The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.Fil: Ginja, Catarina. Universidad de Porto. Facultad de Ciências. Centro de Investigação em Biodiversidade e Recursos Genéticos; PortugalFil: Gama, Luis Telo. Universidade de Lisboa. Faculdade de Medicina Veterinaria; PortugalFil: Cortés, Oscar. Universidad Complutense de Madrid; EspañaFil: Martin Burriel, Inmaculada. Universidad de Zaragoza; EspañaFil: Vega Pla, Jose Luis. Servicio de Cría Caballar de las Fuerzas Armadas. Laboratorio de Investigación Aplicada; EspañaFil: Penedo, Cecilia. University of California; Estados UnidosFil: Sponenberg, Phil. Virginia-Maryland Regional College of Veterinary Medicine; Estados UnidosFil: Cañón Ferreras, Francisco Javier. Universidad Complutense de Madrid; EspañaFil: Sanz, Arianne. Universidad de Zaragoza; EspañaFil: Egito, Andrea Alves do. Embrapa Gado de Corte; BrasilFil: Alvares, Luz Angela. Universidad Nacional de Colombia; ColombiaFil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Agha, Saif. Ain Shams University. Faculty of Agriculture, Animal Production Department; EgiptoFil: Rogberg Muñoz, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Cassiano Lara, Maria Aparecida. Centro de Genética e Reprodução. Instituto de Zootecnia; BrasilFil: Delgado, Juan Vicente. Universidad de Córdoba; EspañaFil: Martinez, Amparo. Universidad de Córdoba; Españ

Pedigree analysis of a highly fragmented population, the Lidia cattle breed

The aim of the study was to analyze the pedigree information of the Lidia bovine breed based on animals registered in the Herdbook and belonging to those lineages recognized as conforming to the official breed standard. Pedigree records of 272,574 animals belonging to 83 herds classified in 30 lineages were used. The average number of equivalent generations known was 4.5 (varying among lineages from 4 in Braganza to 5.2 in Baltasar Iban). The generation interval (7.5 years) was longer than that estimated in other cattle breeds. The effective size was less than 50 and consequently the estimated increase in inbreeding per generation was greater than 1% in all the lineages analyzed. The increase in inbreeding level expected for the next 50 years varied from 7.4% in Braganza to 31.3% in Diego Garrido. The ratios among the effective number of founders, the effective number of ancestors and the effective number of founder genomes was considered evidence that genetic drift explained most of the loss of genetic variability in the Lidia bovine breed due to the reduced effective population sizes of the lineages, more than bottlenecks did, as they have been less dramatic. The lineage allele loss due to the genetic drift and the effect of inbreeding are the major concerns in managing the genetic diversity of the Lidia bovine breed. The analysis of pedigree information still remains as the main useful resource to establish genetic diversity conservation guidelines in the Lidia bovine breed. Minimizing inbreeding increase within lineages in the sub-divided Lidia breed must be the major concern in managing the genetic diversity of this breed.INIA and European Regional Development (Fund nos. RZ2004-00009-00-00 and RZ2008-00005-C02-02)Depto. de Producción AnimalFac. de VeterinariaTRUEpu

Inbreeding depression and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection

Author contributions: Conceptualization: Oscar Cortes, Javier Cañon and Carlos Carleos. Analysis: Carlos Carleos and Javier Cañon. Oscar Cortes wrote the first draft of the manuscript. Carlos Carleos, Javier Cañon, Sara Andrino and María Fernanadez review and editing the article. All authors contributed to the interpretations of the results, the discussion and prepared the final manuscript. All authors read and approved the final manuscript.Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree-based inbreeding coefficients. However, with the development of single-nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding depression in 6 growth and 2 reproductive traits in the Asturiana de los Valles cattle breed using both genealogical and molecular information. The pedigree group comprised 225,848 records and an average equivalent number of complete generations of 2.3. The molecular data comprised genotypes of 2693 animals using the Affymetrix medium-density chip. Using the pedigree information, three different inbreeding coefficients were estimated for the genotyped animals: the full pedigree coefficient (FPED), and the recent and ancient inbreeding coefficients based on the information of the last three generations (FPED3G), respectively. Using the molecular data, seven inbreeding coefficients were calculated. Four of them were estimated based on runs of homozygosity (ROH), considering (1) the total length (FROH), (2) segments shorter than 4 megabases (FROH17). Additionally, the three inbreeding coefficients implemented in the Plink software (FHAT1-3) were estimated. Inbreeding depression was estimated using linear mixed-effects model with inbreeding coefficients used as covariates. All analysed traits (birth weight, preweaning average daily gain, weaning weight adjusted at 180 days, carcass weight, calving ease, age at first calving, calving interval) showed a statistically significant non-zero effect of inbreeding depression estimated from the pedigree group, except for the Postweaning Average Daily Gain trait. When inbreeding coefficients were based on the genomic group, statistically significant inbreeding depression was observed for two traits, Preweaning Average Daily Gain and Weaning Weight based on FROH, FROH>17, and FHAT3 inbreeding coefficients. Nevertheless, similar to inbreeding depression estimated based on pedigree information, estimates of inbreeding depression based on genomic information had no relevant economic impact. Despite this, from a long-term perspective, genotyped data could be included to maximize genetic progress in genetic programs following an optimal genetic contribution strategy and to consider individual inbreeding load instead global inbreeding. ROH islands were identified on chromosomes 2, 3, 8, 10, and 16. Such regions contain several candidate genes for growth development, intramuscular fat, body weight and lipid metabolism that are related to production traits selected in Asturiana de los Valles breed.Ministerio de Ciencia e Innovación (España)Principado de AsturiasDepto. de Producción AnimalFac. de VeterinariaTRUEpu

