Jose Luis Vega-Pla - Academia.edu (original) (raw)

Papers by Jose Luis Vega-Pla

PLoS ONE, 2013

Several studies based on a variety of genetic markers have attempted to establish the origins of ... more Several studies based on a variety of genetic markers have attempted to establish the origins of horse domestication. Thus far a discrepancy between the results of mitochondrial DNA analysis, which show high levels of diversity, and results from the Y-chromosome, with almost no genetic variability, has been identified. Most previous work on the horse Y-chromosome has focused on widespread, popular breeds or local Asian breeds. It is possible that these breeds represent a reduced set of the genetic variation present in the species. Additional genetic variation may be present in local breeds and ancient feral populations, such as the Retuertas horse in Spain. In this study we analyzed the Y-chromosome of the Retuertas horse, a feral horse population on the Iberian Peninsula that is at least several hundred years old, and whose genetic diversity and morphology suggests that it has been reproductively isolated for a long time. Data from the Retuertas horse was compared to another 11 breeds from the region (Portugal, Spain and France) or likely of Iberian origin, and then to data from 15 more breeds from around the globe. We sequenced 31 introns, Zinc finger Y-chromosomal protein (ZFY) and anonymous Y-linked fragments and genotyped 6 microsatellite loci found on the Y-chromosome. We found no sequence variation among all individuals and all breeds studied. However, fifteen differences were discovered between our data set and reference sequences in GenBank. We show that these likely represent errors within the deposited sequences, and suggest that they should not be used as comparative data for future projects.

Research in Veterinary Science, 2002

The genetic variability within the Uruguayan Creole horse and its relationship to a group of geog... more The genetic variability within the Uruguayan Creole horse and its relationship to a group of geographically or historically related breeds (Spanish Pure-bred, Barb, Quarter horse, Paso Fino, Peruvian Paso, Arabian and Thoroughbred horse), was evaluated using 25 loci (seven of blood groups, nine of protein polymorphisms and nine microsatellites) analyzed on a total of 145 Uruguayan Creole horses. In this study, blood group and protein polymorphism variants that are considered to be breed markers of Spanish Pure-bred and Barb horses were detected in the Creole breed. Conversely, some microsatellites and protein polymorphisms alleles were found uniquely in the Creole horse. American horse breeds together with Barb and Arabian horses clearly formed a separate cluster from the Spanish pure-bred and Thoroughbred breeds, as shown by an UPGMA dendrogram based on Nei's standard genetic distance. Data in this study provided evidence for considerable genetic variation within Uruguayan Creole horses and of a distinctive breed profile. Both traits were most likely inherited from the XVIth century Spanish horses, more closely related to Barb than to Spanish Pure-bred.

PLoS ONE, 2012

Background: American Creole cattle presumably descend from animals imported from the Iberian Peni... more Background: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources.

Pesquisa Agropecuária Brasileira, 2008

The objective of this work was to evaluate the genetic diversity of Brazilian Pantaneiro horse by... more The objective of this work was to evaluate the genetic diversity of Brazilian Pantaneiro horse by microsatellite markers, investigate the effect of genetic bottlenecks and estimate genetic differentiation among four horse breeds. Genetic variation was estimated through allele ...

Livestock Science, 2008

The Tzotziles, a Mayan native group located in Chiapas, Southern Mexico, have sheep breeding as o... more The Tzotziles, a Mayan native group located in Chiapas, Southern Mexico, have sheep breeding as one of their principal means of subsistence. Sheep were introduced in the Americas by the Spaniards in the first half of the XVI Century. Three populations of sheep from Chiapas-Café, Chamula and Chiapas-were typed with 27 microsatellites. Genetic distances were calculated for three Iberian breeds, Spanish Merino, Churra, two Canary Islands breeds, Canaria and Palmera, and the French Mutton Merino (Precoce). In the case of Chiapas sheep most of the markers showed Hardy-Weinberg equilibrium and the fixation index of Fst (0.095) showed a moderate level of genetic differentiation. The three distinct sheep subpopulations (Café, Chamula and Chiapas) are genetically differentiated inside the Chiapas sheep population. These breeds could be historically related to Spanish sheep populations, but have diverged significantly as a result of genetic drift and selection.

