1,721,009 research outputs found
Accomplishments and new challenges in dairy genetic evaluations
No full textThis review presents the evolution of dairy
genetic methods to estimate breeding values.
For centuries, human action has shaped animal
populations by choosing progenitors of the
next generation. Since the twentieth century,
applied concepts were integrated into a new
discipline, quantitative genetics. The past
quarter-century in genetic evaluation of dairy
cattle has been marked by evolution in
methodology and computer capacity, expansion
in the array of evaluated traits, and globalization.
Selection index was replaced by
mixed model procedures and animal models
replaced by sire and sire-maternal grandsire
models. Recently, application of Bayesian theory
to breeding values prediction and variance
components estimation has become standard.
Individual test-day observations have been
used more effectively in the estimation of lactation
yield as direct input to evaluation models.
Computer speed and storage are less limiting
in choosing procedures. National evaluations
combined internationally provide evaluations
for bulls from all participating countries
on each of the national scales, facilitating
choices from among many more bulls.
Selection within countries has increased
inbreeding and the use of similar genetics
across countries reduces the previously available
genetic diversity. Finally, considerable
progress in genomics has created a new tool,
genomic selection. The collection and analysis
of several types of phenotypic data to evaluate
genetic merit will continue to be the most
important tool for genetic progress in the foreseeable
future. Information will increasingly
be obtained from smaller reference populations
and the extrapolation from these data
will require careful validation
Threshold and linear models for the genetic analysis of bull fertility in the Italian Brown Swiss population
No full text
Comparison between different statistical models for the prediction of direct genetic component on embryo establishment and survival in Italian Brown Swiss dairy cattle
Full text linkThe aims of this study were to infer variance components and heritability for the direct component on embryo establishment and survival related traits and to compare different statistical models in terms of goodness-of-fit and predictive ability. Embryo establishment and survival (EES) was defined as the outcome of an AI event, its direct effect was represented as the effect of the service sire from which semen was taken. Indicators of EES were calving per service (CS) and non-return at 56. d after service (NR56). Insemination records from the Italian Brown Swiss population reared in the Alps were used. Data included 124,206 inseminations performed by 86 technicians on 28,873 cows in 1400 herds. Services were recorded from 1999 to 2008. Linear-sire, linear-animal, threshold-sire, and threshold-animal models were used to estimate (co)variance components for CS and NR56. Four levels of complexity within each model were tested, so that 16 different models were compared for each of the two fertility traits. Comparison was assessed on the basis of the goodness-of-fit and predictive ability. Paternal half-sibs groups were created as average outcome of the inseminations from a given service sire. Goodness-of-fit was evaluated by regressing the service sire estimated breeding value from each model to paternal half-sibs average CS or NR56. Predictive ability was assessed through sums of chi-squared and percentage of wrong predictions. Predictors were the respective service sire's estimated breeding values constructed on a reduced (independent) training dataset, including years from 1999 to 2005, and predictands were the paternal half-sibs means for every bull in the remaining years (2006-2008). Prediction of EES was considered differently according to whether service sires had observations in the training dataset (prediction of proven bulls) or they had not (prediction of young bulls). Estimates of heritability ranged from 0.011 to 0.119 for CS, and from 0.005 to 0.054 for NR56. In general, threshold models explained a larger proportion of additive genetic variance than linear models, and animal models yielded higher heritabilities than sire models. Calving per service was much more predictable than NR56, but no significant differences were found among models. Although heritabilities were low, the prediction of future EES of a paternal half-sib group is feasibl
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
No full textIn the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (similar to 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding
A first characterization of the microbiota-resilience link in swine
Full text linkBackground: The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not directly observable, we estimated it using four distinct indicators based on daily feed consumption variability, assuming animals with greater intake variation may face challenges in maintaining stable physiological status. These indicators were analyzed both as linear and categorical variables. In our first set of analyses, we explored the microbiota-resilience link using PERMANOVA, α-diversity analysis, and discriminant analysis. Additionally, we quantified the ratio of estimated microbiota variance to total phenotypic variance (microbiability). Finally, we conducted a Partial Least Squares-Discriminant Analysis (PLS-DA) to assess the classification performance of the microbiota with indicators expressed in classes. Results: This study offers four key insights. Firstly, among all indicators, two effectively captured resilience. Secondly, our analyses revealed robust relationship between microbial composition and resilience in terms of both composition and richness. We found decreased α-diversity in less-resilient animals, while specific amplicon sequence variants (ASVs) and KEGG pathways associated with inflammatory responses were negatively linked to resilience. Thirdly, considering resilience indicators in classes, we observed significant differences in microbial composition primarily in animals with lower resilience. Lastly, our study indicates that gut microbial composition can serve as a reliable biomarker for distinguishing individuals with lower resilience. Conclusion: Our comprehensive analyses have highlighted the host-microbiota and resilience connection, contributing valuable insights to the existing scientific knowledge. The practical implications of PLS-DA and microbiability results are noteworthy. PLS-DA suggests that host-microbiota interactions could be utilized as biomarkers for monitoring resilience. Furthermore, the microbiability findings show that leveraging host-microbiota insights may improve the identification of resilient animals, supporting their adaptive capacity in response to changing environmental conditions. These practical implications offer promising avenues for enhancing animal well-being and adaptation strategies in the context of environmental challenges faced by livestock populations. 7uyXcYriZkKxPgmfB9NKtx Video Abstract
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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