieros Agrónomos, Madrid, Spain
| | - Carmen Barragán
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Ana I. Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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Toro MA, Sánchez-Murcia PA, Moreno D, Ruiz-Santaquiteria M, Alzate JF, Negri A, Camarasa MJ, Gago F, Velázquez S, Jiménez-Ruiz A. Probing the dimerization interface of Leishmania infantum trypanothione reductase with site-directed mutagenesis and short peptides. Chembiochem 2013; 14:1212-7. [PMID: 23744811 DOI: 10.1002/cbic.201200744] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/22/2013] [Indexed: 11/07/2022]
Abstract
Binding at the interface: We tested the inhibitory activity of a set of peptide sequences derived from an α-helix of the dimeric trypanothione reductase from Leishmania infantum. Replacement of a glutamic acid residue with a lysine promoted monomer dissociation and enzyme inhibition.
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Affiliation(s)
- Miguel A Toro
- Departamento de Biología de Sistemas, Unidad Asociada de I+D+I al CSIC, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
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23
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Toro MA. Jim Crow: a great population geneticist. J Anim Breed Genet 2012; 129:425-6. [PMID: 23148967 DOI: 10.1111/jbg.12015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M A Toro
- Universidad Politécnica de Madrid.
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Castro L, Toro MA. Imitation or innovation? Unselective mixed strategies can provide a better solution. Theory Biosci 2012; 131:273-9. [PMID: 22865234 DOI: 10.1007/s12064-012-0161-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 07/13/2012] [Indexed: 10/28/2022]
Abstract
Current theory about the evolution of social learning in a changing environment predicts the emergence of mixed strategies that rely on some selective combination of social and asocial learning. However, the results of a recent tournament of social learning strategies [Rendell et al. Science 328(5975):208-213, 2010] suggest that the success relies almost entirely on copying to learn behavior. Those authors conclude that mixed strategies are vulnerable to invasion by individuals using social learning strategies alone. Here we perform a competition using unselective strategies that differ only in the degree of social versus asocial learning. We show that, under the same conditions of the aforementioned tournament, a pure social learning strategy can be invaded by an unselectively mixed strategy and attain an equilibrium where the latter is majority. Although existing theory suggests that copying other individuals unselectively is not adaptive, we show that, at this equilibrium, the average individual fitness of the population is higher than for a population of pure asocial learners, overcoming Rogers' paradox in finite populations.
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Rodríguez-Ramilo ST, Fernández J, Toro MA, Bouza C, Hermida M, Fernández C, Pardo BG, Cabaleiro S, Martínez P. Uncovering QTL for resistance and survival time to Philasterides dicentrarchi in turbot (Scophthalmus maximus). Anim Genet 2012; 44:149-57. [PMID: 22690723 DOI: 10.1111/j.1365-2052.2012.02385.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2012] [Indexed: 01/22/2023]
Abstract
Disease resistance-related traits have received increasing importance in aquaculture breeding programs worldwide. Currently, genomic information offers new possibilities in breeding to address the improvement of this kind of traits. The turbot is one of the most promising European aquaculture species, and Philasterides dicentrarchi is a scuticociliate parasite causing fatal disease in farmed turbot. An appealing approach to fight against disease is to achieve a more robust broodstock, which could prevent or diminish the devastating effects of scuticociliatosis on farmed individuals. In the present study, a genome scan for quantitative trait loci (QTL) affecting resistance and survival time to P. dicentrarchi in four turbot families was carried out. The objectives were to identify QTL using different statistical approaches [linear regression (LR) and maximum likelihood (ML)] and to locate significantly associated markers for their application in genetic breeding strategies. Several genomic regions controlling resistance and survival time to P. dicentrarchi were detected. When analyzing each family separately, significant QTL for resistance were identified by the LR method in two linkage groups (LG1 and LG9) and for survival time in LG1, while the ML methodology identified QTL for resistance in LG9 and LG23 and for survival time in LG6 and LG23. The analysis of the total data set identified an additional significant QTL for resistance and survival time in LG3 with the LR method. Significant association between disease resistance-related traits and genotypes was detected for several markers, a single one explaining up to 22% of the phenotypic variance. Obtained results will be essential to identify candidate genes for resistance and to apply them in marker-assisted selection programs to improve turbot production.
