1,721,021 research outputs found
A comparison of principal component regression and genomic REML for genomic prediction across populations
No full textBackground: Genomic prediction faces two main statistical problems: multicollinearity and n ≪ p (many fewer observations than predictor variables). Principal component (PC) analysis is a multivariate statistical method that is often used to address these problems. The objective of this study was to compare the performance of PC regression (PCR) for genomic prediction with that of a commonly used REML model with a genomic relationship matrix (GREML) and to investigate the full potential of PCR for genomic prediction. Methods: The PCR model used either a common or a semi-supervised approach, where PC were selected based either on their eigenvalues (i.e. proportion of variance explained by SNP (single nucleotide polymorphism) genotypes) or on their association with phenotypic variance in the reference population (i.e. the regression sum of squares contribution). Cross-validation within the reference population was used to select the optimum PCR model that minimizes mean squared error. Pre-corrected average daily milk, fat and protein yields of 1609 first lactation Holstein heifers, from Ireland, UK, the Netherlands and Sweden, which were genotyped with 50 k SNPs, were analysed. Each testing subset included animals from only one country, or from only one selection line for the UK. Results: In general, accuracies of GREML and PCR were similar but GREML slightly outperformed PCR. Inclusion of genotyping information of validation animals into model training (semi-supervised PCR), did not result in more accurate genomic predictions. The highest achievable PCR accuracies were obtained across a wide range of numbers of PC fitted in the regression (from one to more than 1000), across test populations and traits. Using cross-validation within the reference population to derive the number of PC, yielded substantially lower accuracies than the highest achievable accuracies obtained across all possible numbers of PC. Conclusions: On average, PCR performed only slightly less well than GREML. When the optimal number of PC was determined based on realized accuracy in the testing population, PCR showed a higher potential in terms of achievable accuracy that was not capitalized when PC selection was based on cross-validation. A standard approach for selecting the optimal set of PC in PCR remains a challenge
LASSO and SVM: an alternative approach to identify associated genome regions for simple and complex traits in cattle
Full text linkVariable selection via the LASSO regression analysis followed by a classification of phenotypes into two groups of cases and controls using SVM was performed to identify genomic regions associated with phenotypic traits of interest. This approach was successfully validated by identifying previously known genomic associations for two Mendelian traits and a complex polygenic trait in Swiss cattle populations. Furthermore, new associated regions for the trait multiple birth were found in Holstein. Therefore, this approach proved to be a valuable alternative to identify associated genomic regions for inherited traits in livestock
Successful trio-based reverse genetic screen in an endangered local cattle breed
Full text linkWe scanned the genomic data of almost one thousand Evolèner cattle, representing the by far smallest local cattle population of Switzerland, whereof only pedigree records are available. A reverse genetic screen using 94k SNP markers in 585 trios mapped recessive deleterious loci using homozygous haplotype deficiency. We found two haplotypes, EH1 and EH2, with moderate allele frequencies of >0.10. Mining for candidate variants was carried out by linkage analysis of the predicted haplotype status and whole-genome sequencing variant catalogue of seven Evolèner bulls. This led to the detection of two perfectly linked missense variants affecting conserved residues: GBE1:p.Arg437Gln for EH1, and LRRC8A:p.Ala73Val for EH2. No homozygous animals were observed in >5,100 cattle of various breeds including Evolèner. The presented study showed that very limited data can lead to the identification of candidate variants and thereby help to improve reproduction success in an endangered indigenous breed of cattle
Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
Full text linkBy its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. We used whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the VarGoats goat genome project. Phylogenetic analyses indicated five domestic haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, southern Asia and Africa. Sharing of haplogroups reveals male-mediated introgressions: from Asia into Madagascar and, more recently, into the South-African Boer goat; then from this breed into other southeastern African goats; and from Europe into native Korean and Ugandan goats. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of domestic species with a wide geographic range
Genetic associations for pathogen-specific clinical mastitis and patterns of peaks in somatic cell count
