Departamento de Mejora Genética Animal
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA)
Crta. A Coruńa Km. 7,5. 28040 Madrid
(SPAIN)
Phone: 34-91 3471487
FAX: 34-91 3478743 E-mail
RESEARCH LINES AND SCIENTIFIC INTERESTS
Strategies
for controlling rates of inbreeding in selection and conservation programmes.
Genetic aspects of conservation of species in captivity.
Design and management of conservation programmes.
Development of germplasm banks to store genetic
diversity
Use of molecular markers in conservation
Breeding programmes and QTL detection in aquaculture
Improvement of Aquaculture
production by the use of biotechnological tools (Aquagenomics)
(CONSOLIDER CSD2007-00002)
Ministerio de Educación
y Ciencia.
Novel
tree breeding strategies (NovelTree) (211868)
European Commission.
Conservation and
sustainable management of the Menorquín horse breed
through the genetic and morphologic characterisation. Strategies for the maintenance of the genetic diversity
(RZ2008-000011-00-00)
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria
Management
and analysis of diversity in structured populations in the fields of
conservation of genetic resources and animal breeding. (CGL2009- 13278-C02-02)
Ministerio de Ciencia
e Innovación
J. Porta and J. Fernández ()
Accuracy of coancestry estimators when used in
aquaculture for the distribution of breeders into tanks.
Aquaculture (in preparation)
L. O. Seno, J. Fernández, V. L. Cardoso, L. A. García-Cortes, M. A. Toro, D. O. Santos, L. G.
Albuquerque, de G. M. F. Camargo and H. Tonhati (2011)
Selection
strategies for dairy buffaloes: genetic and economic approach.
Animal (submitted).
E. Sánchez-Molano, A. Cerna, M. A. Toro, J. Fernández, C. Bouza, M. Hermida, B. G. Pardo, S. Cabaleiro and P.Martínez (2011)
Detection of growth-related QTL in turbot (Scophthalmus maximus).
BMC Genomics (submitted).
S. T. Rodríguez-Ramilo, M. A. Toro, C. Bouza,
M. Hermida, B. G. Pardo, S. Cabaleiro,
P. Martínez, and J. Fernández (2011)
QTL
detection for disease resistance related traits in turbot (Scophthalmus maximus).
BMC Genomics (submitted).
C. Amador, M. A. Toro and J. Fernández (2011)
Removing exogenous information using pedigree data.
Conservation Genetics (submitted).
M.A.R. de Cara, J. Fernández, M.A. Toro and B. Villanueva
(2011)
Using genome-wide information to minimise the loss of diversity in
conservation programmes.
Journal of Animal Breeding and Genetics (submitted).
B. Villanueva, J. Fernández, L.A.
García-Cortés, L. Varona, H. D. Daetwyler and
M. A. Toro (2011)
Accuracy of
genome-wide evaluation for disease resistance in aquaculture breeding
programmes.
Journal of Animal Science doi:
10.2527/jas.2010-3814 [PDF]
J.
Fernández, T.H.E.
Meuwissen, M. A. Toro and A. Mäki-Tanila (2011)
Management of genetic diversity in small farm animal
populations.
Animal doi:10.1017/S1751731111000930 [PDF]
M. A. Toro, T.H.E. Meuwissen, J. Fernández, I. Shaat and A. Mäki-Tanila (2011)
Assessing the genetic diversity in small farm animal
populations.
Animal doi:10.1017/S1751731111000498 [PDF]
V. Ávila, J. Fernández, H. Quesada and A. Caballero
(2011)
An experimental evaluation with Drosophila
melanogaster of a novel dynamic system for the
management of subdivided populations in conservation programmes.
Heredity 106: 765–774 [PDF]
G. Gandini, L. Avon, D. Bohte-Wilhelmus, E.
Bay, F. G. Colinet, Z. Choroszy,
C. Díaz, D. Duclos, J. Fernández, N. Gengler, R.
Hoving-Bolink, F. Kearney, T. Lilja,
A. Mäki-Tanila, D. Martín-Collado,
M. Maurice-van Eijndhoven, M. Musella,
F. Pizzi, K. Soini, M. A.
Toro, F. Turri, H. Viinalas,
the EURECA Consortium and S. J. Hiemstra (2010)
Motives and values in farming local cattle breeds in Europe: a survey
on 15 breeds.
Animal Genetic Resources 47: 45–58
[PDF]
S. T. Rodríguez-Ramilo, M. A. Toro and J. Fernández (2010)
Usefulness of the clustering methodologies to discriminate between
purebred and crossbred individuals.
Spanish Journal of Agriculture Research 8(2): 347-355 [PDF]
A. Caballero, S. T.
Rodríguez-Ramilo, V. Ávila and J. Fernández (2010)
Management of genetic diversity of subdivided populations in conservation
programmes.
Conservation Genetics 11:409–419
[PDF]
J.
Fernández and S.
