Detecting the footprint of selection on the genomes of Murciano-Granadina goats

Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86 Mb), 4 (41.80-49.95 Mb), 11 (65.74 Mb), 12 (31.24 and 52.51 Mb), 17 (34.76-37.67 Mb), 22 (31.75 Mb), and 26 (26.69-31.05 Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78 days post-partum, early lactation; 216 days post-partum, late lactation; 285 days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.

Caracterización genética del pavo domestico de traspatio mexicano

El pavo de traspatio mexicano es una raza autóctona en peligro de extinción, ya que en la actualidad se ha perdido la costumbre de conservar los recursos genéticos autóctonos de cada población, procurando el cruzamiento con animales de líneas comerciales para la producción de carne de pavo, dañando y perdiendo el acervo genético de los pavos autóctonos de México. El objetivo del presente trabajo es realizar la caracterización genética del pavo de traspatio mexicano mediante el uso de microsatélites y estudiar la posible estructura genética de esta población. Se analiza un panel de 38 microsatélites en 51 muestras de pavo de traspatio, tomadas de diferentes zonas de la ciudad de Veracruz, México. Se han evaluado los principales parámetros de diversidad genética: heterocigosidad esperada y observada, número de alelos, estadísticos F y Análisis Factorial de Correspondencia mediante el programa informático GENETIX. Se calculan las distancias genéticas entre individuos (DSA) con las que se ha construido un dendrograma utilizando el programa POPULATIONS. El árbol se visualiza con el programa TREEVIEW. Se estudia la estructura genética con el programa STRUCTURE. Todos los microsatélites utilizados han resultado polimórficos, encontrándose un mínimo de 2 alelos en el microsatélite MNT 264 y un máximo de 14 alelos en los marcadores MNT274 y RHT024, con un número medio de alelos de 6.79. Los valores medios de HE y HO son 0.619 y 0.620 respectivamente. Los estadísticos F muestran los siguientes valores en el total de la muestra: FIS 0.128 (P

Modelling for the inheritance of multiple births and fertility in endangered equids: Determining risk factors and genetic parameters in donkeys (Equus asinus)

Multiple births or twinning in equids are dangerous, undesirable situations that compromise the life of the dam and resulting offspring. However, embryo vitrification and freezing techniques take advantage of individuals whose multiple ovulations allow flushing more fertilised embryos from the oviduct to be collected, increasing the productivity and profitability of reproductive techniques. Embryo preservation is especially important in highly endangered populations such as certain donkey (Equus asinus) breeds; for which conventional reproductive techniques have previously been deemed inefficient. For instance, becoming an effective alternative to artificial insemination with frozen semen to preserve the individuals' genetic material. The objective of this study was to examine the historical foaling records of Andalusian donkeys to estimate prevalence, risk factors, phenotypic and genetic parameters for multiple births, assessing the cumulative foal number born per animal, maximum foal number per birth and multiple birth number per animal. We designed a Bayesian General Animal Mixed Model with single records considering the 'fixed' effects of birth year, birth season, birth month, sex, farm, location, and husbandry system. Age was considered and included as a linear and quadratic covariate. Gibbs sampling reported heritability estimates ranging from 0.18 ± 0.101 to 0.24 ± 0.078. Genetic and phenotypic correlations ranged from 0.496 ± 0.298 to 0.846 ± 0.152 and 0.206 ± 0.063 to 0.607 ± 0.054, respectively. Predicted breeding values obtained enable the potential selection against/for these traits, offering a new perspective for donkey breeding and conservation.