Livestock Science, 2006

A total of 393 individuals belonging to the Canary Goat Group were typed with 27 microsatellites.... more A total of 393 individuals belonging to the Canary Goat Group were typed with 27 microsatellites. A mean of 5.91 alleles per population per marker was typed, the gene diversity varied between 0.29 and 0.84 and F IS values between 0.45 and À0.48. The fixation index F ST was only 0.04 demonstrating a poor level of interbreed differentiation. The unrooted neighbour-joining tree was built from Reynolds distances, the individual tree from Das distances and the correspondence analysis detected admixtures between the populations. Microsatellite analysis is one of the best tools to characterize and define a breed and to support the traditional methods for goat breed differentiation based exclusively on morphological criteria. In this way, the existence of four populations in the Canary Goat Group was recognized although poorly differentiated. The Palmera, South Tenerife and North Tenerife have enough genetic evidences to be considered as breeds. Remaining populations from Fuerteventura Island, known as the Majorera breed, and Gran Canaria, Gomera and Lanzarote Islands, known as crossbreed, constitute a homogeneous genetic group, for this reason, all of them should be considered as the same breed. Furthermore it is the most numerous and widespread goat population over the Canary Archipelago. D

Livestock Science, 2010

A total of 61 individuals belonging to the Guaymi (GY) and Guabala (GUA) populations were typed w... more A total of 61 individuals belonging to the Guaymi (GY) and Guabala (GUA) populations were typed with 27 microsatellites. A mean of 5.61 (GUA) and 7.5 (GY) alleles per population was typed, and Fis values were 0.053 (GUA) and 0.033 (GY). The exclusive alleles of each population were 67 (GY) compared to the 16 observed in the GUA population, while 135 alleles are shared by both. The Ho and He were 0.628 (GUA) and 0.710 (GY) and 0.648 (GUA) and 0.724 (GY) respectively. The fixation index Fst was 0.068 demonstrating a moderate level of genetic differentiation. The effective number of migrants per generations was 3.40 between GY and GUA. A comparison with most popular breeds in Panama Bos indicus (GYR, BRH, SIN, GUZ and NEL) and Bos taurus (FRI, SPA and HER) was made because of possible crossbreeding. The AMOVA and a NeighborNet tree performed, provided a detailed interrelationship network, and show an important difference between Panama creoles cattle population and most popular breeds. Strategies for preserving the original Panama cattle creole population should be considered in order to prevent the breed from becoming extinct and to strengthen the breed's capability in future breeding programs.

Journal of Heredity, 2007

Journal of Equine Veterinary Science, 2013

ABSTRACT In order to determine whether the high level of inbreeding of the Retuertas endangered H... more ABSTRACT In order to determine whether the high level of inbreeding of the Retuertas endangered Horses may increase the vulnerability to oxidative stress of the sperm, the susceptibility to lipid peroxidation (LPO) of sperm membranes was evaluated in cooled extended ejaculates. Extended ejaculates (INRA 96) from four Retuertas horses and nine ejaculates from pure Spanish horses were received within 24 hours of collection at our laboratory. An aliquot was analyzed and served as time 0 control. The rest of the ejaculates were split into two additional aliquots: the first aliquot served as an incubation control and the second aliquot received an oxidative insult (Fe2SO4). Membrane LPO, motility parameters, membrane integrity, and mitochondrial membrane potential were evaluated. The oxidative insult induced a significant increase in the percentage of sperm with LPO in the Retuertas horses (P < .05). Total and progressive motility were not affected by the oxidative insult in both groups. However, curvilinear velocity (VCL), average velocity (VAP), straightness index (STR), and amplitude of lateral head displacement (ALH) were significantly affected by the treatment (P < .05) in the Retuertas horse population. The membrane integrity of sperm in this group was also affected: the percentage of sperm with intact membranes decreased (57.31% ± 7.76% vs. 47.52% ± 8.28%); and the percentage of necrotic sperm increased (33.27% ± 7.83% vs. 44.85% ± 9.16%) (P < .05). Finally, the oxidative insult increased the population with low mitochondrial membrane potential in these wild horses. We concluded that the high level of inbreeding of this particular breed apparently leads to a higher susceptibility to lipid peroxidation.