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Affiliation(s)
- S T Rodríguez-Ramilo
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain
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26
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Rodríguez-Ramilo ST, Toro MA, Bouza C, Hermida M, Pardo BG, Cabaleiro S, Martínez P, Fernández J. QTL detection for Aeromonas salmonicida resistance related traits in turbot (Scophthalmus maximus). BMC Genomics 2011; 12:541. [PMID: 22047500 PMCID: PMC3216323 DOI: 10.1186/1471-2164-12-541] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 11/02/2011] [Indexed: 11/25/2022] Open
Abstract
Background 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. Results 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. Conclusions 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.
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Affiliation(s)
- Silvia T Rodríguez-Ramilo
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
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Sánchez-Molano E, Cerna A, Toro MA, Bouza C, Hermida M, Pardo BG, Cabaleiro S, Fernández J, Martínez P. Detection of growth-related QTL in turbot (Scophthalmus maximus). BMC Genomics 2011; 12:473. [PMID: 21958071 PMCID: PMC3195100 DOI: 10.1186/1471-2164-12-473] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 09/29/2011] [Indexed: 01/27/2023] Open
Abstract
Background 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. Results 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. Conclusions 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.
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Affiliation(s)
- Enrique Sánchez-Molano
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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Moreno A, Salgado C, Piqueras P, Gutiérrez JP, Toro MA, Ibáñez-Escriche N, Nieto B. Restricting inbreeding while maintaining selection response for weight gain in Mus musculus. J Anim Breed Genet 2011; 128:276-83. [PMID: 21749474 DOI: 10.1111/j.1439-0388.2011.00933.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An experiment with mice was designed to test the relative efficiency of three selection methods that help to minimize the rate of inbreeding during selection. A common house mice (Mus musculus) population was selected for 17 generations to increase the weight gain between 21 and 42 days. The population was split at random into three lines A, B and C where three selection methods were applied: individual selection and random mating, weighted selection with random mating and individual selection with minimum coancestry mating, respectively. There were three replicates for each line. Cumulated selection response was similar in the three lines, but there were differences in the level of inbreeding attained (in percentage): 31.24 (method A), 24.72 (method B) and 27.88 (method C). As consequence, lines B and C (weighted selection and minimum coancestry) showed a lower value of deterioration of fitness traits (the intrauterine mortality and the mortality at birth) than line A (random mating).
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Affiliation(s)
- A Moreno
- Departamento de Producción Animal, ETS Ingenieros Agrónomos, UPM, Ciudad Universitaria s/n, Madrid, Spain
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Villanueva B, Fernández J, García-Cortés LA, Varona L, Daetwyler HD, Toro MA. Accuracy of genome-wide evaluation for disease resistance in aquaculture breeding programs. J Anim Sci 2011; 89:3433-42. [PMID: 21742941 DOI: 10.2527/jas.2010-3814] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Current aquaculture breeding programs aimed at improving resistance to diseases are based on challenge tests, where performance is recorded on sibs of candidates to selection, and on selection between families. Genome-wide evaluation (GWE) of breeding values offers new opportunities for using variation within families when dealing with such traits. However, up-to-date studies on GWE in aquaculture programs have only considered continuous traits. The objectives of this study were to extend GWE methodology, in particular the Bayes B method, to analyze dichotomous traits such as resistance to disease, and to quantify, through computer simulation, the accuracy of GWE for disease resistance in aquaculture sib-based programs, using the methodology developed. Two heritabilities (0.1 and 0.3) and 2 disease prevalences (0.1 and 0.5) were assumed in the simulations. We followed the threshold liability model, which assumes that there is an underlying variable (liability) with a continuous distribution and assumed a BayesB model for the liabilities. It was shown that the threshold liability model used fits very well with the BayesB model of GWE. The advantage of using the threshold model was clear when dealing with disease resistance dichotomous phenotypes, particularly under the conditions where linear models are less appropriate (low heritability and disease prevalence). In the testing set (where individuals are genotyped but not measured), the increase in accuracy for the simulated schemes when using the threshold model ranged from 4 (for heritability equal to 0.3 and prevalence equal to 0.5) to 16% (for heritability and prevalence equal to 0.1) when compared with the linear model.