Low genome-wide homozygosity in 11 Spanish ovine breeds

The population of Spanish sheep has decreased from 24 to 15 million heads in the last 75 years due to multiple social and economic factors. Such a demographic reduction might have caused an increase in homozygosity and inbreeding, thus limiting the viability of local breeds with excellent adaptations to harsh ecosystems. The main goal of our study was to investigate the homozygosity patterns of 11 Spanish ovine breeds and to elucidate the relationship of these Spanish breeds with reference populations from Europe, Africa and the Near East. By using Ovine SNP50 BeadChip data retrieved from previous publications, we have found that the majority of studied Spanish ovine breeds have close genetic relatedness with other European populations; the one exception is the Canaria de Pelo breed, which is similar to North African breeds. Our analysis has also demonstrated that, with few exceptions, the genomes of Spanish sheep harbor fewer than 50 runs of homozygosity (ROH) with a total length of less than 350 Mb. Moreover, the frequencies of very long ROH (>30 Mb) are very low, and the inbreeding coefficients (F_ROH ) are generally small (F_ROH  < 0.10), ranging from 0.008 (Rasa Aragonesa) to 0.086 (Canaria de Pelo). The low levels of homozygosity observed in the 11 Spanish sheep under analysis might be due to their extensive management and the high number of small to medium farms.

Effect of different olive oil-derived antioxidants (hydroxytyrosol and 3,4-dihydroxyphenylglycol) on the quality of frozen-thawed ram sperm

The aim of the present study was to evaluate the effect of the addition of different concentrations of two olive oil-derived antioxidants, hydroxytyrosol (3,4-dihydroxyphenylethanol, HT) and 3,4-dihydroxyphenylglycol (DHPG), on ovine semen during the freezing-thawing process. Sperm was collected, pooled and diluted with commercial extenders and then divided into aliquots supplemented with different concentrations (10 μg/ml, 30 μg/ml, 50 μg/ml and 70 μg/ml) of HT, DHPG and a mixture (MIX) of both antioxidants. A control group, without antioxidant, was also prepared. Sperm motility, viability, acrosome integrity, mitochondrial membrane potential and lipid peroxidation (LPO) were assessed. The results showed that frozen-thawed ram spermatozoa exhibited lower values for motility, membrane integrity, acrosome and mitochondrial membrane potential than fresh samples (P ≤ 0.01). However, when antioxidants were added, thawed spermatozoa exhibited relatively low LPO, recording values similar to fresh spermatozoa; by contrast, the control group of frozen-thawed spermatozoa without antioxidants exhibited significantly higher LPO (P ≤ 0.01). The addition of a HT+DHPG mixture (MIX) had a negative impact on sperm membrane and acrosome integrity, suggesting that a pure antioxidant supplementation has the potential to offer superior results. In conclusion, HT and DHPG exhibited a positive effect on the frozen-thawed spermatozoa inasmuch as they reduced the LPO. These olive oil-derived antioxidants have the potential to improve frozen-thawed sperm quality, although further studies should be carried out to analyse the antioxidant effect at different times after thawing.

The legacy of Columbus in American horse populations assessed by microsatellite markers

Criollo horse populations descend from horses brought from the Iberian Peninsula over the period of colonization (15th to 17th century). They are spread throughout the Americas and have potentially undergone genetic hybridization with other breeds in the recent past. In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of "all other Criollo breeds" had the closest genetic relationship with breeds originating from the Iberian Peninsula, specifically with the Celtic group. For the whole set of Criollo breeds analysed, the estimated genetic contribution from other breeds was approximately 50%, 30% and 20% for the Celtic, Iberian and Arab-Thoroughbred groups, respectively. The spatial distribution of genetic diversity indicates that hotspots of genetic diversity are observed in populations from Colombia, Ecuador, Brazil, Paraguay and western United States, possibly indicating points of arrival and dispersion of Criollo horses in the American continent. These results indicate that Criollo breeds share a common ancestry, but that each breed has its own identity.

El Cerdo Criollo Costero: Valioso recurso zoogenético local de la provincia de Buenos Aires Argentina

El cerdo Criollo costero (CCC), forma parte de la cultura popular de la provincia de Buenos Aires. Se utiliza para producir carne y chacinados desde el principio de la colonización española hasta la actualidad. A pesar de esto, nunca se lo ha valorado zootécnicamente y no ha sido tenido en cuenta como recurso genético en la producción porcina moderna. El mayor número de ejemplares se mantiene como cerdo cimarrón en una amplia zona costera de la provincia. No se han estudiado aún sus características productivas ni su importancia económica y social. Se plantea aquí la necesidad de constituir un centro genético porcino local, destinado a caracterizar productivamente este recurso genético local para lograr un aprovechamiento más racional.

