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Cervantes I.,Complutense University of Madrid | Pastor J.M.,Provincial Branch of the Andalusian Regional Government Plaza de la Constitucion | Gutierrez J.P.,Complutense University of Madrid | Goyache F.,SERIDA Deva | Molina A.,University of Cordoba, Spain
Livestock Science | Year: 2011

The aim of this study was to compare different methodologies to compute the effective size when the genealogies are not available (or are shallow) in three rare Spanish ruminant populations. For this purpose the authors used molecular information from three Spanish local ruminant populations (the Pajuna cattle, Payoya goat and Merino de Grazalema sheep populations). Several methods based on molecular or pedigree data were applied to estimate the effective population size in the three studied populations. Estimates based on increase in molecular coancestry (Nefm) in Pajuna (8.5) and Payoya (16.7) populations were 2- and 3-fold lower than those obtained using the linkage disequilibrium method. However, Nefm in Merino de Grazalema population reached a higher value (110.5 vs 86.2). Regarding the effective size using temporal methods (F statistics and coalescence theory), the results for Pajuna were very similar across methodologies with values ranging from 6.0 to 7.8. In the Payoya goat, the results obtained ranged from 15.0 to 33.4. For Merino de Grazalema was not possible to estimate the Ne using temporal methods. Regarding the genealogical methods, pedigrees highly compatible with molecular information were generated from the genotypes of the individuals, the correlations between the molecular and the genealogical coancestry matrix were high from 0.82 to 0.94. The effective population sizes based on individual increase in inbreeding were similar for Pajuna (17.0) and Payoya (18.1) and for Merino de Grazalema was 24.2. The Ne based on an increase in coancestry (Nec) was higher in all cases ranging from 20.2 for Pajuna to 38.3 for Merino de Grazalema. The Nec for Payoya was 27.1. We can conclude that there is no single value of molecular-based Ne for each population, because high ranges for effective size where found across methodologies. However, the assessed ranking was steady: the Pajuna is the most endangered population, followed by Payoya and Merino de Grazalema. When the priority for conservation is of concern, all methods seem to be useful, but it is not possible to combine them. It is recommendable to use the same method across populations to define the risk status of the list of populations. Moreover, if a precise value of Ne is needed, for example, to define the size of sampled animals to be genotyped under a genomic selection scenario, different methodologies would lead to different conclusions. Further research seems to be needed on this issue. © 2010 Elsevier B.V. Source


Menendez J.,Asociacion de Criadores de Gochu Asturcelta ACGA | Goyache F.,SERIDA Deva
Archivos de Zootecnia | Year: 2011

The aim of the present study is the caracterization of the growth of Gochu Asturcelta piglets. In this first approach we studied 191 born weights and 146 weaning weights from 12 sows located in the Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA). The average birth weigth was 1439 ± 279 g, the weaning weigth 12.840 ± 3.055 kg with a weaning age of 42 days and a preweaning daily gain of 268 ± 0.061 g/day. The lineal models adjusted for the analysis of the environmental factors of higher significance for the characters under study showed that the birth weight is not affected by piglet sex, 48 h piglet survival or litter number (p>0.05). The weaning weigth was significantly affected by litter number (p= 0.046) and sow age at birth (p= 0.014). The weaning weight of third birth piglets were significantly higher to the first birth. The preweaning daily gain was significantly affected by litter number, age of the sow at birth and weaning age. The weaning weight was not affected by piglet sex (p= 0.68). The third litter growth 34 g/day faster than first birth litter. The present study is the first approach to the characterization of the production ability of Gochu Asturcelta breed. Source


Goyache F.,SERIDA Deva | Molina A.,University of Cordoba, Spain | Valera M.,University of Seville
Journal of Animal Breeding and Genetics | Year: 2011