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Affiliation(s)
- B Villanueva
- Departamento de Mejora Genética Animal, INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Carretera de La Coruña km 7,5, 28040 Madrid, Spain.
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Abstract
Estimation of non-additive genetic effects in animal breeding is important because it increases the accuracy of breeding value prediction and the value of mate allocation procedures. With the advent of genomic selection these ideas should be revisited. The objective of this study was to quantify the efficiency of including dominance effects and practising mating allocation under a whole-genome evaluation scenario. Four strategies of selection, carried out during five generations, were compared by simulation techniques. In the first scenario (MS), individuals were selected based on their own phenotypic information. In the second (GSA), they were selected based on the prediction generated by the Bayes A method of whole-genome evaluation under an additive model. In the third (GSD), the model was expanded to include dominance effects. These three scenarios used random mating to construct future generations, whereas in the fourth one (GSD + MA), matings were optimized by simulated annealing. The advantage of GSD over GSA ranges from 9 to 14% of the expected response and, in addition, using mate allocation (GSD + MA) provides an additional response ranging from 6% to 22%. However, mate selection can improve the expected genetic response over random mating only in the first generation of selection. Furthermore, the efficiency of genomic selection is eroded after a few generations of selection, thus, a continued collection of phenotypic data and re-evaluation will be required.
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Tapio M, Ozerov M, Tapio I, Toro MA, Marzanov N, Cinkulov M, Goncharenko G, Kiselyova T, Murawski M, Kantanen J. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia. BMC Genet 2010; 11:76. [PMID: 20698974 PMCID: PMC2931448 DOI: 10.1186/1471-2156-11-76] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 08/10/2010] [Indexed: 11/19/2022] Open
Abstract
Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.
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Affiliation(s)
- Miika Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, 31600 Jokioinen, Finland
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Boettcher PJ, Tixier-Boichard M, Toro MA, Simianer H, Eding H, Gandini G, Joost S, Garcia D, Colli L, Ajmone-Marsan P. Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources. Anim Genet 2010; 41 Suppl 1:64-77. [PMID: 20500756 DOI: 10.1111/j.1365-2052.2010.02050.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.
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Affiliation(s)
- P J Boettcher
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome 00153, Italy.
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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Rodríguez-Ramilo ST, Toro MA, Fernández J. Assessing population genetic structure via the maximisation of genetic distance. Genet Sel Evol 2009; 41:49. [PMID: 19900278 PMCID: PMC2776585 DOI: 10.1186/1297-9686-41-49] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 11/09/2009] [Indexed: 01/23/2023] Open
Abstract
Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm) of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium, performs well under different simulated scenarios and with real data. Therefore, it could be a useful tool to determine genetically homogeneous groups, especially in those situations where the number of clusters is high, with complex population structure and where Hardy-Weinberg and/or linkage equilibrium are present.
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Affiliation(s)
- Silvia T Rodríguez-Ramilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Crta, A Coruña Km, 7,5, 28040 Madrid, Spain.
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Abstract
Optimization of contributions of parents to progeny by minimizing the average coancestry of the progeny is an effective strategy for maintaining genetic diversity in ex situ conservation programs, but its application on the basis of molecular markers has the negative collateral effect of homogenizing the allelic frequencies at each locus. Because one of the objectives of a conservation program is to preserve the genetic composition of the original endangered population, we devised a method in which markers are used to maintain the allele frequency distribution at each locus as closely as possible to that of the native population. Contributions of parents were obtained so as to minimize changes in allele frequency for a set of molecular markers in a population of reduced size. We used computer simulations, under a range of scenarios, to assess the effectiveness of the method in comparison with methods in which contributions of minimum coancestry are sought, either making use of molecular markers or genealogical information. Our simulations indicated that the proposed method effectively maintained the original distribution of allele frequencies, particularly under strong linkage, and maintained acceptable levels of genetic diversity in the population. Nevertheless, contributions of minimum coancestry determined from pedigree information but ignoring the genealogy previous to the conservation program, was the most effective method for maintaining allelic frequencies in realistic situations.