Transcriptomic characterization of innate and acquired immune responses in red-legged partridges (Alectoris rufa): a resource for immunoecology and robustness selection

Author Contributions: Conceived and designed the experiments: NS JC SD. Performed the experiments: NS. Analyzed the data: NS IG. Contributed reagents/materials/analysis tools: NS JC IG SD. Wrote the paper: NS JC SD.Present and future challenges for wild partridge populations include the resistance against possible disease transmission after restocking with captive-reared individuals, and the need to cope with the stress prompted by new dynamic and challenging scenarios. Selection of individuals with the best immune ability may be a good strategy to improve general immunity, and hence adaptation to stress. In this study, non-infectious challenges with phytohemagglutinin (PHA) and sheep red blood cells allowed the classification of red-legged partridges (Alectoris rufa) according to their overall immune responses (IR). Skin from the area of injection of PHA and spleen, both from animals showing extreme high and low IR, were selected to investigate the transcriptional profiles underlying the different ability to cope with pathogens and external aggressions. RNA-seq yielded 97 million raw reads from eight sequencing libraries and approximately 84% of the processed reads were mapped to the reference chicken genome. Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR. Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis. These findings indicate that the immune system ability to respond to aggressions (either diseases or stress produced by environmental changes) involves extensive transcriptional and post-transcriptional regulations, and expand our understanding on the molecular mechanisms of the avian immune system, opening the possibility of improving disease resistance or robustness using genome assisted selection (GAS) approaches for increased IR in partridges by using genes such as AVN or BF2 as markers. This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.Ministerio de Ciencia, Innovación y UniversidadesEuropean CommissionDepto. de Producción AnimalFac. de VeterinariaTRUEpu

Candidate gene analysis of osteochondrosis in Spanish Purebred horses

Equine osteochondrosis (OC) is a frequent developmental orthopaedic disease with high economic impact on the equine industry and may lead to premature retirement of the animal as a result of chronic pain and lameness. The genetic background of OC includes different genes affecting several locations; however, these genetic associations have been tested in only one or few populations, lacking the validation in others. The aim of this study was to identify the genetic determinants of OC in the Spanish Purebred horse breed. For that purpose, we used a candidate gene approach to study the association between loci previously implicated in the onset and development of OC in other breeds and different OC locations using radiographic data from 144 individuals belonging to the Spanish Purebred horse breed. Of the 48 polymorphisms analysed, three single nucleotide polymorphisms (SNPs) located in the FAF1, FCN3 and COL1A2 genes were found to be associated with different locations of OC lesions. These data contribute insights into the complex gene networks underlying the multifactorial disease OC, and the associated SNPs could be used in a marker-assisted selection strategy to improve horse health, welfare and competitive lifespan.Ministerio de Ciencia, Innovación y UniversidadesDepto. de Producción AnimalFac. de VeterinariaTRUEpu

A Primer Extension Assay for simultaneous use in cattle Genotype Assisted Selection, Parentage and Traceability analysis

Supplementary data to this article can be found online at doi:10.1016/j.livsci.2010.10.011.The use of genotype information as an aid to selection can be a cheap and effective way to improve the genetic progress in beef cattle breeds, specially in the case of high cost phenotypic recording which is true for many economic traits in beef cattle. SNPs located at candidate genes underlying economic traits allow prediction of the genetic merit of individuals and, combined with parentage and traceability analysis, guarantee consumer protection. Here we present a cost-effective technology, the Capillary Primer-Extension Assay, to genotype validated mutations which identify differences between individuals in candidate genes associated directly or potentially with meat tenderness, marbling and muscle growth, milk yield, protein and fat content, sex or coat colour. We genotyped 70 SNPs in 8 beef, 3 dairy and one semi-feral (never selected for any production trait) breeds and present a panel of 53 SNPs with the aim of enabling a reasonable tool for parentage analysis, animal identification and production of markers usable in GAS in small local breeds for which other tools are unaffordable.Ministry of Science and Innovation (MICINN) RZ2008-00006-CO2-2Depto. de Producción AnimalFac. de VeterinariaTRUEpu