Genetic relationships among American donkey populations: insights into the process of colonization

This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed.

Diversidad genética y estructura de población de cabras autóctonas nigerianas usando marcadores microsatélites DNA

Se analizaron 29 microsatélites para evaluar la diversidad genética de tres razas caprinas Nigerianas y establecer las relaciones genéticas entre ellas utilizando las razas Saanen y Kalahari como poblaciones outgroup. Se analizaron 244 distribuidas de la siguiente manera: en Sahel (47), Maradi (47) y WestAfrican Dwarf (67), Kalahari (47) y Saanen (36). El ADN se extrajo a partir de sangre conservada en tarjetas FTA Classic siguiendo las instrucciones del fabricante y se amplificaron los microsatélites mediante PCR. Se calcularon el número medio de alelos (MNA), las heterocigocidades observada (Ho) y esperada (He) y las distancias genéticas entre pares de poblaciones. Se hizo una prueba de equilibrio Hardy-Weinberg (HWE) y un análisis de la estructura genética de las poblaciones mediante el programa STRUCTURE. La diversidad genética encontrada fue alta con valores de MNA entre 6,69 y 8,79 para Kalahari y West African Dwarf, respectivamente. Los valores de Ho oscilaron entre un 59 % para West African Dwarf y un 64,9 % para Saanen. La He más alta se encontró en la raza West African Dwarf (70 %), mientras que el valor más bajo se observó en la raza Saanen (He= 66,5 %). Los valores medios de Fis para las poblaciones estudiadas variaron entre 0,055 en Kalahari y 0,148 en West African Dwarf. La distancia genética más elevada fué la encontrada entre Saanen y Maradi (0,386) y la menor entre Maradi y Sahel (0,025). La prueba de equilibrio de HWE reveló que dieciocho, diecisiete, trece, veintitrés y veintiún loci estaban en equilibrio HWE (p>0,05) en las razas Maradi, West African Dwarf, Sahel, Saanen y Kalahari, respectivamente. Una representación gráfica del análisis de estructura genética reveló que las cabras de Nigeria descienden de un ancestro común diferente de las razas sudafricanas y europeas que fueron utilizadas como grupos externos.

The biodiversity and genetic structure of Balearic sheep breeds

The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was found among the Balearic sheep breeds for the microsatellites scored. The whole mean value of observed heterozygosity amounted to 0.62, whereas the expected heterozygosity value was 0.69, suggesting the presence of a great degree of genetic variability, although a significant deficit of heterozygotes was detected for some markers. Genetic distance estimates showed that Balearic sheep are differentiated from the other Spanish breeds and in particular, from the Merino type. The Ibicenca breed showed the highest distance value from other breeds. The neighbour-net method of analysis clustered the Roja Mallorquina, Menorquina and Mallorquina breeds. The Structure results clearly demonstrated the genetic differentiation among the four Balearic sheep breeds, with the Ibicenca and Formentera races joined, with slight migration among them. Few external genetic influences from the Spanish mainland breeds were detected.

Technical note: Advantages and limitations of authenticating Palmera goat dairy products by pyrosequencing the melanocortin 1 receptor (MC1R) gene

Inferring the breed of origin of dairy products can be achieved through molecular analysis of genetic markers with a population-specific pattern of segregation. The goal of the current work was to generate such markers in goats by resequencing several pigmentation genes [melanocortin 1 receptor (MC1R), v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT), tyrosinase (TYR), and tyrosinase-related protein 2 (TYRP2)]. This experiment revealed 10 single nucleotide polymorphisms (SNP), including 5 missense mutations and 1 nonsense mutation. These markers were genotyped in 560 goats from 18 breeds originally from Italy, the Iberian Peninsula, the Canary Islands, and North Africa. Although the majority of SNP segregated at moderate frequencies in all populations (including 2 additional markers that were used as a source of information), we identified a c.764G>A SNP in MC1R that displayed highly divergent allelic frequencies in the Palmera breed compared with the Majorera and Tinerfeña breeds from the Canary Islands. Thus, we optimized a pyrosequencing-based technique that allowed us to estimate, very accurately, the allele frequencies of this marker in complex DNA mixtures from different individuals. Once validated, we applied this method to generating breed-specific DNA profiles that made it possible to detect fraudulent cheeses in which Palmero cheese was manufactured with milk from Majorera goats. One limitation of this approach, however, is that it cannot be used to detect illegal manufacturing where Palmero dairy products are produced by mixing milk from Palmera and Majorera goats, because the c.764G>A SNP segregates in both breeds.

Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers

In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha. Genetic variability was assessed by analyzing a panel of 25 microsatellite markers from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability with observed and expected heterozygosities of 0.583 and 0.603, respectively. The mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of them in Hardy Weinberg equilibrium. The level of endogamy was low (F_IS = 0.0475). A factorial analysis of correspondence was used to assess the genetic differences between Pampa Rocha and other pig breeds; genetic distances were calculated, and a tree was designed to reflect the distance matrix. Individuals were also allocated into clusters. This analysis showed that the Pampa Rocha breed was separated from the other breeds along the first and second axes. The neighbour-joining tree generated by the genetic distances D_A showed clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to clusters showed a clear separation of Pampa Rocha pigs. These results provide insights into the genetic variability of Pampa Rocha pigs and indicate that this breed is a well-defined genetic entity.

Genetic diversity analysis of the Uruguayan Creole cattle breed using microsatellites and mtDNA markers

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 FIS index was 0.037. The D-loop analysis revealed three haplotypes (UY1, UY2 and UY3), belonging to the European matriline group, with a haplotype diversity of 0.532. The history of the population, changes in the effective population size, bottlenecks, and genetic drift are possible causes of the genetic variability patterns that we detected.

Genetic diversity, structure, and breed relationships in Iberian cattle

In Iberia there are 51 officially recognized cattle breeds of which 15 are found in Portugal and 38 in Spain. We present here a comprehensive analysis of the genetic diversity and structure of Iberian cattle. Forty of these breeds were genotyped with 19 highly polymorphic microsatellite markers. Asturiana de los Valles displayed the greatest allelic diversity and Mallorquina the least. Unbiased heterozygosity values ranged from 0.596 to 0.787. The network based on Reynolds distances was star-shaped with few pairs of interrelated breeds and a clear cluster of 4 breeds (Alistana/Arouquesa/Marinhoa/Mirandesa). The analysis of the genetic structure of Iberian cattle indicated that the most probable number of population clusters included in the study would be 36. Distance results were supported by the STRUCTURE software indicating a relatively recent origin or possible crossbreeding or both between pairs or small groups of breeds. Five clusters included 2 different breeds (Betizu/Pirenaica, Morucha/Avileña, Parda de Montaña/Bruna de los Pirineos, Barrosã/Cachena, and Toro de Lidia/Brava de Lide), 3 breeds (Berrenda en Negro, Negra Andaluza, and Mertolenga) were divided in 2 independent clusters each, and 2 breeds were considered admixed (Asturiana de los Valles and Berrenda en Colorado). Individual assignation to breeds was not possible in the 2 admixed breeds and the pair Parda de Montaña/Bruna de los Pirineos. The relationship between Iberian cattle reflects their geographical origin rather than their morphotypes. Exceptions to this geographic clustering are most probably a consequence of crossbreeding with foreign breeds. The relative genetic isolation within their geographical origin, the consequent genetic drift, the adaptation to specific environment and production systems, and the influence of African and European cattle have contributed to the current genetic status of Iberian cattle, which are grouped according to their geographical origin. The greater degree of admixture observed in some breeds should be taken into account before using molecular markers for genetic assignment of individuals to breeds.