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Affiliation(s)
- María Saura
- Departamento Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
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Estellé J, Gil F, Vázquez JM, Latorre R, Ramírez G, Barragán MC, Folch JM, Noguera JL, Toro MA, Pérez-Enciso M. A quantitative trait locus genome scan for porcine muscle fiber traits reveals overdominance and epistasis. J Anim Sci 2008; 86:3290-9. [PMID: 18641172 DOI: 10.2527/jas.2008-1034] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Muscle histochemical characteristics are decisive determinants of meat quality. The relative percentage and diameters of the different muscular fiber types influence crucial aspects of meat such as color, tenderness, and ultimate pH. Despite its relevance, however, the information on muscle fiber genetic architecture is scant, because histochemical muscle characterization is a laborious task. Here we report a complete QTL scan of muscle fiber traits in 160 animals from a F(2) cross between Iberian and Landrace pigs using 139 markers. We identified 20 genome regions distributed along 15 porcine chromosomes (SSC1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, and X) with direct and(or) epistatic effects. Epistasis was frequent and some interactions were highly significant. Chromosomes 10 and 11 seemed to behave as hubs; they harbored 2 individual QTL, but also 6 epistatic regions. Numerous individual QTL effects had cryptic alleles, with opposite effects to phenotypic pure breed differences. Many of the QTL identified here coincided with previous reports for these traits in the literature, and there was overlapping with potential candidate genes and previously reported meat quality QTL.
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Affiliation(s)
- J Estellé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Castro L, Toro MA. Iterated prisoner's dilemma in an asocial world dominated by loners, not by defectors. Theor Popul Biol 2008; 74:1-5. [PMID: 18490041 DOI: 10.1016/j.tpb.2008.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 04/01/2008] [Accepted: 04/13/2008] [Indexed: 11/29/2022]
Abstract
Cooperation among genetically unrelated individuals can arise when pairs of individuals interact repeatedly in the Prisoner's Dilemma. However, the conditions allowing the evolution of reciprocal cooperation become extremely restrictive as the size of the cooperative group increases, because defectors can exploit cooperators more efficiently in larger groups. Here we consider three strategies: Tit for Tat, defector, and loner. Loner beats defector in a non-cooperative world. However, a cooperative strategy Tit for Tat (TFT(0)) that stops cooperation after the first iteration when there is at least one defector in the group, can invade a world of loners, even in sizable groups, if both the TFT(0) and the defector strategies arise at the same frequency by mutation.
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Affiliation(s)
- Laureano Castro
- Departamento de Mejora Genética Animal, SGIT-INIA, Carretera de La Coruña km. 7, 28040 Madrid, Spain
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López-Fanjul C, Fernández A, Toro MA. The effect of dominance on the use of the QST - FST contrast to detect natural selection on quantitative traits. Genetics 2007; 176:725-7. [PMID: 17339213 PMCID: PMC1893017 DOI: 10.1534/genetics.106.062901] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
We propose that assortative mating can arise through a mechanism of sexual selection by active female choice of partners based on a 'self-seeking like' decision rule. Using a mathematical model, we show that a gene can be selected that make females to choose mates that are similar to themselves with respect to an arbitrary tag, even if two independent and unlinked genes determine the preference and the tag. The necessary requisite for this process to apply is an asymmetry between partners, such that the female can choose the male but this one must always accept to mate. The fitness advantage is due to linkage disequilibrium built up between both genes. Simulations have been run to check the algebraic results and to analyse the influence of several factors on the evolution of the system. Any factor that favors linkage disequilibrium also favors the evolution of the preference allele. Moreover, in a large population subdivided in small subpopulations connected by migration, the assortative mating homogenizes the population genotypic structure for the tags in contrast to random mating that maintains most of the variation.