Detection of selection signatures for agonistic behaviour in cattle

The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine-rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2-activating protein (PLAA) at BTA8.Depto. de Producción AnimalFac. de VeterinariaTRUEpu

New single nucleotide polymorphisms in Alectoris identified using chicken genome information allow Alectoris introgression detection

Using the chicken genome, 114 polymorphisms (109 SNPs and 5 INDELs) were identified in the Alectoris genus by polymerase chain reaction–single strand conformation polymorphism. Using these, a panel of SNPs is described, which allows easy detection of introgression of Alectoris chukar in wild Alectoris rufa populations, when used with a primer extension protocol. The selected polymorphisms were genotyped and their allelic frequencies estimated on 98 A. rufa partridges sampled from nonrestocking Spanish areas, and 63 A. chukar partridges from Greek and Spanish farms. Power calculations to determine an optimum subset of markers for a given significance level were performed.CDTI Art, 83 LOU (nº 15172006 – 41472006)Depto. de Producción AnimalFac. de VeterinariaTRUEpu

Dietary inulin supplementation modifies significantly the liver transcriptomic profile of broiler chickens

Inclusion of prebiotics in the diet is known to be advantageous, with positive influences both on health and growth. The current study investigated the differences in the hepatic transcriptome profiles between chickens supplemented with inulin (a storage carbohydrate found in many plants) and controls. Liver is a major metabolic organ and has been previously reported to be involved in the modification of the lipid metabolism in chickens fed with inulin. A nutrigenomic approach through the analysis of liver RNA hybridized to the Affymetrix GeneChip Chicken Genome Array identified 148 differentially expressed genes among both groups: 104 up-regulated (≥1.4-fold) and 44 down-regulated (≤0.6-fold). Quantitative real-time PCR analysis validated the microarray expression results for five out of seven genes tested. The functional annotation analyses revealed a number of genes, processes and pathways with putative involvement in chicken growth and performance, while reinforcing the immune status of animals, and fostering the production of long chain fatty acids in broilers supplemented with 5 g of inulin kg−1 diet. As far as we are aware, this is the first report of a microarray based gene expression study on the effect of dietary inulin supplementation, supporting further research on the use of this prebiotic on chicken diets as a useful alternative to antibiotics for improving performance and general immunity in poultry farming, along with a healthier meat lipid profile.Universidad Complutense de Madrid / Banco Santander Central HispanoDepto. de Producción AnimalFac. de VeterinariaTRUEpu

The Southwestern fringe of Europe as an important reservoir of caprine biodiversity

Background: Portugal and Spain, with six and 22 officially recognized caprine breeds, encompass 25 % of the European Union goat census. Many of these populations have suffered strong demographic declines because of competition with exotic breeds and the phasing-out of low income rural activities. In this study, we have investigated the consequences of these and other demographic processes on the genetic diversity, population structure and inbreeding levels of Iberian and Atlantic goats. Methods: A sample of 975 individuals representing 25 officially recognized breeds from Portugal and Spain, two small populations not officially recognized (Formentera and Ajuí goats) and two ecotypes of the Tinerfeña and Blanca Celtibérica breeds were genotyped with a panel of 20 microsatellite markers. A wide array of population genetics methods was applied to make inferences about the genetic relationships and demography of these caprine populations. Results: Genetic differentiation among Portuguese and Spanish breeds was weak but significant (FST = 0.07; P < 0.001), which is probably the consequence of their short splitting times and extensive gene flow due to transhumance. In contrast, Canarian goats were strongly differentiated because of prolonged geographic isolation. Most populations displayed considerable levels of diversity (mean He = 0.65). Conclusions: High diversity levels and weak population structures are distinctive features of Portuguese and Spanish breeds. In general, these local breeds have a reduced census, but are still important reservoirs of genetic diversity. These findings reinforce the need for the implementation of management and breeding programs based on genetic data in order to minimize inbreeding, maintain overall genetic and allelic diversities and breed identities, while at the same time taking into account the within-breed genetic structure.This study has been partially supported by the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) RZ2004-00037-00-00, RZ2006- 00005-C02-00, RZ2007-00005-C02-01 and RZ2007-00005-C02-02 projectsCatarina Ginja was supported by a grant from the Fundação para a Ciência e a Tecnologia (Ref. SFRH/BCC/52687/2014)Carolina Bruno de Sousa was supported by a grant from the Fundação para a Ciência e a Tecnologia (Ref. SFRH/BM/1770/2004)Depto. de Producción AnimalFac. de VeterinariaTRUEpu