Drift across the Atlantic: genetic differentiation and population structure in Brazilian and Portuguese native goat breeds

Brazilian goat breeds are believed to derive mainly from animals brought by Portuguese settlers since the 16th century. We used microsatellite markers in a sample of 436 animals to study genetic variability and differentiation of the six Portuguese (PT) and six Brazilian (BR) goat breeds currently recognized in the two countries. These breeds were also compared with an outgroup represented by a sample of Alpine (ALP) goats. The effective number of alleles and allelic richness were slightly higher in PT than in BR breeds. The global F(ST) was nearly 0.11 when PT and BR breeds were considered, with a mean pairwise F(ST) of about 0.03 among PT breeds, 0.07 among BR breeds and 0.15 between PT and BR breeds. The dendrogram illustrating relationships between populations and the correspondence analysis indicate the existence of two very distinct clusters, corresponding to the countries of origin of the breeds studied, which are nearly equidistant from the Alpine outgroup. The analysis with structure confirmed the separation between PT and BR breeds but suggests that some BR breeds, especially Graúna and Canindé, may share a common ancestry with PT breeds. The divergence observed between PT and BR breeds may result from founder effects and genetic drift but could also reflect the introduction in Brazil of goats originating from other regions, e.g., West Africa.

Consumo de agua de ovinos alimentados con diferentes niveles de nopal (opuntia ficus indica) en Brasil

En 45 ovinos machos Santa Inés (peso vivo medio de 27,50 ± 0, 48 kg) se evaluó el consumo de agua, al consumir raciones con niveles crecientes (0, 25, 50, 75, 100%) de nopal (Opuntia fícus indica Mill) en sustitución al maíz molido. El diseño fue en bloques al azar con nueve repeticiones. El consumo de materia seca respondió de modo cuadrático, perjudicando el peso final, que disminuyó, con el aumento del nopal en la dieta. Aumentó el consumo de materia natural disminuyendo el de agua, el consumo total de agua aumentó en el tratamiento con mayor cantidad de nopal. La relación de consumos: agua voluntaria/materia seca, disminuyó al aumentar el nopal. El nopal constituye una reserva de agua para ovinos Santa Inés en condiciones semiáridas de Brasil.

Genetic characterization of Latin-American Creole cattle using microsatellite markers

Genetic diversity in and relationships among 26 Creole cattle breeds from 10 American countries were assessed using 19 microsatellites. Heterozygosities, F-statistics estimates, genetic distances, multivariate analyses and assignment tests were performed. The levels of within-breed diversity detected in Creole cattle were considerable and higher than those previously reported for European breeds, but similar to those found in other Latin American breeds. Differences among breeds accounted for 8.4% of the total genetic variability. Most breeds clustered separately when the number of pre-defined populations was 21 (the most probable K value), with the exception of some closely related breeds that shared the same cluster and others that were admixed. Despite the high genetic diversity detected, significant inbreeding was also observed within some breeds, and heterozygote excess was detected in others. These results indicate that Creoles represent important reservoirs of cattle genetic diversity and that appropriate conservation measures should be implemented for these native breeds in order to minimize inbreeding and uncontrolled crossbreeding.

Análisis preliminar de parámetros genéticos para el carácter de prolificidad en la oveja canaria de pelo

En este trabajo se presentan los valores de los parámetros genéticos para prolificidad de la oveja Canaria de Pelo, obtenidos a partir de la utilización de un modelo animal con observaciones repetidas sobre la información generada en los núcleos de control de rendimiento cárnico de la raza. El modelo de análisis genético incluyó como efectos fijos: ganadería, año, época y número de parto; y como efectos aleatorios, el genotipo aditivo del animal y el efecto ambiental permanente. Se utilizaron, como base de información, un total de 7657 partos registrados en 2889 animales de 5 ganaderías entre los años 1996 y 2008, lo que supuso un promedio de 2,65 partos registrados por animal, suficiente para obtener una buena estimación del efecto ambiental permanente. Los valores observados para la heredabilidad y para la repetibilidad fueron de 0,05 y de 0,1 respectivamente, valores dentro de los límites de la especie. También se aportan valores de las varianzas aditiva, fenotípica total y ambiental permanente. Ésta es la primera estimación de parámetros genéticos que se realiza en esta raza con datos de campo, lo que supone un importante avance en el esquema de selección de la misma.