We introduce a simple method to estimate effective population size from increase in coancestry (δcjk) for all pairs of individuals j and k in a reference subpopulation. An increase in pairwise coancestry for any pair of individuals j and k can be defined assuming that a hypothetical mating between them would give an individual with an inbreeding coefficient equal to cjk, where cjk is the coancestry coefficient between the individuals j and k. The equivalent measure to discrete generations value (gjk) corresponding to the individual jk can be computed by averaging discrete equivalents generations of its parents (gj and gk). The mean increase in coancestry for all pairs of individuals in a reference subpopulation can be used to estimate a realized effective population size based on coancestries that would provide information on the effective size of a population under random mating. Performance of the new parameter was tested on simulated and empirical (horse) populations with different mating strategies and population structures. The routines needed to compute the introduced parameters have been included in a new version of the program ENDOG. © 2011 Blackwell Verlag GmbH. Source


Alvarez I.,SERIDA Deva | Traore A.,SERIDA Deva | Fernandez I.,SERIDA Deva | Cuervo M.,SERPA S.A. | And 5 more authors.
Molecular Biology Reports | Year: 2014

A total of 350 samples were analyzed to estimate zebu gene proportions into two different taurine cattle breeds of Burkina Faso (Lobi and N'Dama) using 38 microsatellites and various statistical methodologies. West African and East African zebu samples were sequentially used as reference parental populations. Furthermore, N'Dama cattle from Congo, the composite South African Bonsmara cattle breed and a pool of European cattle were used successively as second parental populations. Independently of the methodology applied: (a) the use of West African zebu samples gave higher admixture coefficients than the East African zebu; (b) the higher zebu proportions were estimated when the European cattle was used as parental population 2; and (c) the use of the N'Dama population from Congo as parental population 2 gave the more consistent zebu proportion estimates for both the Lobi and the N'Dama breeds. In any case, the zebu admixture proportions estimated were not negligible and were always higher in the N'Dama cattle than in the Lobi cattle of Burkina Faso. This suggested that the introgression of Sahelian zebu genes into the taurine cattle of Southern West Africa can follow a complex pattern that can depend on local agro-ecological features. The current research pointed out that the estimation of admixture coefficients is highly dependent on both the assumptions underlying the methodologies applied and the selection of parental populations. Our analyses suggest that either too high or nil genetic identity between the parental and the expectedly derived populations must be avoided. © 2014 Springer Science+Business Media. Source


Alvarez I.,SERIDA Deva | Fernandez I.,SERIDA Deva | Lorenzo L.,Centro Ecuestre El Asturcon | Payeras L.,AECABMA | And 2 more authors.
Journal of Animal Breeding and Genetics | Year: 2012

Pedigree information and 179 mtDNA sequences from two endangered Spanish horse breeds, the Asturcón pony (143) and the Mallorquí horse (36), were analysed to asses: (i) the pedigree and molecular maternal genetic diversity of the two breeds; (ii) the concordance between the dam lines recorded in the corresponding studbooks and the mtDNA haplotypes identified; and (iii) to assess the losses of maternal genetic variability occurred from the foundation of the studbooks to present. Up to 50 Asturcón and 18 Mallorquí founder dam lines were identified in the studbooks analysed. Up to 315 Asturcón mares and 51 Mallorquí mares that foaled in the last 5years of recording formed a reference population. Only 35 Asturcón and 13 Mallorquí founder dam lines were represented in their reference populations. Sequences from a total of 38 Asturcón and 12 Mallorquí dam lines could be obtained. The 179 sequences obtained gave 15 different haplotypes, 11 and 9 of them being identified, respectively, in the Asturcón pony and in the Mallorquí horse. Five different haplotypes (roughly two-thirds of the sequences) were shared by the two horse breeds. Most dam lines analysed had a single mtDNA haplotype. However, more than one haplotype was detected within eight of the dam lines in Asturcón pony. The found inconsistencies are likely to result from deficiencies in genebank management. The maternal Ne (mNe) computed using the dam line information was higher in the Asturcón pony (20.5) than in the Mallorquí horse (15.9), while these figures were on the opposite direction for the haplotypic line information (6.4 and 9.4, respectively). The ratio of the computed mNe values to the actual number of founder dam lines were always higher in the Mallorquí horse probably due to a more balanced distribution of individuals kept for reproduction among studs. Consequences for the conservation programmes of the analysed breeds are discussed. © 2012 Blackwell Verlag GmbH. Source

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