Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.

Performance of genomic selection under a single-step approach in autochthonous Spanish beef cattle populations

This study evaluated different strategies for implementing a single-step genomic selection programme in two autochthonous Spanish beef cattle populations (Pirenaica-Pi and Rubia Gallega-RG). The strategies were compared in terms of accuracy attained under different scenarios by simulating genomic data over the known genealogy. Several genotyping approaches were tested, as well as, other factors like marker density, effective population size, mutation rate and heritability of the trait. The results obtained showed gains in accuracy with respect to pedigree BLUP evaluation in all cases. The greatest benefit was obtained when the candidates to selection had their genotypes included in the evaluation. Moreover, genotyping the individuals with the most accurate predictions maximized the gains but other suboptimal strategies also yielded satisfactory results. Furthermore, the gains in accuracy increased with the marker density reaching a plateau at around 50,000 markers. Likewise, the effective population size and the mutation rate have also shown an effect, both increasing the accuracy with decreasing values of these population parameters. Finally, the results obtained for the RG population showed greater gains compared to the Pi population, probably attributed to the wider implantation of artificial insemination.

Detección de regiones genómicas con elevado desequilibrio de ligamiento en poblaciones de vacuno de carne españolas con análisis de BovineHD BeadChip

El objetivo de este trabajo fue evaluar el patrón de desequilibrio de ligamiento a lo largo del genoma en siete poblaciones españolas autóctonas de vacuno de carne (Asturiana de los Valles, Avileña Negra-Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta y Rubia Gallega). Para ello, se utilizó el BovineHD BeadChip con el que se genotiparon 171 tríos formados por individuo/padre/madre. Después del filtrado, se dispuso de 573.134 SNP. A partir de esta información se definió un parámetro que mide el desequilibrio medio del genoma por regiones de 1Mb en cada una de las poblaciones. Los resultados mostraron que el desequilibrio de ligamiento es muy heterogéneo a lo largo del genoma y que, además, esta heterogeneidad es consistente entre poblaciones. Las causas de esta heterogeneidad pueden ser, o bien estructurales y atribuibles a una menor tasa de mutación y/o recombinación, o bien consecuencia de procesos de selección estabilizadora.

Consumer Beliefs and Attitudes Towards Dry-cured Ham and Protected Designation of Origin Teruel Ham in Two Spanish Regions Differing in Product Knowledge

This work compared the responses of a consumer survey on beliefs and attitudes towards dry-cured ham and protected designation of origin (PDO) Teruel ham carried out in two Spanish regions differing in Teruel ham knowledge: Aragon (high knowledge) and Catalonia (lower knowledge). Results revealed that only small differences were found regarding dry-cured ham consumption habits. With regard to beliefs related to factors affecting ham quality, differences were even lesser; raw material and maturing process, as well as marbling, colour and flavour and proper saltiness were rated as the most important quality factors. Nevertheless, large significant differences were evident between both regions in knowledge, consumption, beliefs and attitudes towards PDO Teruel ham. However, there were no differences regarding the willingness to pay a higher price for PDO ham. Multiple correspondence analysis of all data revealed large effects of age, education, income level and size of the place of residence, independent from the region of origin of the consumer.

Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip

The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Nei's D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

Monitoring changes in the demographic and genealogical structure of the main Spanish local beef breeds

