Gijón, Spain
Gijón, Spain

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Cervantes I.,Complutense University of Madrid | 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.


Avarez I.,SERIDA Deva | Fernandez I.,SERIDA Deva | Goyache F.,SERIDA Deva
Animal | Year: 2012

Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (Dm) matrices showed that the pair CalvanaChianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (CT = 1.8%). The Calvana breed made null or negative within-breed contributions (W = 0.0%; CW = 0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (T = 0.7%; CT = 1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (T = 2.1%; CT = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (T = 0.47%; CT = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock. © 2011 The Animal Consortium.


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.


PubMed | INRAB Benin, British Petroleum, University of Koudougou, Fundacion CETEMAS and 2 more.
Type: Comparative Study | Journal: Tropical animal health and production | Year: 2015

A total of 1015 adult cows belonging to nine West African cattle breeds were assessed for 16 body measurements and 18 qualitative traits to ascertain the existence of geographical patterns of variation. Sampling was carried out in 29 different provinces of Mali, Burkina Faso and Benin. For body measurements, taurine breeds took lower average values than the zebu breeds. Sanga cattle took intermediate values. Qualitative traits did not allow to differentiate among cattle groups (taurine, zebu or sanga) or breeds. Principal component analysis identified two factors explaining 56.4 and 9.2% of the variance for body measurements, respectively. Two correspondence analysis dimensions computed on qualitative traits explained a small proportion of the variability (20.8 and 13.5%, respectively). Contour plots were constructed using the eigenvalues computed for each individual and either factor or dimension identified; confidence regions calculated confirmed that body measurements clearly differentiated zebu and taurine cattle breeds while qualitative traits did not. Factor 1 was projected on a geographical map, using provinces as nodes, to assess breed-free variation for body measurements. A pattern of continuous variation from the Sahel area southwards was identified. Probably, breeding decisions promoting the crosses between zebu-like and taurine cattle are underlying this geographical pattern of variation. The implementation of selection strategies aiming at the increase of the productivity of native West African taurine cattle breeds while avoiding looses in trypanotolerant ability would be highly advisable.


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.


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.


Ferencakovic M.,University of Zagreb | Curik I.,University of Zagreb | Perez-Pardal L.,SERIDA Deva | Royo L.J.,SERIDA Deva | And 7 more authors.
Animal Genetics | Year: 2013

Variation in mitochondrial DNA (mtDNA) and Y-chromosome haplotypes was analysed in nine domestic sheep breeds (159 rams) and 21 mouflon (Ovis musimon) sampled in the East Adriatic. Mitochondrial DNA analyses revealed a high frequency of type B haplotypes, predominantly in European breeds, and a very low frequency of type A haplotypes, which are more frequent in some Asian breeds. Mitochondrial haplotype Hmt-3 was the most frequent (26.4%), and 37.1%, 20.8% and 7.6% of rams had haplotypes one, two and three mutations remote from Hmt-3 respectively. In contrast, Y-chromosome analyses revealed extraordinary paternal allelic richness: HY-6, 89.3%; HY-8, 5.0%; HY-18, 3.1%; HY-7, 1.3%; and HY-5, 1.3%. In fact, the number of haplotypes observed is comparable to the number found in Turkish breeds and greater than the number found in European breeds so far. Haplotype HY-18 (A-oY1/135-SRYM18), identified here for the first time, provides a link between the haplotype HY-12 (A-oY1/139-SRYM18) found in a few rams in Turkey and haplotype HY-9 (A-oY1/131-SRYM18) found in one ram in Ethiopia. All mouflons had type B mtDNA haplotypes, including the private haplotype (Hmt-55), and all were paternally monomorphic for haplotype HY-6. Our data support a quite homogeneous maternal origin of East Adriatic sheep, which is a characteristic of European breeds. At the same time, the high number of haplotypes found was surprising and intriguing, and it begs for further analysis. Simultaneous analysis of mtDNA and Y-chromosome information allowed us to detect a large discrepancy between maternal and paternal lineages in some populations. This is most likely the result of breeder efforts to 'upgrade' local populations using rams with different paternal origins. © 2012 The Authors.


Menendez J.,Breeders Association of Gochu Asturcelta ACGA | Alvarez I.,SERIDA Deva | Fernandez I.,SERIDA Deva | Goyache F.,SERIDA Deva
Czech Journal of Animal Science | Year: 2016

The Breeders Association of Gochu Asturcelta (ACGA) initiated a recovery programme with six founders (three boars and three sows) in 2002. Information provided by a total of 3156 records (515 litters, 109 boars, and 309 sows) with father and mother known included in the Gochu Asturcelta herdbook was analyzed. The aim of the analyses was to assess if the mating policy implemented by the breeders association ACGA has been successful in preserving the genetic background of the founders in the present population. Two reference populations were defined: 232 individuals born in 2013 and 2014 (PopO), and 18 individuals born in 2012 and 2013 and kept for reproduction (PopR). Mean inbreeding was very high (0.230 ± 0.078 for the whole pedigree) with mean individual increase in inbreeding (ΔFi) of 0.067 ± 0.021 for PopO and PopR. However, mean ΔFi tended to keep steady values (around 0.07) after 2009. The number of founders identified for PopO and PopR was 4 and 5, respectively. The ratio between the effective number of ancestors (fa) and effective number of founders (fe) was roughly 1 for both PopO and PopR. This suggests that the ACGA's mating policy has avoided an extreme bottleneck in the population. However, drift caused noticeable losses of genetic diversity: ratio between the founder genome equivalents (fg) and fe was around 0.6 for the two reference populations. The current results highlight the need of unbalancing further genetic contributions to the population towards descendants of a very poorly represented founder (Fema 1).


Del Coz J.J.,University of Oviedo | Diez J.,University of Oviedo | Bahamonde A.,University of Oviedo | Goyache F.,SERIDA Deva
Information Sciences | Year: 2012

In most cases, the main goal of machine learning and data mining applications is to obtain good classifiers. However, final users, for instance researchers in other fields, sometimes prefer to infer new knowledge about their domain that may be useful to confirm or reject their hypotheses. This paper presents a learning method that works along these lines, in addition to reporting three interesting applications in the field of population genetics in which the aim is to discover relationships between species or breeds according to their genotypes. The proposed method has two steps: first it builds a hierarchical clustering of the set of classes and then a hierarchical classifier is learned. Both models can be analyzed by experts to extract useful information about their domain. In addition, we propose a new method for learning the hierarchical classifier. By means of a voting scheme employing pairwise binary models constrained by the hierarchical structure, the proposed classifier is computationally more efficient than previous approaches while improving on their performance. © 2012 Elsevier Inc. All rights reserved.


PubMed | SERIDA Deva
Type: Journal Article | Journal: 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 NDama) using 38 microsatellites and various statistical methodologies. West African and East African zebu samples were sequentially used as reference parental populations. Furthermore, NDama 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 NDama population from Congo as parental population 2 gave the more consistent zebu proportion estimates for both the Lobi and the NDama breeds. In any case, the zebu admixture proportions estimated were not negligible and were always higher in the NDama 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.

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