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.

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 (FIS = 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 DA 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.

Porcine colonization of the Americas: a 60k SNP story.

The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.

Identificación por catálogo y detección molecular de bovinos Holstein portadores de braquiespina en Uruguay / Identification through sire catalogues analysis and molecular detection of brachyspina carriers in Uruguayan Holstein

Resumen El síndrome de braquiespina es una condición genética de la raza Holstein, detectada en el año 2006. Es causado por una deleción de 3.3 Kb en el gen FANCI localizado en el cromosoma bovino 21. La mutación fue identificada en poblaciones de Holstein de Europa, América del Norte y Asia. Dada la importancia económica del defecto y su amplia distribución mundial, el objetivo de este trabajo ha sido la identificación de animales portadores en el núcleo de selección genética de la raza en Uruguay y el diagnóstico molecular del alelo deletéreo en animales del rodeo nacional. En el presente estudio se analizaron 2598 registros de toros Holstein del catálogo de padres del sistema de evaluación genética lechera, los registros de toros pertenecientes a los catálogos de semen Holstein disponible para Uruguay de los años 2014 al 2018; y 71 vacas pertenecientes al rodeo general. Se encontraron 28 toros portadores de braquiespina de un total de 377 toros con información genética del catálogo de padres y cuatro vacas portadoras de un total de 71 genotipificadas en nuestro laboratorio. Se demostró una disminución en el ingreso de semen de animales portadores al país entre los años 2014 y 2018. La frecuencia significativa de animales portadores en Uruguay evidencia la necesidad de implementar estrategias que permitan eliminar gradualmente el defecto de la población.

Abstract Brachyspina syndrome is a hereditary recessive disease of recent identification in the Holstein breed. It is caused by a deletion of 3.3Kb in the FANCI gene located in the bovine chromosome 21. The mutation was identified in Holstein populations of Europe, North America and Asia. Given the economic importance of the defect and its wide distribution, the objective of this work was the identification of carrier animals in the genetic selection nucleus of the breed in Uruguay and the molecular verification of the deleterious allele in animals of the national herd. In the present study, 2598 records of Holstein bulls were analyzed from the list of parents of the dairy genetic evaluation system, records of bulls belonging to the Holstein semen catalogs available for Uruguay from 2014 to 2018; and 71 cows belonging to the general herd. Twenty-eight brachyspina carrier bulls were found of a total of 377 bulls with genetic information from the list of parents and four carrier cows of a total of 71 genotyped in our laboratory. A decrease in the income of semen from carrier animals to the country between 2014 and 2018 was demonstrated. The significant frequency of carrier animals in Uruguay evidences the need to implement strategies to gradually eliminate the population defect.

Localization of the fragile X chromosome break points in Holstein-Friesian cattle (Bos taurus).

Chromosome fragility is generally believed to affect cattle reproductive performance. Lymphocytes were cultured and the long arm of the X-chromosome was measured in 19 bovines that had been presented as repeat breeders, freemartin cotwins, or as having had anestrus or abortions. The positions of the break points on the X-chromosome were estimated by a measuring compass, starting at the centromere. Relative measurements were calculated from the ratio of break point distance from the centromere to the total Xq length. In our study the break points were found to be mainly in the middle of the long arm (X = 0.52; sigma=0.046). Giemsa banding showed that the break points were located in a large negative G-band observed in region 3 of the long arm. The relationship of these findings to animal reproductive problems is discussed.

Genomic polymorphism in Uruguayan Creole cattle using RAPD and microsatellite markers.

Uruguayan Creole cattle inhabit areas that cannot sustain conventional farming. They have adapted to fragile environments and are influenced only by natural selection. In this study, random amplified polymorphic DNA (RAPD) and microsatellite (MS) markers were used to analyse Creole cattle genome polymorphism. A comparative analysis using the RAPD technique was performed in pooled DNA of three cattle breeds (Holstein Friesian, Creole and Hereford) in order to evaluate their amplification patterns. A primary screening of RAPD primers allowed us to select and use those with higher percentage of GC base composition. A total of 215 loci ranging between 300 and 2500 bp were amplified. Bandsharing frequency (BSF) among breeds showed that less related fingerprints were observed between Creole and Hereford cattle (0.77), while the highest similarity frequency corresponded to Holstein Friesian compared to Hereford (0.81). Specific RAPD bands were identified in the three DNA pools and they were tested in every individual of each breed. It may be possible to isolate and sequence these bands to create breed-specific molecular markers. The identification of multiple alleles of the MSCYP 21 in Creole cattle with an heterozygosity of He = 0.846 supported the variability of this genetic resource. The use of molecular markers such as RAPD s and microsatellites is proposed to establish genetic distance among American Creole cattle and possibly related ancestral Iberian breeds.