Demographic and pedigree analyses describe the structure and dynamics of livestock populations. We studied information recorded in the herdbooks of Asturiana de los Valles (AV; N = 458,806), Avileña-Negra Ibérica (ANI; N = 204,623), Bruna dels Pirineus (BP; N = 62,138), Morucha (Mo; N = 65,350), Pirenaica (Pi; N = 217,428), Retinta (Re; N = 135,300), and Rubia Gallega (RG; N = 235,511) beef breeds from their creation until 2009. All breeds have increased in the number of registered cows in recent years. In all breeds, herds do not behave as isolated entities and a high rate of exchange of breeding males between herds exists. A percentage of herds (12-52%) make some type of selection and sell bulls to other herds. There were large differences in average number of progeny per bull, ranging from 15.6 (AV) to 373.7 animals (RG, with a high incidence of AI). Generation interval estimates ranged from 4.7 (AV) to 7.6 (RG) yr in the sire pathway and from 5.95 (AV) to 7.8 (Mo) yr in the dam pathway. Density of pedigrees varied among breeds, with Pi, ANI, and Re having the more dense pedigrees, with average completeness indexes of more than 96% in the first generation and 80% when 6 generations were considered. A general increase in average inbreeding was observed in all breeds in the years analyzed. For animals born in 2009, average inbreeding coefficients ranged from 0.6 (BP) to 7.2% (Re) when all animals were considered and from 3.6 (Pi) to 17.6% (BP) when only inbred animals were considered. Due to the lack of completeness of pedigrees in most populations, inbreeding coefficients may be considered as a lower bound of the true parameters. The proportion of inbred animals tended to increase in the periods analyzed in all breeds. Differences between inbreeding and coancestry rates (except in RG) suggest the presence of population structure. Effective population size (Ne) based on the inbreeding rate estimated by regression ranged from 43 to 378 for Re and BP, whereas Ne estimates based on coancestry were greater, with a range of 100 for RG to 9,985 for BP. These facts suggest that an adequate mating policy can help to monitor inbreeding so as not to lose genetic variability. Effective number of ancestors in 2009 for 6 of the breeds ranged from 42 (RG) to 220 (AV), with BP having much a greater value, and was lower than was the effective number of founders in all breeds, suggesting the existence of bottlenecks.

The bovine annexin 9 gene (ANXA9) is significantly associated with milk-fat yield in a Spanish Holstein-Friesian population

On the basis of QTL studies for milk-fat yield trait on BTA3, annexin 9 protein (ANXA9), fatty acid transport protein type 3 (SLC27A3) and diacylglycerol O-acyltransferase 1 (DGAT1) were selected as candidate genes. Three different single nucleotide polymorphisms (SNPs) of bovine ANXA9, SLC27A3 and DGAT1 genes have been tested in a selective genotyping design for milk-fat yield. Significant allele frequency differences were found for ANXA9 (p=0.02), in Holstein-Friesian animals with high and low breeding values for milk-fat yield. Regression analysis also showed a significant effect (p=0.0207) between estimated breeding values (EBVs) for fat milk content and ANXA9 polymorphism. So ANXA9 gene falls into a significant quantitative trait loci interval for milk-fat yield that was previously reported on bovine chromosome 3 in other dairy populations. Our results suggest that the ANXA9 gene polymorphism or a linked segregating QTL contributes to variation in milk-fat yield.

Bayesian estimates of genetic parameters for pre-conception traits, gestation length and calving interval in beef cattle

A total of 5253 records obtained from 2081 Rubia Gallega beef cows managed using artificial insemination as the only reproduction system were analysed to estimate genetic parameters for days to first insemination (DFI), days from first insemination to conception (FIC), number of inseminations per conception (IN), days open (DO), gestation length (GL) and calving interval (CI) via multitrait Bayesian procedures. Estimates of the mean of posterior distribution of the heritability of DFI, FIC, IN, DO, GL and CI were, respectively, 0.050, 0.078, 0.071, 0.053, 0.037 and 0.085 and the corresponding estimates for repeatability of these traits were 0.116, 0.129, 0.147, 0.138, 0.082 and 0.132, respectively. No significant genetic correlations associated to DFI or GL were found. However, genetic correlations between the other four analysed traits were high and significant. Genetic correlations between FIC and IN, DO and CI were similar and higher than 0.85. Genetic correlations of IN-DO and IN-CI were over 0.65. The highest genetic correlation was estimated for the pair DO-CI (0.992) that can be considered the same trait in genetic terms. Results indicated that DFI can be highly affected by non-genetic factors thus limiting its usefulness to be used as an earlier indicator of reproductive performance in beef cattle. Moreover, GL could not be associated to the reproductive performance of the cow before conception. The other four analysed traits, FIC, IN, DO and CI, have close genetic relationships. The inclusion of IN as an earlier indicator of fertility in beef cattle improvement programs using artificial insemination as the main reproductive system can be advisable due to the low additional recording effort needed.

