Análisis genómico de diversidad y estructura genómica de las poblaciones bovinas de la raza mexicana de Lidia

First documented in the 13th Century on the Iberian Peninsula, the Lidia cattle breed has since been the preferred breed for producing bulls for social celebrations known as “bullfighting”, an expression of regional cultural identity in several countries. Specialization of the breed in Mexico began in the late 19th Century when four Mexican families imported a small number of Lidia animals from Spain. Of these original imports, only the lines derived from the Llaguno and González families remain. Different breeding strategies were implemented in the Llaguno family. Antonio Llaguno crossed the recently imported Spanish animals among each other, resulting in what is currently recognized in Mexico as the “Pure” line. Julián Llaguno crossed Creole dams with Spanish sires, creating the line known as “Impure”. In addition, Lidia breed lines such as Domecq, Murube and Santa Coloma were brought to Mexico between 1996 and 1997. The present study objective was to use SNP molecular markers to analyze genomic diversity, population structure, endogamy levels and genetic relationships between Lidia lines in Mexico. Five lines within the Mexican population were studied: Antonio Llaguno, Julián Llaguno, González, Domecq and Santa Coloma. All five lines were found to be genetically distinct, although the Antonio and Julián Llaguno lines are more similar than the others. Genetic isolation between the different lines of the Lidia breed in Mexico has resulted in their being unique.La raza bovina de Lidia ha sido seleccionada desde el siglo XIII para participar en festejos sociales reconocidos bajo el término de “Tauromaquia”. En la actualidad forman parte de la identidad de las culturas regionales de varios países. En México, la raza se especializó a finales del siglo XIX cuando cuatro familias mexicanas importaron un número reducido de bovinos de España. De estas importaciones actualmente solo permanecen las líneas derivadas de las familias Llaguno y González. En la familia Llaguno se llevaron diferentes estrategias de reproducción. Antonio Llaguno cruzó los recién importados bovinos españoles entre sí; de dichas cruzas derivó la línea que actualmente es reconocida como “Pura”. Por otro lado, Julián Llaguno realizó cruzas entre hembras criollas con machos españoles, línea conocida como “Impura”. Por último, entre1996 y 1997, un grupo de ganaderos importó bovinos pertenecientes a ciertos encastes españoles como Domecq, Murube, Santa Coloma, entre otros. El objetivo del presente estudio fue investigar la diversidad genómica, estructura poblacional, niveles de endogamia y relaciones genéticas entre las poblaciones de Lidia mexicana, utilizando marcadores moleculares de tipo SNP. La población fue dividida en cinco grupos: Antonio Llaguno, Julián Llaguno, González, y dos grupos que incluían bien importaciones recientes de origen Domecq, o bien importaciones recientes de origen Santa Coloma. Los resultados permiten apreciar diferentes orígenes genéticos dentro de la familia Llaguno en función de su origen histórico: Antonio y Julián. En el resto de grupos también se observa una clara diferenciación genética. Este aislamiento genético entre poblaciones de Lidia mexicana es una característica de su singularidad

Genomic Tools for Effective Conservation of Livestock Breed Diversity

Human concern about the status of genetic diversity in livestock breeds and their conservation has increased, as intense selection and reduced population sizes in many breeds has caused losses on the global livestock genetic biodiversity. Traditionally, pedigree data provided by the breeders were used to estimate genetic diversity parameters, but over the past decades, technology has made possible the development of genomic markers. The result has been new opportunities to estimate genetic diversity in more detail, and to improve selection as well as prioritizing animals for conservation of genetic resources. The aim of the review is to summarize the evolution of livestock genomic markers and to explore the potential of the newest high-throughput technologies for estimation and conservation of livestock genetic diversity. More accurate diversity parameters are observed when genomic information is used for selection decisions instead of the traditional estimates using pedigree data. It is also possible to estimate additional parameters such as linkage disequilibrium to calculate effective population size or to minimize the genetic relatedness among the selected individuals based on runs of homozygosity. For long-term perspectives, new methods on genome editing are considered as new perspectives to reach a genetic diversity balance

Red-legged partridge (Alectoris rufa) de-novo transcriptome assembly and identification of gene-related markers