Journal of Animal Science, 2008

Population structure and genetic diversity in the Portuguese native breeds of pigs Alentejano (AL... more Population structure and genetic diversity in the Portuguese native breeds of pigs Alentejano (AL), Bísaro (BI), and Malhado de Alcobaça (MA) and the exotic breeds Duroc (DU), Landrace (LR), Large White (LW), and Pietrain were analyzed by typing 22 microsatellite markers in 249 individuals. In general, the markers used were greatly polymorphic, with mean total and effective number of alleles per locus of 10.68 and 4.33, respectively, and an expected heterozygosity of 0.667 across loci. The effective number of alleles per locus and expected heterozygosity were greatest in BI, LR, and AL, and least in DU. Private alleles were found in 9 of the 22 markers analyzed, mostly in AL, but also in the other breeds, with the exception of LW. The proportion of loci not in Hardy-Weinberg equilibrium in each breed analyzed ranged between 0.23 (AL) and 0.41 (BI, LW, and Pietrain), mostly because of a less than expected number of heterozygotes in those loci. With the exception of MA, all breeds showed a significant deficit in heterozygosity (F(IS); P &amp;lt; 0.05), which was more pronounced in BI (F(IS) = 0.175) and AL (F(IS) = 0.139), suggesting that inbreeding is a major concern, especially in these breeds that have gone through a genetic bottleneck in the recent past. The analysis of relationships among breeds, assessed by different methods, indicates that DU and AL are the more distanced breeds relative to the others, with the closest relationship being observed between LR and MA. The degree of differentiation between subpopulations (F(ST)) indicates that 0.184 of the total genetic variability can be attributed to differences among breeds. The analysis of individual distances based on allele sharing indicates that animals of the same breed generally cluster together, but subdivision is observed in the BI and LR breeds. Furthermore, the analysis of population structure indicates there is very little admixture among breeds, with each one being identified with a single ancestral population. The results of this study confirm that native breeds of pigs represent a very interesting reservoir of allelic diversity, even though the current levels of inbreeding raise concerns. Therefore, appropriate conservation efforts should be undertaken, such as adopting strategies aimed at minimizing inbreeding, to avoid further losses of genetic diversity.

Genetics and Molecular Research, 2013

The Uruguayan Creole cattle population (N = 600) is located in a native habitat in south-east Uru... more The Uruguayan Creole cattle population (N = 600) is located in a native habitat in south-east Uruguay. We analyzed its genetic diversity and compared it to other populations of American Creole cattle. A random sample of 64 animals was genotyped for a set of 17 microsatellite loci, and the D-loop hyper-variable region of mtDNA was sequenced for 28 calves of the same generation. We identified an average of 5.59 alleles per locus, with expected heterozygosities between 0.466 and 0.850 and an expected mean heterozygosity of 0.664. The polymorphic information content ranged from 0.360 to 0.820, and the global F IS index was 0.037. The D-loop analysis revealed three haplotypes (UY1, UY2 and UY3), belonging to the European ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (2): 1119-1131 (2013) E. Armstrong et al.

Genetics and Molecular Biology, 2006

The Uruguayan Creole cattle genetic reserve consists of a herd of about 600 animals (bulls, cows ... more The Uruguayan Creole cattle genetic reserve consists of a herd of about 600 animals (bulls, cows and calves) located in an indigenous habitat of 650 hectares. In a previous study, a random sample from this herd showed high heterozygosity and a Hardy-Weinberg equilibrium for markers of major genes related to milk production. To study its genetic diversity we genotyped a sample of bulls (N = 19 out of 23 for the whole herd) using the PCR reaction with a set of 17 microsatellite markers. Between two and seven different alleles were identified per microsatellite in a total of 73 alleles. The expected mean heterozygosity (He) per locus was between 0.465 and 0.801, except for microsatellite HEL13 which gave a He value of 0.288. The expected mean heterozygosity was 0.623 and the polymorphic information content (PIC) was between 0.266 for HEL13 and 0.794 for CSSM66. The genetic diversity found in polymorphic markers in the breeding bulls of this Creole cattle population supports previous genetic analyses using major production genes and indicate that further studies should be carried out on this population to provide data of interest to cattle production.