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Affiliation(s)
- Laureano Castro
- Departamento de Mejora Genética Animal, Instituto de Investigacion y Tecnologia Agraria y Alimentaria, SGIT-INIA, Carretera de La Coruña km. 7, 28040 Madrid, Spain
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Abstract
We show that mutual benefit cooperation can favor the evolution of a preference to interact with individuals that are similar to themselves with respect to one or several arbitrary cultural tags. One necessary requisite to obtain this result is an asymmetry between partners in such a way that one of them (actor) proposes the cooperation and elects the partner, whereas the other (receiver) never rejects the offer because cooperation always reports benefits. The advantage of individuals possessing allele for preferential assortment is due to receiving more offers of mutually beneficial cooperation when there is linkage disequilibrium between the assortment locus and the cultural tags. An especially favorable scenario for the evolution of such preference is a subdivided metapopulation. In this case, the homogeneity within populations and the divergence between populations is favored, facilitating the existence of ethnic groups.
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Affiliation(s)
- Laureano Castro
- Departamento de Mejora Genética Animal, SGIT-INIA, Carretera de La Coruña km. 7, 28040 Madrid, Spain
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Abstract
Four major problems can affect the efficiency of methods developed to estimate relatedness between individuals from information of molecular markers: (i) some of them are dependent on the knowledge of the true allelic frequencies in the base population; (ii) they assume that all loci are unlinked and in Hardy-Weinberg and linkage equilibrium; (iii) pairwise methods can lead to incongruous assignations because they take into account only two individuals at a time; (iv) most are usually constructed for particular structured populations (only consider a few relationship classes, e.g. full-sibs vs. unrelated). We have developed a new approach to estimate relatedness that is free from the above limitations. The method uses a 'blind search algorithm' (actually simulated annealing) to find the genealogy that yield a co-ancestry matrix with the highest correlation with the molecular co-ancestry matrix calculated using the markers. Thus (i and ii) it makes no direct assumptions about allelic frequencies or Hardy-Weinberg and linkage equilibrium; (iii) it always provide congruent relationships, as it considers all individuals at a time; (iv) degrees of relatedness can be as complex as desired just increasing the 'depth' (i.e. number of generations) of the proposed genealogies. Computer simulations have shown that the accuracy and robustness against genotyping errors of this new approach is comparable to that of other proposed methods in those particular situations they were developed for, but it is more flexible and can cope with more complex situations.
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Affiliation(s)
- J Fernández
- Departamento de Mejora Genética Animal. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.
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Abstract
Within the area of sex allocation, one of the topics that has attracted a lot of attention is the sex ratio problem. Fisher (1930) proposed that equal numbers of males and females have been promoted by natural selection and it has an adaptive significance. But the empirical success of Fisher's theory remains doubtful because a sex ratio of 0.50 is also expected from the chromosomal mechanism of sex determination. Another way of approaching the subject is to consider that Fisher's argument relies on the underlying assumption that offspring inherit their parent's tendency in biased sex ratio and therefore that genetic variance for this trait exists. Here, we analyzed sex ratio data of 56,807 piglets coming from 550 boars and 1893 dams. In addition to classical analysis of heterogeneity we performed analyses fitting linear and threshold animal models in a Bayesian framework using Gibbs sampling techniques. The marginal posterior mean of heritability was 2.63 x 10(-4) under the sire linear model and 9.17 x 10(-4) under the sire threshold model. The probability of the hypothesis p(h(2) = 0) fitting the last model was 0.996. Also, we did not detect any trend in sex ratio related to maternal age. From an evolutionary point of view, the chromosomal sex determination acts as a constraint that precludes control of offspring sex ratio in vertebrates and it should be included in the general theory of sex allocation. From a practical view that means that the sex ratio in domestic species is hardly susceptible to modification by artificial selection.
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Affiliation(s)
- M A Toro
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain.