Effects of 5-azacytidine on lymphocyte-metaphases of Creole cows carrying the rob(1;29).

The Robertsonian translocation rob(1;29) is the most important chromosomal abnormality in cattle. It has been demonstrated that carriers of this chromosomal alteration exhibit reduced fertility due to an early embryonic loss. In the present study we analyzed the effects of DNA methylation inhibitor 5-azacytidine (5-aza-C) on metaphase lymphocytes from Uruguayan Creole cows carrying the rob(1;29). The analysis was focused on the chromatin structure of rob(1;29) comparing it to active and inactive BTAX chromosomes. Lymphocyte cultures were treated with 5-aza-C (1 x 10(-3)M) for 2 h to analyze regions of chromatin decondensation. A comparative analysis of chromatin decondensation among rob(1;29), active BTAX and inactive BTAX showed significant differences (p=1.07 x 10(-7)). Post-hoc pair-wise comparisons using the Mann-Whitney U-test showed significant differences between rob(1;29) and active BTAX (p=1.97 x 10(-5)) and between the active BTAX and inactive BTAX (p=2.55 x 10(-7)). Nevertheless, rob(1;29) did not show significant differences when compared to inactive BTAX (p=0.078). Robertsonian translocation rob(1;29) showed a despiralization pattern similar to the inactive X chromosome. Pericentromeric despiralization in rob(1;29) and the inactive X chromosome was similar, with an average value and standard error of 0.75+/-0.11 and 0.75+/-0.083, respectively. A single condensed region was observed in the inactive X chromosome, whereas in rob(1;29) two regions of condensation, one proximal to the centromere and another proximal to the telomere were detected. Our results show that rob(1;29) and the inactive X chromosome present instability regions susceptible to 5-aza-C. Further studies will be needed to understand the nature and expression pattern of genes located in chromatin condensed regions of rob(1;29).

Molecular approach of the fragile chromosomal region Xq31-34 in cattle (Bos taurus) by microdissection and DOP-PCR / Aproximação molecular da região cromossômica frágil Xq31-34 em bovinos (Bos taurus) utilizando microdissecação cromossômica e DOP-PCR

Fragile sites (FS) are chromosomal regions where the normal compactation of chromatine is not observed. FRAXA (Fra Xq27.3, X sexual chromosome) is one of the most studied FS in humans. FRAXA is an expansion of the trinucleotide CGG located in the gene FMR-1. In cattle, sites of chromosomal fragility were reported in BTAX, associated with different pathologies and fertility impairment. Chromosomal microdissection has became a valuable tool for isolating chromatine fragments. In this work, it was combined the chromosomal microdissection technique with DOP-PCR in order to carry out a molecular analysis of the fragile chromosomal region BTAXq31-34. In that region, polymorphic DNA-RAPD sequences (GC rich) are present and sequences of the gene FMR-1 are missing. The results showed the usefulness of the microdissection-DOP-PCR technique for molecular characterization of fragile chromosomal sites in cattle.

Os sítios frágeis (FS) são regiões de cromossomo onde a compactação normal da cromatina não é realizada. O FRAXA (Fra Xq27.3, cromossomo sexual X) é um dos FS mais estudados em seres humanos. O FRAXA apresenta expansão do trinucleotídeo CGG localizado no gene FMR-1. Em bovinos, existem estudos informando sobre fragilidade cromossômica em BTAX associada com diversas patologias e alterações na fertilidade. A microdissecação cromossômica é uma valiosa técnica para isolar fragmentos de cromatina. Neste trabalho, combinou-se a técnica de microdissecação de cromossomo com DOP-PCR para executar a análise molecular da região do sitio frágil cromossômico BTAXq31-34. Naquela região estão presentes seqüências do polimorfo DNA-RAPD (rico em GC), em que as seqüências do gene FMR-1 estão ausentes. Os resultados mostram a utilidade da técnica de microdissecação-DOP-PCR para a caracterização molecular de sítios frágeis cromossômicos em bovinos.