Association of polymorphisms in the bovine FASN gene with milk-fat content

Fatty acid synthase (FASN) is a multifunctional protein that carries out the synthesis of fatty acids so it plays a central role in de novo lipogenesis in mammals. Previously, we defined the genetic structure and expression of the bovine FASN gene. Our mapping studies placed FASN on BTA19 (19q22) where several quantitative trait loci (QTL) affecting milk-fat content and related traits have been described. This study was conducted to identify polymorphisms in the bovine FASN gene and to study their association with milk-fat content. The bovine FASN gene was screened for polymorphisms in two cattle breeds. Sequence analysis revealed several single nucleotide polymorphisms (SNPs), and two of them were analysed: a G>C substitution in the untranslated exon 1 (g.763G>C), altering a potential Sp1 transcription factor-binding site, and an A>G substitution in exon 34 (g.16009A>G), which determines a non-conservative substitution of threonine by alanine. Allele-specific amplification of the SNPs in FASN revealed significant frequency differences for both polymorphisms in Holsteins with high and low breeding values for milk-fat content. The intragenic haplotypes comprising exon 1 (alleles G and C) and exon 34 (alleles A and G) polymorphisms were studied, and the existence of linkage disequilibrium between these SNPs was found (D(CG) = 0.048, P < 0.001). Our results suggest that the FASN gene polymorphisms contribute to variation in milk-fat content. We propose that the bovine FASN gene is a candidate gene for a milk-fat content QTL.

Prediction of fertility by centrifugal countercurrent distribution (CCCD) analysis: correlation between viability and heterogeneity of ram semen and field fertility

The prediction of the fertilizing ability of a sire or a given insemination dose is a primary aim in the field of artificial insemination. Centrifugal countercurrent distribution analysis (CCCD) was used to determine the relationship between some sperm parameters and the in vivo fertility rate obtained with the same sample after cervical artificial insemination. A total of 522 ewes from 26 different farms was inseminated with 53 ejaculates obtained from 25 mature Rasa aragonesa rams. Semen was diluted to 1.6 x 10(9) cells ml-1 and doses of 0.25 ml were prepared and kept at 15 degrees C until used for insemination. The same ejaculates were used for analysis of standard semen parameters and CCCD analysis. Sperm motility, concentration and viability were determined before and after CCCD. Post-CCCD parameters were derived from the analysis of the profile obtained after CCCD. The recovered viability showed the highest correlation with fertility, especially in the central chambers (V2), r = 0.415, P < 0.005). The ejaculate heterogeneity also showed a positive correlation with field fertility (r = 0.23), with a tendency towards significance (P < 0.1). The mean fertility value of all ejaculates used in this study was 46.75%, ranging from 12.5% to 75.0%. Ejaculates were classified into two categories according to their fertility: higher and lower than the mean value. Only the viability recovered in the central chambers (V2) was a parameter with a predictive capacity to discriminate between the two groups (P < 0.05). A predictive equation for field fertility with a correlation coefficient r = 0.488 and a very high level of significance (P < 0.005) was deduced by multiple analysis: PF = 6.02 + 0.069V2 + 0.315H (where PF is predictive fertility, V2 is the recovered viability in the CCCD profile central chambers and H is heterogeneity).

Semantic codes are not used in integrating information across eye fixations in reading: evidence from fluent Spanish-English bilinguals

The question of whether meaning can be extracted from unidentified parafoveal words was examined using fluent Spanish-English bilinguals. In Experiment 1, subjects fixated on a central cross, and a preview word was presented to the right of fixation in parafoveal vision. During the saccade to the parafoveal preview word, the preview was replaced by the target word, which the subject was required to name. In Experiment 2, subjects read sentences containing the target word, and, as in the naming task, a preview word was replaced by the target word when the subject's saccade crossed a boundary location. In both experiments, preview words were identical to the target word, translations, orthographic controls for the translations, or unrelated words in the opposite language. In both experiments, the preview benefit from the translation conditions was no greater than would be predicted by the orthographic similarity of the preview to the target. Hence, the data indicated that subjects obtained no useful semantic information from words seen parafoveally that enabled them to identify them more quickly on the subsequent fixation.

Novel popout and familiar popout in a brightness discrimination task

A single novel word among several familiarized words may be localized more effectively than the familiarized words (novel popout). Early demonstrations of novel popout attributed the effect to the capture of attentional resources by novel stimuli. Christie and Klein (1995, 1996) argued that differential recollection of novel versus familiar words could alternatively account for the popout effect. In the present experiments, participants judged which of four locations contained a physically brighter word. A bright novel word was localized significantly better than a bright familiar word in one-novel/three-familiar arrays, inconsistent with a retrievability account of novel popout. However, a bright familiar word was also localized better than a bright novel word in three-novel/one-familiar arrays, inconsistent with the mismatch theory proposed by Johnston and Hawley (1994). The results suggest that familiarity and novelty provide a perceptual segregation of the odd item; superior brightness discrimination at that location may be due either to attentional capture or to locational ambiguity within the larger group.