No full textGenetic associations were estimated between pathogen-specific cases of clinical mastitis (CM), lactational average somatic cell score (LACSCS), and patterns of peaks in somatic cell count (SCC) which were based on deviations from the typical lactation curve for SCC. The dataset contained test-day records on SCC in 94 781 lactations of 25 416 cows of different parities. Out of these 94 781 lactations, 41 828 lactations had recordings on occurrence of pathogen-specific CM and on SCC, and 52 953 lactations had recordings on SCC only. A total of 5,324 lactations with cases of CM were recorded. Analysed pathogens were Staphylococcus aureus, coagulase negative staphylococci, Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis, and culture-negative samples. Pattern definitions were based on three or five consecutive test-day recordings of SCC. They differentiated between short or longer periods of increased SCC, and also between lactations with and without recovery. Occurrence of pathogen-specific CM and presence of patterns of peaks in SCC were both scored as binary traits. Variance components for sire, maternal grandsire, and permanent animal effects were estimated using AS-REML. The estimated heritability for overall CM was 0.04, and similar heritabilities for pathogen-specific CM were estimated. Heritabilities for the patterns of peaks in SCC ranged from 0.01 to 0.06. Heritabilities for LACSCS were 0.07 to 0.08. Genetic correlations with patterns of peaks in SCC differed for each pathogen. Generally, genetic correlations between pathogen-specific CM and patterns of peaks in SCC were stronger than the correlations with LACSCS. This suggests that genetic selection purely on diminishing presence of peaks in SCC would decrease the incidence of pathogen-specific CM more effectively than selecting purely on lower LACSCS..RE: 22 ref.; SC: 0D; 0V; 0I; 0A; ZA; CA; BE; VE; XURL: E-MAILSource type: Electronic(1)[email protected]; http://upei-resolver.asin-risa.ca?sid=SP:CABI&id=pmid:&id=&issn=1357-7298&isbn=&volume=77&issue=2&spage=187&pages=187-195&date=2003&title=Animal%20Science&atitle=Genetic%20associations%20for%20pathogen-specific%20clinical%20mastitis%20and%20patterns%20of%20peaks%20in%20somatic%20cell%20count.&aulast=Haas&pid=%3Cauthor%3EHaas%2c%20Y%20de%3bBarkema%2c%20H%20W%3bSchukken%2c%20Y%20H%3bVeerkamp%2c%20R%20F%3C%2Fauthor%3E%3CAN%3E20033154657%3C%2FAN%3E%3CDT%3EJournal%20article%3C%2FDT%3
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
The effect of pathogen-specific clinical mastitis on the lactation curve for somatic cell count
No full textData from 274 Dutch herds recording clinical mastitis (CM) over an 18-mo period were used to investigate the effect of pathogen-specific CM on the lactation curve for somatic cell count (SCC). Analyzed pathogens were Staphylococcus aureus, coagulase-negative staphylococci, Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis, other streptococci, and the culture-negative samples. The dataset contained 178,754 test-day records on SCC, recorded in 26,411 lactations of 21,525 cows of different parities. In lactations without both clinical and subclinical mastitis, SCC was high shortly after parturition, decreased to a minimum at 50 days in milk (DIM), and increased slowly toward the end of the lactation. Effects of CM on lactation curves for SCC differed among the pathogens isolated. Before a case of clinical E. coli mastitis occurred, SCC was close to the SCC of lactations without both clinical and subclinical mastitis, and after the case of CM had occurred, SCC returned rather quickly to a low level again. Similar curves were found for lactations with cases of CM associated with culture-negative samples. Before a case of clinical Staph. aureus mastitis occurred, average SCC was already high, and it remained high after the occurrence. Effects of CM associated with Strep. dysgalactiae, Strep. uberis, and other streptococci on the lactation curve for SCC were comparable. They showed a continuous increase in SCC until the case of pathogen-specific CM occurred, and afterwards SCC stayed at a higher level. Using SCC test-day records, these typical characteristics of each pathogen may be used to find more effective indicators of CM.LR: 20061115; PUBM: Print; JID: 2985126R; 0 (Coagulase); ppublishSource type: Electronic(1
Genetic parameters of pathogen-specific incidence of clinical mastitis in dairy cows
No full textData from 274 Dutch herds recording clinical mastitis (CM) over an 18-month period were used to quantify the genetic variation for overall and pathogen-specific CM. Analysed pathogens were Staphylococcus aureus, coagulase negative staphylococci (CNS), Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis and other streptococci. The data set contained 47 563 lactations of 28 695 cows of different parities. Cases of overall and pathogen-specific CM were treated as all-or-none traits. Variance components for the sire, maternal grandsire and permanent environmental effect were estimated using generalized linear mixed models with a logit link function for the binary traits. Average number of days at risk and in milk on trial was 198 days. The estimated heritability for overall CM was 0.04, and similar heritabilities for the pathogen-specific CM were estimated. Repeatability across lactations was low for overall and pathogen-specific CM (0.10 to 0.14). Genetic correlations with milk yield and somatic cell score (SCS) differed according to pathogen. For instance, the incidence rate of clinical E. coli mastitis was slightly unfavourably correlated with milk yield at 150 days (0.13) but stronger with SCS (0.74). Whereas, the genetic correlations with clinical Str. dysgalactiae mastitis were 0.70 and 0.16, respectively. The expected correlated responses showed that current selection practices (using milk yield and SCS) will be effective in reducing the incidence of E. coli and CNS but less effective in reducing the incidence of S. aureus and Str. dysgalactiae, even with a large relative weight for SCS in the selection index..RE: 38 ref.; SC: ZA; 0D; 0A; 0V; 0I; VE; CA; BE; XURL: E-MAILSource type: Electronic(1)[email protected]; http://upei-resolver.asin-risa.ca?sid=SP:CABI&id=pmid:&id=&issn=1357-7298&isbn=&volume=74&issue=2&spage=233&pages=233-242&date=2002&title=Animal%20Science&atitle=Genetic%20parameters%20of%20pathogen-specific%20incidence%20of%20clinical%20mastitis%20in%20dairy%20cows.&aulast=Haas&pid=%3Cauthor%3EHaas%2c%20Y%20de%3bBarkema%2c%20H%20W%3bVeerkamp%2c%20R%20F%3C%2Fauthor%3E%3CAN%3E20023035591%3C%2FAN%3E%3CDT%3EJournal%20article%3C%2FDT%3
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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