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.

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.

Genetic diversity and patterns of population structure in Creole goats from the Americas

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora-type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well-differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.

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.

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.

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.

Genomic analysis of the origins of extant casein variation in goats

The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.

Efecto socioeconómico sobre las características fanerópticas de gallinas autóctonas de Ecuador

Se caracterizaron fanerópticamente 244 aves: 207 gallinas 84,84% y 37 gallos 15,16% en 25 localidades de 6 provincias del Ecuador, Región Sierra: Bolívar 31, Chimborazo 70, Tungurahua 35, Cotopaxi 32; Región Costa: Guayas 28; Región Amazónica: Morona Santiago 38. Mediante observación directa, los datos recogidos fueron tabulados en el programa estadístico SPSS versión Statistic 19, como estadísticos descriptivos se obtuvo frecuencias; además se realizó, la prueba Chi-cuadrado de Pearson y La V de Cramer (P ≤0,05). La provincia de Bolívar parroquia Chimbo, obtuvo los mayores valores de la mediana para color de plumas, tipo de cresta, color de piel y presencia de plumas en el cuello 6,50; 1,00; 1,00; 1,00 respectivamente. La coloración del plumaje que se presentó fue marrón café 17,21%, seguido del jaspeado 16,80%, negro 14,34% y barrado 10,25%. La forma más frecuente de las crestas fue la sencilla con 76,74%, seguida de tipo nuez 8,20%. La piel de las aves presentó una coloración amarilla en la mayoría de los casos 52,46%. El mayor porcentaje de los animales presenta emplumado de tipo normal 94,26 % y 5,74 % cuello desnudo. Las aves estudiadas son poblaciones heterogéneas con gran variabilidad en cuanto a características fanerópticas, que permitiría la creación de líneas productivas que conserven su fenotipo y rusticidad, tomando en consideración la preferencia de los consumidores y productores que ejecuten bajo sistemas de producción tradicionales, culturales, sociales y económicamente sustentables en beneficio de las familias campesinas salvaguardando la soberanía alimentaria y los saberes ancestrales.

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.

Resistencia y resiliencia a las enfermedades en las razas de rumiantes locales: un enfoque en América del Sur

La pérdida de variabilidad genética de interés ha tomado importancia no sólo la producción, sino también porque puede tener un efecto negativo en la epidemiología de las enfermedades animales. La actividad ganadera puede presentar considerables pérdidas económicas periódicas debido a la eliminación de animales, la reducción de la productividad, la falta de expresión del potencial genético de los animales, los costes de tratamiento, la asistencia laboral y profesional, el cierre del comercio debido a los obstáculos sanitarios y la competencia con los mercados extranjeros. Por lo tanto, la resistencia a las enfermedades es un atributo deseado en la producción ganadera y la salud animal puede estar limitando en los sistemas de producción de ganado. Existe cierta confusión en la terminología: la resistencia se define como la capacidad del huésped para ejercer cierto grado de control sobre el ciclo de vida del patógeno, mientras que la tolerancia define el impacto de la infección en el rendimiento animal. Un concepto muy cercano a la tolerancia es la resiliencia, que se puede definir como mantener la capacidad productiva del animal frente a la infección. Existen numerosos informes que indican las razas locales como un importante reservorio de resistencia genética natural a las enfermedades como un proceso de adaptabilidad al medio ambiente. Refiriéndose a las principales enfermedades de los animales domésticos (tuberculosis, brucelosis, fiebre aftosa, etc.), numerosos genes han sido identificados y estudiados como biomarcadores de resistencia y tolerancia como los genes BOLA, CD, NOD y SLC11A1 entre los más importantes. Aunque el factor limitante para que los programas de reproducción incluyan resistencia a enfermedades genéticas es la necesidad de cuantificar los fenotipos de resistencia. Esto puede ser costoso y logísticamente difícil, y es una barrera significativa para la selección de la resistencia a las enfermedades. Por esta razón, las características de resistencia a la enfermedad son un objetivo atractivo para los estudios genómicos y generalmente son objeto de estos estudios.

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

Heat stress has divergent effects on the milk microbiota of Holstein and Brown Swiss cows

Heat stress (HS) is one of the pivotal causes of economic losses in dairy industries and affects welfare and performance, but its effect on milk microbiota remains elusive. It is also unclear if and how different breeds may cope with HS in sustaining productive performance. The objectives of this study were to compare (1) the performance of 2 dairy breeds, namely Holstein and Brown Swiss, subjected to HS and (2) the different effects of HS on the milk microbiota of the 2 breeds in thermal comfort conditions and HS. The study was carried out on 36 dairy cows, 18 per breed. The HS was induced by switching off the cooling system during a natural heat wave for 4 d. In addition to the temperature-humidity index, animal stress was confirmed by measuring respiratory frequency and rectal temperature twice daily at 0400 h and 1500 h. The HS affected the 2 breeds differently. The rectal temperature increased with HS in both breeds. Milk yield recording and sampling were performed during the morning milking of d 1 (at 0400 h) and afternoon milking of d 4 (at 1700 h). Productive parameters were also different: milk yield, FCM, ECM, protein and casein content, and renneting parameters were decreased in Holstein cows but remained unaffected in Brown Swiss cows. The HS also modified the milk microbiota of the 2 breeds differently. During HS, the Brown Swiss cows had milk microbiota that was richer (α diversity) than that of the Holstein cows. Comparing the time points before and during HS within breeds showed that Brown Swiss cow milk microbiota was less affected by HS than Holstein cow milk microbiota. Under the same thermal comfort condition, milk microbiota did not discriminate between Brown Swiss and Holstein. Consistently with α and β diversity, the number of operational taxonomic units (OTU) at the genus level that changed their abundance during HS was higher in Holstein (74 OTU) than in Brown Swiss (only 20 OTU). The most significant changes in abundance affected Acinetobacter, Chryseobacterium, Cutibacterium, Enterococcus, Lactococcus, Prevotella-9, Serratia, and Streptococcus. In conclusion, the present report confirms and extends previous studies by demonstrating that Brown Swiss cows regulate their body temperature better than the Holstein breed. The relative thermal tolerance to HS compared with Holstein cows is also confirmed by changes in milk uncultured microbiota, which were more evident in Holstein cows than in Brown Swiss cows.