Implementation of an extended ZINB model in the study of low levels of natural gastrointestinal nematode infections in adult sheep

Background: In this study, two traits related with resistance to gastrointestinal nematodes (GIN) were measured in 529 adult sheep: faecal egg count (FEC) and activity of immunoglobulin A in plasma (IgA). In dry years, FEC can be very low in semi-extensive systems, such as the one studied here, which makes identifying animals that are resistant or susceptible to infection a difficult task. A zero inflated negative binomial model (ZINB) model was used to calculate the extent of zero inflation for FEC; the model was extended to include information from the IgA responses. Results: In this dataset, 64 % of animals had zero FEC while the ZINB model suggested that 38 % of sheep had not been recently infected with GIN. Therefore 26 % of sheep were predicted to be infected animals with egg counts that were zero or below the detection limit and likely to be relatively resistant to nematode infection. IgA activities of all animals were then used to decide which of the sheep with zero egg counts had been exposed and which sheep had not been recently exposed. Animals with zero FEC and high IgA activity were considered resistant while animals with zero FEC and low IgA activity were considered as not recently infected. For the animals considered as exposed to the infection, the correlations among the studied traits were estimated, and the influence of these traits on the discrimination between unexposed and infected animals was assessed. Conclusions: The model presented here improved the detection of infected animals with zero FEC. The correlations calculated here will be useful in the development of a reliable index of GIN resistance that could be of assistance for the study of host resistance in studies based on natural infection, especially in adult sheep, and also the design of breeding programs aimed at increasing resistance to parasites

Mitochondrial DNA variability in spanish sheep breeds

Mitochondrial DNA variability was studied in indigenous Iberian sheep and results analysed for each of the four morphological trunks. Three maternal lineages, B, A and C were identified. Mean nucleotide diversity for each of the ovine groups was estimated, showing a lower value for the churro trunk, intermediate values for entrefino and merino trunks, while the iberian group had the greatest mitochondrial diversity. Within the churro trunk all mitochondrial DNA sequences belonged to haplogroup B, also known as European type, and among churro breeds Latxa sheep showed the lowest diversity of all Iberian sheep analysed. A few animals of the entrefino trunk showed a maternal A, or Asiatic, lineage, namely Spanish Manchega and Portuguese Serra da Estrela sheep. In the merino group Merino Branco breed showed differences with the rest of sheep, particularly much greater nucleotide diversity and the presence of animals of maternal lineage A. On the other hand, moderate diversity was evident among the rest of merino populations, as it was the case of Spanish pure Merino for which all animals belonged to maternal lineage B. Finally, the iberian trunk showed the highest mean nucleotide diversity and in this group maternal lineage C was identified. The presence of this mitochondrial DNA type was evident in both breeds corresponding to this trunk: Montesina and Ojalada. This result is of particular relevance since this maternal lineage has been discovered quite recently and mainly in Asiatic ovines.Se estudió la variabilidad en el DNA mitocondrial en distintas razas ovinas ibéricas y los resultados obtenidos se analizaron para cada uno los cuatro troncos etnológicos. Se identificaron los tres linajes maternos conocidos como B, A y C. La diversidad nucleotídica promedio estimada para cada uno de los grupos ovinos fue menor para el tronco churro, intermedia para los grupos entrefino y merino, mientras que el tronco ibérico mostró la mayor diversidad mitocondrial. En el tronco churro todas las secuencias de DNA mitocondrial correspondieron al haplogrupo B, también denominado europeo, y entre sus razas la Latxa fue la de menor diversidad de todos las razas Ibéricas analizadas. En el tronco entrefino se identificaron unos pocos animales del linaje materno A, o asiático, en concreto en la raza española Manchega y en la portuguesa Serra da Estrela. En la agrupación merina se encontraron diferencias entre la raza Merino Branco y el resto, mostrando la primera una diversidad nucleotídica muy superior, así como la presencia de algunos animales del linaje A. Por el contrario, en el resto de las poblaciones merinas, entre ellas el Merino puro español, se detectó una variabilidad moderada y sus animales pertenecían en todos los casos al linaje materno B. Finalmente, el tronco ibérico presentó el valor promedio más elevado de diversidad nucleotídica y en esta agrupación ovina se identificó el linaje materno C. La presencia de este tipo de DNA mitocondrial fue puesta de manifiesto en ambas razas representantes de este tronco, Montesina y Ojalada. Este resultado es de particular relevancia dado que este linaje materno ha sido descubierto no hace mucho tiempo y fundamentalmente en ovinos asiáticos

Estimation of genetic parameters for cheese-making traits in Spanish Churra sheep