Concreteness, context availability, and imageability ratings and word associations for abstract, concrete, and emotion words

Normative values on various word characteristics were obtained for abstract, concrete, and emotion words in order to facilitate research on concreteness effects and on the similarities and differences among the three word types. A sample of 78 participants rated abstract, concrete, and emotion words on concreteness, context availability, and imagery scales. Word associations were also gathered for abstract, concrete, and emotion words. The data were used to investigate similarities and differences among these three word types on word attributes, association strengths, and number of associations. These normative data can be used to further research on concreteness effects, word type effects, and word recognition for abstract, concrete, and emotion words.

Bayesian analysis of Wood's lactation curve for Spanish dairy cows

A Bayesian procedure is presented to analyze test day performances in the scope of Wood's lactation function: atb (exp (-ct)), where a, b, and c = parameters, and t = time-dependent variable. The procedure has been applied to 148,557 test day controls corresponding to records for 15,349 first lactations of Spanish dairy cows. The procedure uses all available information and reduces the presence of atypical lactations. Moreover, the posterior marginal distribution of (co)variance components, breeding values, and systematic effects for the underlying variables of Wood's function are provided. The posterior means of the heritabilities were 0.43, 0.17, 0.40, and 0.29 for the parameters a (initial milk yield), b (ascent to peak), c (descent from peak), and total milk yield, respectively. Selection for total milk yield implies a great effect on the initial milk yield (a) but only minor effects on ascent to peak (b) and descent from peak (c).

Novel popout without novelty

Localization of a novel word in an array with several familiar words is typically enhanced relative to localization in an all-novel array (between-array novel popout) and sometimes enhanced relative to familiar words in one-novel arrays (within-array novel popout). Christie and Klein (1996) have questioned the reality of the latter effect, suggesting that it may be an artifact of guessing bias. The present Experiment 1 replicated within-array novel popout with the novel word probed at chance (i.e., on only one quarter of trials). Experiments 2 and 3 demonstrated a similar popout effect for a categorically unrelated word among three categorically related words, despite superior performance on all-related arrays relative to all-unrelated arrays. Repetition of constant sets of words within the experimental context is therefore unnecessary for a popout effect, contrary to assertions by Johnston and Hawley (1994). Interitem associations appear to be sufficient to produce a popout effect; as such, "novel popout" appears to be a misnomer for a phenomenon that does not depend on novelty.

Bayesian inference of variance components for litter size in Rasa Aragonesa sheep

Variance components were estimated for litter size in Rasa Aragonesa sheep, a meat breed from northern Spain, to determine whether selective breeding for litter size is a reasonable strategy to improve reproductive performance. We assumed an animal mixed effect threshold model with a binary response variable. Marginal estimates of the genetic parameters were obtained in the underlying scale using Bayesian inference, implemented via the Gibbs sampling procedure and a data augmentation approach. Posterior marginal means of heritability and repeatability were .077 and .141, respectively. Moreover, the 95% highest marginal posterior density region of heritability ranged from .051 to .101. Therefore, we conclude that litter size is a trait that could be selected for in breeding programs. The effect of the loss of pedigree information, a common feature of sheep production, on the estimation of the genetic parameters was also studied using simulation. The results indicate that the lack of pedigree information has little effect on our estimates of heritability.

Model determination in a case of heterogeneity of variance using sampling techniques