The red-legged partridge (Alectoris rufa) has a great socio-economic importance as a game species and is reared by millions in farms in several European countries. The ability to respond to a wide spectrum of pathogens and environmental changes is key for farm-reared animals that, as such, face even higher pathogen exposure and specifically for those submitted to restocking programs. In this study, RNA-sequencing and de-novo assembly of genes expressed in different immune tissues were performed. The raw FASTQ files were submitted to the NCBI SRA database with accession number PRJNA289204. A total of 94.2 million reads were obtained and assembled into 51,403 contigs using OASES software. The final annotated partridge immune transcriptome comprises almost 7000 unigenes, available as FASTA in the supplementary material. A total of 12,828 microsatellites and 33,857 Single Nucleotide Polymorphisms (SNPs) were identified. The candidate gene sequences and the large number of potential genetic markers from the red-legged partridge transcriptome reliably identified through the use for the first time of a high coverage 100-bp paired-end RNA-seq protocol, provide new tools for future studies in this and related species, thus contributing to the ongoing development of genomic resources in avian species. Further investigation into candidate genes and gene-associated markers will help to uncover individual variability in the resistance to infections and other external aggressions in partridges

Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle

Background: Aggressive behavior is an ancient and conserved trait, habitual for most animals in order to eat, protect themselves, compete for mating and defend their territories. Genetic factors have been shown to play an important role in the development of aggression both in animals and humans, displaying moderate to high heritability estimates. Although such types of behaviors have been studied in different animal models, the molecular architecture of aggressiveness remains poorly understood. This study compared gene expression profiles of 16 prefrontal cortex (PFC) samples from aggressive and non-aggressive cattle breeds: Lidia, selected for agonistic responses, and Wagyu, selected for tameness. Results: A total of 918 up-regulated and 278 down-regulated differentially expressed genes (DEG) were identified, representing above-chance overlap with genes previously identified in studies of aggression across species, as well as those implicated in recent human evolution. The functional interpretation of the up-regulated genes in the aggressive cohort revealed enrichment of pathways such as Alzheimer disease-presenilin, integrins and the ERK/MAPK signaling cascade, all implicated in the development of abnormal aggressive behaviors and neurophysiological disorders. Moreover, gonadotropins, are up-regulated as natural mechanisms enhancing aggression. Concomitantly, heterotrimeric G-protein pathways, associated with low reactivity mental states, and the GAD2 gene, a repressor of agonistic reactions associated with PFC activity, are down-regulated, promoting the development of the aggressive responses selected for in Lidia cattle. We also identified six upstream regulators, whose functional activity fits with the etiology of abnormal behavioral responses associated with aggression. Conclusions: These transcriptional correlates of aggression, resulting, at least in part, from controlled artificial selection, can provide valuable insights into the complex architecture that underlies naturally developed agonistic behaviors. This analysis constitutes a first important step towards the identification of the genes and metabolic pathways that promote aggression in cattle and, providing a novel model species to disentangle the mechanisms underlying variability in aggressive behavior

A novel missense variant in endothelin‐2 ( EDN2 ) causes a growth and respiratory lethal syndrome in bovine

The high level of fragmentation of the Spanish Lidia cattle breed, divided into lineages called ‘castas’ and into herds within lineages based on reproductive isolation, increases the risk of homozygosity and the outbreak of recessive genetic defects. Since 2004, an increasing number of calves have been identified in a Lidia herd with signs of severe growth retardation, respiratory alterations and juvenile lethality, which constitutes a novel inherited syndrome in cattle and was subsequently termed growth and respiratory lethal syndrome. We performed a genome-wide association study on a cohort of 13 affected calves and 24 putative non-carrier parents, mapping the disease to a wide 6 cM region on bovine chromosome 3 (p A|p.Cys50Tyr) in exon 2 of the endothelin 2 (EDN2) gene. Bioinformatic analyses of p.Cys50Tyr effects predicted them to be damaging for both the structure and the function of the edn2 protein, and to create a new site of splicing that may also affect the pattern of pre-mRNA splicing and exon definition. Sanger sequencing of this variant on the rest of the sample set confirmed the segregation pattern obtained with whole genome re-sequencing. The identification of the causative variant and the development of a diagnostic genetic test enable the efficient design of matings to keep the effective population size as high as possible, as well as providing insights into the first EDN2-associated hereditary disease in cattle or other species

Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas

A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a conservation plan at the end of the 21th century in order to preserve this important genetic reservoir. However, Morenas Gallegas bovine breeds never have been analyzed with genomic tools and this information may be crucial to develop conservation plans. The aim of the study was to analyze their genetic diversity and genetic relationships with a set of local and cosmopolitan European bovine breeds using single nucleotide polymorphisms. Our results show own genetic signatures for the Morenas Gallegas breeds which form a separate cluster when compared to the Spanish breeds analyzed, with the exception of the Cachena breed. The genetic diversity levels of the Morenas Gallegas were intermediate or high, and low inbreeding coefficients can be found except for the Frieiresa breed (11%). Vianesa breed evidenced two lineages depending on the Frieiresa component influence. The Morenas Gallegas bovine breeds group represent an important Spanish bovine genetic reservoir and despite their classification within a single generic group, the five breeds show their own genetic uniqueness