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López-Fanjul C, Fernández A, Toro MA. The effect of genetic drift on the variance/covariance components generated by multilocus additive x additive epistatic systems. J Theor Biol 2005; 239:161-71. [PMID: 16242726 DOI: 10.1016/j.jtbi.2005.08.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 05/10/2005] [Accepted: 07/23/2005] [Indexed: 11/19/2022]
Abstract
The effect of population bottlenecks on the components of the genetic variance/covariance generated by n neutral independent additive x additive loci has been studied theoretically. In its simplest version, this situation can be modelled by specifying the allele frequencies and homozygous effects at each locus, and an additional factor measuring the strength of the n-th order epistatic interaction. The variance/covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t bottlenecks of size N (derived components). Formulae were obtained giving the derived components (and the between-line variance) as functions of the ancestral ones (alternatively, in terms of allele frequencies and effects) and the corresponding inbreeding coefficient F(t). The n-th order derived component of the genetic variance/covariance is continuously eroded by inbreeding, but the remaining components may increase initially until a critical F(t) value is attained, which is inversely related to the order of the pertinent component, and subsequently decline to zero. These changes can be assigned to the between-line variances/covariances of gene substitution and epistatic effects induced by drift. Numerical examples indicate that: (1) the derived additive variance/covariance component will generally exceed its ancestral value unless epistasis is weak; (2) the derived epistatic variance/covariance components will generally exceed their ancestral values unless allele frequencies are extreme; (3) for systems showing equal ancestral additive and total non-additive variance/covariance components, those including a smaller number of epistatic loci may generate a larger excess in additive variance/covariance after bottlenecks than others involving a larger number of loci, provided that F(t) is low. Our results indicate that it is unlikely that the rate of evolution may be significantly accelerated after population bottlenecks, in spite of occasional increments of the derived additive variance over its ancestral value.
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Affiliation(s)
- Carlos López-Fanjul
- Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense, 28040 Madrid, Spain.
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Abstract
This study investigated, through stochastic computer simulation, the extra gains expected from marker-assisted selection (MAS) in an infinitesimal model with linkage. The trait under selection was assumed to be controlled by 2,000 loci of additive small effect and evenly distributed in c chromosomes of one Morgan each (and c = 5, 10, 20, or 30). This approach differs from previous studies on the benefits of MAS that have considered mixed inheritance models. Marker information was used together with pedigree information to compute the relationship matrix used in BLUP genetic evaluations. The MAS schemes were compared with schemes where genetic evaluations were performed using standard BLUP (i.e., the relationship matrix is obtained using pedigree information only). When the number of markers was large enough (approximately one marker every 10 cM), there were increases in the accuracy of selection with MAS, and this led to extra gains compared with standard BLUP for all genome sizes considered. The benefit from MAS increased over generations. At the last generation of selection (Generation 10), the response from MAS was 11, 9, 7, and 5% greater than with standard BLUP for genomes with 5, 10, 20, and 30 chromosomes, respectively. Thus, although small, gains from MAS were nonetheless detectable for genome sizes typical of livestock populations.
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Affiliation(s)
- B Villanueva
- Scottish Agricultural College, Edinburgh EH9 3JG, UK.
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Salgado C, Nieto B, Toro MA, López-Fanjul C, García-Dorado A. Inferences on the role of insertion in a mutation accumulation experiment with Drosophila melanogaster using RAPDs. ACTA ACUST UNITED AC 2005; 96:576-81. [PMID: 15994415 DOI: 10.1093/jhered/esi076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The genetic variability for RAPDs band pattern was studied in a set of 157 mutation accumulation (MA) lines of Drosophila melanogaster. These MA lines were derived from the same isogenic base population and subsequently maintained by full-sib mating during 132 generations. The ancestral pattern of the original isogenic base can be unambiguously established as the consensus pattern of the MA lines and, because these lines are expected to be homozygous, dominance for band pattern is not a concern. Only repeatable changes in band pattern were considered. The number of ancestral bands detected implies that nine-nucleotide targets are enough for repeatable PCR amplification. Compared with the ancestral pattern, one MA line lost one band and two MA lines gained a new one. These results can be accounted for by the insertion of transposable elements occurring at a rate 0.07 < i < 0.21 per whole haploid genome and generation. This range is typical for Drosophila and consistent with the previously observed mobility for the roo family, supporting the generality of previous estimates of spontaneous mutation rates for morphological and fitness traits based on these MA lines. The sequence of one of the new bands suggests that the Idefix family is also active in the lines.