SUMMARY

A sampling determination procedure has been described in a case of heterogeneity of variance. The procedure makes use of the predictive distributions of each data given the rest of the data and the structure of the assumed model. The computation of these predictive distributions is carried out using a Gibbs Sampling procedure. The final criterion to compare between models is the Mean Square Error between the expectation of predictive distributions and real data. The procedure has been applied to a data set of weight at 210 days in the Spanish Pirenaica beef cattle breed. Three proposed models have been compared: (a) Single Trait Animal Model; (b) Heterogeneous Variance Animal Model; and (c) Multiple Trait Animal Model. After applying the procedure, the most adjusted model was the Heterogeneous Variance Animal Model. This result is probably due to a compromise between the complexity of the model and the amount of available information. The estimated heritabilities under the preferred model have been 0.489 ± 0.076 for males and 0.331 ± 0.082 for females. RESUMEN: Contraste de modelos en un caso de heterogeneidad de varianzas usando métodos de muestreo Se ha descrito un método de contraste de modelos mediante técnicas de muestreo en un caso de heterogeneidad de varianza entre sexos. El procedimiento utiliza las distribucviones predictivas de cada dato, dado el resto de datos y la estructura del modelo. El criterio para coparar modelos es el error cuadrático medio entre la esperanza de las distribuciones predictivas y los datos reales. El procedimiento se ha aplicado en datos de peso a los 210 días en la raza bovina Pirenaica. Se han propuesto tres posibles modelos: (a) Modelo Animal Unicaracter; (b) Modelo Animal con Varianzas Heterogéneas; (c) Modelo Animal Multicaracter. El modelo mejor ajustado fue el Modelo Animal con Varianzas Heterogéneas. Este resultado es probablemente debido a un compromiso entre la complejidad del modelo y la cantidad de datos disponibles. Las heredabilidades estimadas bajo el modelo preferido han sido 0,489 ± 0,076 en los machos y 0,331 ± 0,082 en las hembras.

Repetition blindness and bilingual memory: token individuation for translation equivalents

The repetition blindness effect (RB) occurs when individuals are unable to recall a repeated word relative to a nonrepeated word in a sentence or string of words presented in a rapid serial visual presentation task. This effect was explored across languages (English and Spanish) in an attempt to provide evidence for RB at a conceptual level using noncognate translation equivalents (e.g., nephew-sobrino). In the first experiment, RB was found when a word was repeated in an English sentence but not when the two repetitions were in different languages. In the second experiment, RB was found for identical repetitions in Spanish and in English using word lists. However, the cross-language condition produced significant facilitation in recall, suggesting that although conceptual processing had taken place, semantic overlap was not sufficient to produce RB. The results confirm Kanwisher's (1987) token individuation hypothesis in the case of translation equivalents.

The influence of lexical and conceptual constraints on reading mixed-language sentences: evidence from eye fixations and naming times

In two experiments, we explored the degree to which sentence context effects operate at a lexical or conceptual level by examining the processing of mixed-language sentences by fluent Spanish-English bilinguals. In Experiment 1, subjects' eye movements were monitored while they read English sentences in which sentence constraint, word frequency, and language of target word were manipulated. A frequency x constraint interaction was found when target words appeared in Spanish, but not in English. First fixation durations were longer for high-frequency Spanish words when these were embedded in high-constraint sentences than in low-constraint sentences. This result suggests that the conceptual restrictions produced by the sentence context were met, but that the lexical restrictions were not. The same result did not occur for low-frequency Spanish words, presumably because the slower access of low-frequency words provided more processing time for the resolution of this conflict. Similar results were found in Experiment 2 using rapid serial visual presentation when subjects named the target words aloud. It appears that sentence context effects are influenced by both semantic/conceptual and lexical information.

Constraints on priming in spatial memory: naturally learned versus experimentally learned environments

In four experiments, we explored constraints on priming in spatial memory. In Experiments 1 and 2, subjects who were familiar with the locations of buildings on the Vanderbilt campus participated in a recognition test. The subjects' task was to decide whether or not named buildings were on the campus. Foils in this recognition test were realistic but fictional names of buildings. In principle, the subjects could have performed this task without using spatial knowledge; in fact, they must not have used spatial knowledge, because there was no evidence of priming in recognition as a function of the spatial relations between buildings on the campus. This result differs from those obtained in earlier experiments that have examined memory of spatial layouts learned in laboratory settings. In Experiment 3, the fictional foils were replaced by names of buildings in an area of the campus separated geographically from the main campus. Evidently, this change induced subjects to retrieve spatial knowledge, because the spatial priming effect materialized. A fourth experiment replicated the above findings in a single experiment and demonstrated that spatial priming could be obtained when the configuration of buildings was learned experimentally. These results are explained by appealing to the "decontextualization" that takes place in memory over time.

Computer methodology for simulation and prediction of alloimmune responses: expected antibody specificities

The methodology presented here was developed for simulating planned alloimmunization results, with regard to the type and number of expected antibody specificities. The computer program designed for this purpose was adapted to an immunogenetic model using Boolean algebra. It was written to help immunogeneticists avoid handling routine data preceding selection of donor-recipient pairs, specially concerning blood type alloimmunizations in animals: all of the donor-recipient combinations and the expected antibody specificities (their limit number being specified in each particular immunization program) are provided in the print-out.