Identification of nonsense variants in the genomes of 15 Murciano-Granadina bucks and analysis of their segregation in parent-offspring trios.

Nonsense variants can inactivate gene function by causing the synthesis of truncated proteins or by inducing nonsense mediated decay of messenger RNAs. The occurrence of such variants in the genomes of livestock species is modulated by multiple demographic and selective factors. Even though nonsense variants can have causal effects on embryo lethality, abortions, and disease, their genomic distribution and segregation in domestic goats have not been characterized in depth yet.

The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data.

Background: The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds.

Single and longitudinal genome-wide association studies for dairy traits available in goats with three recorded lactations.

Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2.

Univariate and multivariate genome-wide association studies for hematological traits in Murciano-Granadina goats.

Hematological traits are important indicators of health status, and they are frequently used as criteria for clinical diagnosis. In humans, the genomic architecture of blood traits has been investigated in depth and thousands of associations with genetic variants have been found. In contrast, the association between marker genotypes and the variation of hematological traits has not been investigated in goats yet.

Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats.

Background: Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.

Results: We genotyped 1040 goats with the Goat SNP50 BeadChip.

On the origins of American Criollo pigs: A common genetic background with a lasting Iberian signature.

American Criollo pigs are thought to descend mainly from those imported from the Iberian Peninsula starting in the late 15th century. Criollo pigs subsequently expanded throughout the Americas, adapting to very diverse environments, and possibly receiving influences from other origins. With the intensification of agriculture in the mid-20th century, cosmopolitan breeds largely replaced Criollo pigs, and the few remaining are mostly maintained by rural communities in marginal areas where they still play an important socio-economic and cultural role.

A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats.

Morphological traits are of great importance to dairy goat production given their effect on phenotypes of economic interest. However, their underlying genomic architecture has not yet been extensively characterized. Herein, we aimed to identify genomic regions associated with body, udder, and leg conformation traits recorded in 825 Murciano-Granadina goats.

Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers.

The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique.

Author Correction: The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats.

Background: In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e.

Effect of olive-derived antioxidants (3,4-dihydroxyphenylethanol and 3,4 dihydroxyphenylglycol) on sperm motility and fertility in liquid ram sperm stored at 15°C or 5°C.

The aim of the present study was to evaluate the effect of the addition of two olive oil-derived antioxidants, hydroxytyrosol (3,4-dihydroxyphenylethanol, HT) and 3,4-dihydroxyphenylglycol (DHPG), on ovine semen during liquid storage at 5°C and 15°C. Semen was collected, pooled, diluted and then divided into aliquots supplemented with different concentrations (5 μg/ml, 10 μg/ml, 50 μg/ml and 100 μg/ml) of HT, DHPG and a mixture (MIX) of both antioxidants. Sperm motility characteristics were assessed in the different samples at 0, 6, 24, 48, 72 and 96 hr after cooling, and a fertility trial was also conducted.

Effect of three commercial extenders on sperm motility and fertility in liquid ram semen stored at 15 °C or 5 °C.

The effect of different extenders on sperm motility and fertility was evaluated during liquid storage of ram semen at 5 °C and 15 °C. The semen was collected, pooled and diluted in three commercial extenders: Inra 96® (INRA) based on skimmed milk, Biladyl® A fraction (BIL) based on egg yolk, and Ovixcell® (OVIX) based on soybean lecithin. Then, sperm motility was evaluated at 0, 6, 24, 48, 72 and 96 h.

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.

Vitrification induces critical subcellular damages in ram spermatozoa.

The aim of the present study was to analyse morphological variations in ovine spermatozoa subjected to different cryopreservation protocols using high resolution imaging techniques. Ejaculates were pooled and diluted in Tris-based extender. Aliquots containing 300 × 10 spz/ml were prepared and evaluated a) after the semen collection and pooling, b) after conventional freezing, c) after vitrification of samples maintained at room temperature (22 °C) prior to vitrification, and d) after vitrification of samples maintained at 5 °C prior to vitrification.

Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds.

The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations.

Measuring and modeling for the assessment of the genetic background behind cognitive processes in donkeys.

New productive niches can offer new commercial perspectives linked to donkeys' products and human therapeutic or leisure applications. However, no assessment for selection criteria has been carried out yet. First, we assessed the animal inherent features and environmental factors that may potentially influence several cognitive processes in donkeys.

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach.

Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats.

Molecular Study of the Amazonian Macabea Cattle History.

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered.

A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds.

Background: The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes.

Results: Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina).

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.

Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers.

Background: Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions.

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands.

Background: Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies.

Methods: A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results.