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Affiliation(s)
- C Salgado
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid
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Castro L, Toro MA. Mutual benefit can promote the evolution of preferential interactions and in this way can lead to the evolution of true altruism. Theor Popul Biol 2004; 65:239-47. [PMID: 15066420 DOI: 10.1016/j.tpb.2004.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Indexed: 11/25/2022]
Abstract
We analyse the evolution of the assortment of encounters through active choice of companions among individuals that interact cooperatively in a situation of mutual benefit. Using a simple mathematical model, we show that mutual benefit can favour the evolution of a preference to interact with individuals that are similar to themselves with respect to an arbitrary tag even when both the preference and the tag depend on two independent and unlinked genes. Two necessary requisites to obtain this result are: (i) a small population or a large subdivided metapulation and (ii) an asymmetry between partners in such a way that one of them (donor) proposes the cooperation and elects the partner, whereas the other (receiver) never rejects the offer. We also show that mutual benefit can be the starting point for the evolution of altruistic behaviours as long as there are preferential interactions. This requires that the tag used in the election of partners is the altruistic or selfish behaviour itself.
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Affiliation(s)
- Laureano Castro
- Departamento de Mejora Genética Animal, SGIT-INIA, Carretera de La Coruña km. 7, Madrid 28040, Spain
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Abstract
The effect of population bottlenecks on the components of the genetic covariance generated by two neutral independent epistatic loci has been studied theoretically (additive, covA; dominance, covD; additive-by-additive, covAA; additive-by-dominance, covAD; and dominance-by-dominance, covDD). The additive-by-additive model and a more general model covering all possible types of marginal gene action at the single-locus level (additive/dominance epistatic model) were considered. The covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of the allele frequencies and effects at each locus, the corresponding epistatic effects and the inbreeding coefficient Ft. These expressions show that the contribution of nonadditive loci to the derived additive covariance (covAt) does not linearly decrease with inbreeding, as in the pure additive case, and may initially increase or even change sign in specific situations. Numerical examples were also analyzed, restricted for simplicity to the case of all covariance components being positive. For additive-by-additive epistasis, the condition covAt > covA only holds for high frequencies of the allele decreasing the metric traits at each locus (negative allele) if epistasis is weak, or for intermediate allele frequencies if it is strong. For the additive/dominance epistatic model, however, covAt > covA applies for low frequencies of the negative alleles at one or both loci and mild epistasis, but this result can be progressively extended to intermediate frequencies as epistasis becomes stronger. Without epistasis the same qualitative results were found, indicating that marginal dominance induced by epistasis can be considered as the primary cause of an increase of the additive covariance after bottlenecks. For all models, the magnitude of the ratio covAt/covA was inversely related to N and t.
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Affiliation(s)
- Carlos López-Fanjul
- Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense, 28040 Madrid, Spain.
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Abstract
Populations with small census sizes are at risk because of the loss of genetic variability and the increase of inbreeding and its harmful consequences. For situations with different numbers of males and females, several hierarchical designs have been proposed to control inbreeding through the fixation of individuals' contributions. An alternative method, based on the minimization of global coancestry, has been proposed to determine contributions as to yield of the lowest levels of inbreeding in the population. We use computer simulations to assess the relative efficiency of the different methods. The results show that minimizing the global coancestry leads to equal or lower levels of inbreeding in the short and medium term, although one of the hierarchical designs provides lower asymptotic inbreeding rates and, thus, less net inbreeding in the long term. We also investigate the performance of the alternative methods against departures from the ideal conditions, such as inbred or differentially related base individuals and random failures in the expected contributions. The method of minimization of global coancestry turns out to be more flexible and robust under these realistic situations.
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Affiliation(s)
- J Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain.
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