C. González-Martínez (2010)
SOFSOG: a
suite of programs to avoid inbreeding in the design of open pollinated trees
plantation sites.
Molecular Ecology Resources 10: 393-396 [PDF]
S. T. Rodríguez-Ramilo, M. A. Toro and J. Fernández (2009)
Assessing population genetic structure via the maximisation of the
genetic distance.
Genetics Selection Evolution 41: 49 [http://www.gsejournal.org/content/41/1/49]
P. Martínez, C.
Bouza, M. Hermida, J. Fernández, M. A. Toro, M.
Vera, B. Pardo, A. Millán,
C. Fernández, R. Vilas, A. Vińas, L. Sánchez, A. Felip, F. Piferrer, I. Ferreiro and S. Cabaleiro (2009)
Identification
of the main sex-determining region of turbot (Scophthalmus maximus).
Genetics 183: 1443–1452 [PDF]
J. A.
Godoy, M. Casas and J. Fernández (2009)
Genetic
issues in the implementation of Iberian lynx Ex-situ conservation program.
In: Iberian Lynx Ex-situ Conservation: An Interdisciplinary Approach. Ed.: Vargas, A., Breitenmoser, C., Breitenmoser, U. Fundación Biodiversidad, Madrid, Spain.
[http://www.fundacion-biodiversidad.es/images/stories/recursos/home/2009/LIBRO_LINCE_BLOQUE.pdf]
A. Pérez-Figueroa, M. Saura, J. Fernández, M. A.
Toro and A. Caballero (2009)
METAPOP - A
software for the management and analysis of subdivided populations in
conservation programs.
Conservation
Genetics 10:
1097-1099 [PDF]
M. Saura, A. Pérez-Figueroa, J.
Fernández, M. A. Toro and A. Caballero (2009)
Preserving population allele frequencies in ex situ conservation
programs.
Conservation
Biology 22:
1277-1287 [PDF]
M.
A. Toro, J. Fernández and A. Caballero (2009)
Molecular characterization of breeds and its use in conservation.
Livestock Science 120: 174–195
[PDF]
J.
Fernández and S.
C. González-Martínez (2009)
Allocating
trees to avoid the increase of inbreeding: so far, so good.
Conservation
Genetics 10:
45-57 [PDF]
P.
Martínez and J. Fernández (2008)
Estimating Parentage
Relationships Using Molecular Markers in Aquaculture.
In: Aquaculture
Research Trends. Ed.: Stephen H. Schwartz, pp. 59-112. Nova Science
Publishers, Inc. (ISBN: 978-1-60456-217-0)
J. Fernández, M. A. Toro and A. Caballero (2008)
Management of subdivided populations in conservation programs: development of a
novel dynamic system.
Genetics 179: 683-692 [PDF]
S. T. Rodríguez-Ramilo, M. A. Toro, P. Martínez, J. Castro, C. Bouza
and J. Fernández
(2007)
Accuracy of the pairwise methods in the
reconstruction of family relationships using molecular information of turbot (Scophthalmus maximus).
Aquaculture 273: 434-442
[PDF]
S. T. Rodríguez-Ramilo, M. A. Toro, A.
Caballero and J. Fernández
(2007)
The accuracy of a heritability estimator using molecular information.
Conservation Genetics 8: 1189-1198 [PDF]
J.
Fernández, T. Roughsedge, J. A. Woolliams and
B. Villanueva (2006)
Optimisation of the sampling strategy for establishing a gene bank: storing PrP alleles following a scrapie
eradication plan as a case study.
Animal
Science 82:
813-821. [PDF]
M.
A. Toro , J. Fernández and A. Caballero (2006)
Scientific basis for policies in conservation of farm animal genetic resources.
Proceedings of the 8th World Congress on Genetics Applied to
Livestock Production. Communication No. 33-05. [PDF]
J.
Fernández and M.
A. Toro (2006)
A new method to estimate relatedness from molecular markers.
Molecular
Ecology 15:
1657-1667. [PDF]
B.
Villanueva, R. Pong-Wong, J. Fernández and M.
A. Toro (2005)
Benefits
from marker assisted selection under a polygenic genetic model.
Journal
of Animal Science
83: 1747-1752. [PDF]
J.
Fernández, B.
Villanueva, R. Pong-Wong and M. A. Toro (2005)
Efficiency
of the use of molecular markers in conservation programmes.
Genetics 170: 1313-1321. [PDF]
J.
Fernández, J.
Galindo, B. Fernández, A. Pérez-Figueroa, A. Caballero and E. Rolán-Alvarez (2005)
Genetic differentiation and estimation of effective population size and
migration rates in two sympatric ecotypes of the marine snail Littorina saxatilis.
Journal
of Heredity 96: 460-464. [PDF]
J. Fernández, M. A. Toro and A. Caballero (2004)
Managing individuals' contributions to maximize the allelic diversity
maintained in small, conserved populations.
Conservation Biology 18 (5): 1358-1367.