Artículo de investigaciónThe global production of sheep milk is growing, and the main industrial use of sheep milk is cheese making. The Spanish Churra sheep breed is one of the most important native dairy breeds in Spain. The present study aimed to estimate genetic parameters for a wide range of traits influencing the cheese-making ability of Churra sheep milk. Using a total of 1,049 Churra ewes, we studied the following cheese-making traits: 4 traits related to milk coagulation properties (rennet coagulation time, curd-firming time, and curd firmness at 30 and 60 min after addition of rennet), 2 traits related to cheese yield (individual laboratory cheese yield and individual laboratory dried curd yield), and 3 traits measuring curd firmness over time (maximum curd firmness, time to attain maximum curd firmness, and syneresis). In addition, a list of milk traits, including the native pH of the milk and several milk production and composition traits (milk yield; the fat, protein, and dried extract percentages; and the somatic cell count), were also analyzed for the studied animals. After discarding the noncoagulating samples (only 3.7%), data of 1,010 ewes were analyzed with multiple-trait animal models by using the restricted maximum likelihood method to estimate (co)variance components, heritabilities, and genetic correlations. In general, the heritability estimates were low to moderate, ranging from 0.08 (for the individual laboratory dried curd yield trait) to 0.42 (for the fat percentage trait). High genetic correlations were found within pairs of related traits (i.e., 0.93 between fat and dried extract percentages, −0.93 between the log of the curd-firming time and curd firmness at 30 min, 0.70 between individual laboratory cheese yield and individual laboratory dried curd yield, and −0.94 between time to attain maximum curd firmness and syneresis). Considering all the information provided here, we suggest that in addition to the current consideration of the protein percentage trait for improving cheese yield traits, the inclusion of the pH of milk as a measured trait in the Churra dairy breeding program would represent an efficient strategy for improving the cheese-making ability of milk from this breed.S

Análisis del genoma ovino para la identificación de QTL con influencia sobre caracteres de morfología mamaria: resultados preliminares

Ponencia publicada en ITEA, vol.104El objetivo del presente estudio es la localización de regiones genómicas con influencia sobre caracteres de morfología mamaria en ganado ovino, utilizando la metodología de genome scan, o barrido genómico. Con este fin, se ha analizado una población comercial de ganado ovino de raza Churra, organizada en un diseño hija compuesto por 8 familias de medio-hermanas. Un total de 182 marcadores genéticos, distribuidos uniformemente a lo largo del genoma ovino autosómico, fueron genotipados en la población objeto de estudio. Como medidas cuantitativas se utilizaron las desviaciones calculadas para los caracteres de morfología mamaria considerados en el programa de mejora genética de la raza ovina Churra: inserción de la ubre, posición de los pezones, tamaño de los pezones, profundidad y forma global de la ubre. Para la identificación de los QTL se realizó un análisis de regresión de los fenotipos con marcadores flanqueantes. El análisis del genoma para el conjunto de la población permitió la identificación de 11 regiones asociadas con estos caracteres, al nivel chromosome-wise, en los siguientes cromosomas: 4, 6, 7, 8, 10, 14, 15, 20, 22, 23 y 26. Para las asociaciones significativas se debe realizar una verificación previamente al abordaje del mapeo fino.Analysing the ovine genome to detect QTL for mammary morphology: preliminary results The objective of this work was the identification of chromosomal regions influencing udder morphology traits in dairy sheep by using the genome scan approach. For this purpose, we have analyzed a commercial population of Spanish Churra sheep organized according a daughter design, which included 8 half-sib families. A total of 182 genetic markers, evenly distributed along the ovine autosome, were genotyped in the studied population. As quantitative measurements for the analysis, we used the yield deviations calculated for each of the udder traits considered in the breeding program of Churra sheep: udder attachment, teat position and teat size, udder depth and udder shape. A multimarker regression analysis was used to detect QTL. The whole genome analysis allowed the identification of 11 chromosome-wide significant regions associated with the traits analyzed in the following chromosomes: 4, 6, 7, 8, 10, 14, 15, 20, 22, 23 y 26. Confirmation of the detected effects is required before attempting future fine mapping studies on these regions

Quantum-well states in ultrathin Ag(111) films deposited onto H-passivated Si(111)-(1x1) surfaces

Ag(111) films were deposited at room temperature onto H-passivated Si(111)-(1x1) substrates, and subsequently annealed at 300 C. An abrupt non-reactive Ag/Si interface is formed, and very uniform non-strained Ag(111) films of 6-12 monolayers have been grown. Angle resolved photoemission spectroscopy has been used to study the valence band electronic properties of these films. Well-defined Ag sp quantum-well states (QWS) have been observed at discrete energies between 0.5-2eV below the Fermi level, and their dispersions have been measured along the GammaK, GammaMM'and GammaL symmetry directions. QWS show a parabolic bidimensional dispersion, with in-plane effective mass of 0.38-0.50mo, along the GammaK and GammaMM' directions, whereas no dispersion has been found along the GammaL direction, indicating the low-dimensional electronic character of these states. The binding energy dependence of the QWS as a function of Ag film thickness has been analyzed in the framework of the phase accumulation model. According to this model, a reflectivity of 70% has been estimated for the Ag-sp states at the Ag/H/Si(111)-(1x1) interface.Comment: 6 pages, 6 figures, submitted to Phys. Rev.

Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds

20 p.This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.S

Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.Publishe