Genetics and Molecular Biology, 2008

We investigated the genealogy of the in situ conservation nucleus of the Pantaneiro horse using D... more We investigated the genealogy of the in situ conservation nucleus of the Pantaneiro horse using DNA microsatellites by evaluating 101 horses, the group consisting of 71 adult horses (3 stallions, 40 male and 31 mares) and 27 foals (14 colts and 13 fillies). Genomic DNA was extracted from hair roots and genotyped using 12 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, HMS3 HMS6, HMS7, HTG4, HTG10, LEX33 and VHL20). The number of alleles per locus varied from 6 to 13, with a mean of 7.8 and the expected heterozygosity ranged from 0.544 to 0.734 (mean 0.644). The VLH20, ASB2, HTG10, ASB23 markers had a high (> 0.8) polymorphism information content and the total exclusion probability of the 12 microsatellite loci was 0.99. The genealogical study of the Pantaneiro horse using genetic markers was efficient in detecting mistakes during paternity and maternity designation and is an important tool which can be used together with traditional systems of animal identification. The use of genetic markers is recommended in the systematic control of the genealogical registrations and conservation plans to improve genetic aspects of the Pantaneiro horse.

Animal Genetics, 2006

In the 1980s, a conservation programme involving a feral horse population, the Retuertas horses f... more In the 1980s, a conservation programme involving a feral horse population, the Retuertas horses from the Guadalquivir marshes, was started in the Doñana National Park. The analysis of an extensive genetic survey of this population, which now numbers 100 animals, and 10 additional European and North African breeds using DNA polymorphisms from 22 microsatellites is presented. Highly significant fixation indexes were obtained for all pairwise comparisons between the Retuertas population and other breeds. A population neighbour-joining breed phenogram was built using different distance measures, but the Retuertas population failed to cluster with either of the two major clades of European and North African breeds, highlighting its uniqueness. In fact, the Retuertas population was positioned at the base of the trees, which were rooted using donkey samples. Furthermore, assignment tests and the individual Q-matrices obtained with the structure programme isolated the Retuertas breed from the other breeds with only four K groups. Interestingly, some local semi-feral horses, known as Marismeño, also currently living in the Guadalquivir marshes, have some microsatellite genotypes that fall well within the Retuertas cluster. This raises the possibility of incorporating horses from the Marismeño population in a future conservation programme.

Animal Genetics, 2000

Partition of the genetic variability, genetic structure and relationships among seven Spanish Cel... more Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean F ST » 0 . 08; P < 0 . 01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.

Animal Genetics, 2002

South American horses constitute a direct remnant of the Iberian horses brought to the New World ... more South American horses constitute a direct remnant of the Iberian horses brought to the New World by the Spanish conquerors. The source of the original horses was Spain, and it is generally assumed that the animals belonged to the Andalusian, Spanish Celtic, Barb or Arabian breeds. In order to establish the relationship between Argentinean and Spanish horses, a portion of the mitochondrial D-loop of 104 animals belonging to nine South American and Spanish breeds was analysed using SSCP and DNA sequencing. The variability found both within and between breeds was very high. There were 61 polymorphic positions, representing 16% of the total sequence obtained. The mean divergence between a pair of sequences was 2.8%. Argentinean Creole horses shared two haplotypes with the Peruvian Paso from Argentina, and the commonest haplotype of the Creole horses is identical to one of the Andalusian horses. Even when there was substantial subdivision between breeds with highly significant Wright's Fixation Index (FST), the parsimony and distance-based phylogenetic analyses failed to show monophyletic groups and there was no clear relationship in the trees between the South American and any of the other horses analysed. Although this result could be interpreted as mixed ancestry of the South American breeds with respect to the Spanish breeds, it is probably indicating the retention of very ancient maternal lineages in the breeds analysed.

Page 1. ARCHAEOLOGY MEETS MOLECULAR BIOLOGY Gabriel Dorado1, Víctor Vásquez2, Isabel Rey3, José L... more Page 1. ARCHAEOLOGY MEETS MOLECULAR BIOLOGY Gabriel Dorado1, Víctor Vásquez2, Isabel Rey3, José Luis Vega-Pla4 1Author for correspondence, Dep. ... Yet, as Bob Dylan said in one of his emblematic songs, The times they are a-changin'. ...

Animal Genetics, 2014

For centuries, domestic horses have represented an important means of transport and served as wor... more For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be fourbeat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.