[PDF]
S. T.
Rodríguez-Ramilo, A. Pérez-Figueroa, B. Fernández, J. Fernández and A. Caballero (2004)
Mutation-selection balance accounting for genetic variation for viability in Drosophila
melanogaster as deduced from an inbreeding and
artificial selection experiment.
Journal of Evolutionary Biology 17: 528-541. [PDF]
J. Fernández, M. A. Toro and A. Caballero (2003)
Fixed contributions designs vs. minimization of global coancestry
to control inbreeding in small populations.
Genetics 165: 885-894. [PDF]
J. Vales-Alonso, J. Fernández, F. J. González-Castańo
and A. Caballero (2003)
A parallel optimization approach for controlling allele diversity in
conservation schemes.
Mathematical Biosciences 183 (2): 161-173. [PDF]
J. Fernández, S. T.
Rodríguez-Ramilo, A. Pérez-Figueroa, C. López-Fanjul and A. Caballero (2003)
Lack of nonadditive genetic effects on early fecundity in
Drosophila melanogaster.
Evolution 57 (3): 558-565. [PDF]
J. Fernández, M. A. Toro and A. Caballero (2001)
Practical
implementations of optimal management strategies in conservation programmes: a
mate selection method.
Animal Biodiversity and Conservation 24: 17-24. [PDF]
J. Fernández and A. Caballero (2001)
A comparison of
management strategies for conservation with regard to population fitness.
Conservation Genetics 2: 121-131.
[PDF]
J. Fernández and A. Caballero (2001)
Accumulation of
mutations and equalisation of parental contributions in the conservation of
genetic resources.
Heredity 86: 480-488. [PDF]
J.
Fernández and M.
A. Toro (2001)
Controlling genetic variability by mathematical programming in a
selection scheme on an open-pollinated population of Eucalyptus globulus.
Theoretical
and Applied Genetics 102:
1056-1064. [PDF]
A.
García-Dorado, J. Fernández and C. López-Fanjul (2000)
Temporal uniformity
of the spontaneous mutational variance of quantitative traits in Drosophila melanogaster.
Genetical Research
75: 47-51. [PDF]
M. A. Toro, L. Silió, J. Rodrigáńez, M. C. Rodriguez and J. Fernández (1999)
Optimal use
of genetic markers in conservation programmes.
Genetics
Selection Evolution
31: 255-261. [PDF]
J.
Fernández and M.
A. Toro (1999)
The use of mathematical programming to control inbreeding in selection
schemes.
Journal
of Animal Breeding and Genetics 116: 447-466. [PDF]
J. Fernández and C. López-Fanjul (1997)
Spontaneous mutational
genotype-environment interaction for fitness-related traits in Drosophila melanogaster.
Evolution 51: 856-864. [PDF]
J. Fernández and C. López-Fanjul (1996)
Spontaneous
mutational variances and covariances for
fitness-related traits in Drosophila melanogaster.
Genetics 143: 829-837. [PDF]
MOL_COAN (version 2.0): Software for the calculation of coancestry based on molecular information through a method
of explicit reconstruction of genealogies. Approach does not relay on the knowledge of the allelic frequencies and does
not assume Hardy-Weinberg or linkage equilibrium.
This programme implements the algorithm by Fernández & Toro (Molecular
Ecology 15: 1657-1667)
[Download]
IN_CO_FAM (version 1.0): Software for the detection of incongruous triplets of full-sibs and
incompatible full-sibs families when coancestry is
calculated from molecular information in a pairwise
base
This programme is the one implemented in Rodriguez-Ramilo et al. (Aquaculture
273: 434-442)
[Download]
SOFSOG
(version 1.0):
SOFSOG is a suite of programs which helps to design plantation sites. Distributes the available individuals among different sites
minimising within-site global coancestry.
Then, it yields a plantation design for each site, either following the
classical permutated neighbourhood
strategy or the recently developed method by Fernández and González-Martínez
(Conservation Genetics 10: 45-57). Additionally, the package includes a tool
for calculating the molecular coancestry (Identity By State) from codominant marker
data.
This programme is presented in Fernández and González-Martínez. (Molecular
Ecology Resources, 10: 393-396)
[Download
Windows version] [Download
Mac version]
METAPOP (version 2.0.a1): Metapop
is a new software for management of subdivided populations
in conservation programs. Using molecular marker data or pedigree information,
the software determines the optimal contributions (i.e. number of offspring) of
each individual, the number of migrants, and the particular subpopulations
involved in the exchange of individuals in order to maintain the largest level
of gene diversity in the whole population with a desired control in the rate of
inbreeding. Restrictions can be introduced for the total number of migrants,
and the mating of particular pairs and their contribution. A full genetic
diversity analysis of the population is also carried out.
This programme implements a modification of the algorithm by Fernández et al.
(Genetics 179: 683-692)
[Download]
Full length CV (in Spanish). [PDF]
Updated: 21/07/2011