Diversidade genética de búfalos brasileiros (bubalus bubalis) utilizando microssatélites de DNA

Foi estudada a diversidade genética de búfalos do Brasil utilizando-se vinte e cinco marcadores microssatélites (CSSM41, CSSM8, CSRM60, CSSM33, BM1818, HEL13, MAF65, CSSME70, HSC, BRN, CSSM36, CSSM22, HAUT24, BM1824, SRCRSP8, TGLA227, ILSTS33, INRA23, BM8125, CSSM19, INRA37, CSSM66, ILSTS011, OarFCB48, SPS115). Foram analisadas amostras colhidas ao acaso de cinco populações, ou seja, raças Carabao, Jafarabadi, Mediterrâneo e Murrah, mais o tipo Baio. Em geral, os valores para a diferença entre as heterozigosidades (Ho - He) foram bastantes pequenas, significando equilíbrio nos marcadores utilizados para este tipo de estudo. Os valores do GST demonstraram um nível alto de diferenciação genética e os da estatística F: Fis (f), Fst (q) e Fit (F) demonstraram que os marcadores utilizados permitem inferir informações adequadas sobre as populações, podendo-se deduzir que os grupos Baio, Carabao, Jafarabadi e Mediterrâneo apresentam-se mais homogêneos que o grupo Murrah, o qual mostra níveis altos de endogamia. Os resultados dos estudos de distância genética mostraram que as populações de Baio, Mediterraneo e Murrah, agrupando-se em um cluster comum, demonstra alta similaridade genética, não obstante as suas divergências fenotípicas, confirmando que o grupo Carabao constitui uma diferente subespécie. Os resultados, principalmente das populações de Baio e Carabao, mostram o êxito do trabalho de con-servação genética e a necessidade de se desenvolver novas estratégias para a conservação do germoplasma dos búfalos do Brasil.

Historia de los bovinos en Panamá y su relación con las poblaciones bovinas de iberoamérica

Se hace una revisión histórica sobre el origen de la ganadería en América; se describen las migraciones de bovinos que se realizan desde España hacia las islas y los primeros envíos de animales desde La Española y Santiago hacia tierra firme, como Santa Marta, Colombia; Tamaulipas, México y Santa María La Antigua, Panamá. Se relata el movimiento de animales por todo el territorio panameño, influenciado por la presencia de Pedrarias Dávila como Gobernador de Castilla del Oro y posteriormente como Gobernador de Nicaragua; se plantea la importancia del paso de bovinos por Panamá y su importancia en la conquista del Perú y Ecuador. Y se concluye con la hipótesis histórica de la influencia genética de los bovinos llegados al Nuevo Mundo sobre el territorio Iberoamericano particularmente los bovinos que llegaron a Panamá.

Genetic diversity within and between European pig breeds using microsatellite markers

An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43-0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy-Weinberg expectations (P < 0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright F(ST) index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.

Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs

DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F(ST)), and Reynolds genetic distances. A highly significant average F(ST) of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of F(ST) across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity.

Genetic structure of the Iberian pig breed using microsatellites

An analysis of 25 microsatellite loci in 210 animals has been used to define the genetic structure of the Iberian pig, traditionally classified into several varieties. In addition, a sample of 20 Duroc pigs was used as an outgroup for topology trees. Inter-variety genetic variation was estimated by unbiased average heterozygosity and the number of alleles observed. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were shown for 19 loci across the whole population. By contrast, equilibrium deviation within varieties was much lower. Genetic variation measures, genetic distance values and a neighbour-joining tree were used to estimate subdivision. In addition, an individual tree was constructed to contrast the assignation of animals into varieties. Despite the low bootstrap values obtained in the varieties neighbour-joining tree, the degree of genetic variation found was sufficient to support the division of the Iberian pig into varieties, although in some cases the traditional classification cannot be accepted. These results have shown the value of this marker panel in the study of intra-breed genetic structures.