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1.
Nature ; 625(7994): 329-337, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38200294

RESUMO

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.


Assuntos
Genoma Humano , Genômica , Migração Humana , Populações Escandinavas e Nórdicas , Humanos , Dinamarca/etnologia , Emigrantes e Imigrantes/história , Genótipo , Populações Escandinavas e Nórdicas/genética , Populações Escandinavas e Nórdicas/história , Migração Humana/história , Genoma Humano/genética , História Antiga , Pólen , Dieta/história , Caça/história , Fazendeiros/história , Cultura , Fenótipo , Conjuntos de Dados como Assunto
2.
Genet Sel Evol ; 55(1): 54, 2023 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-37491205

RESUMO

BACKGROUND: In commercial pig production, reduction of harmful social behavioural traits, such as ear manipulation and tail biting, is of major interest. Moreover, farmers prefer animals that are easy to handle. The aim of this experiment was to determine whether selection on social breeding values (SBV) for growth rate in purebred pigs affects behaviour in a weighing crate, lesions from ear manipulation, and tail biting of their crossbred progeny. Data were collected on crossbred F1 pigs allocated to 274 pens, which were progeny of purebred Landrace sows and Yorkshire boars from a DanBred nucleus herd. RESULTS: Behaviour in the weighing crate scored on a three-level scale showed that groups of pigs with high SBV for growth rate were significantly calmer than groups of pigs with low SBV (P < 0.027). When the mean SBV in the group increased by 1 unit, the proportion of pigs that obtained a calmer score level was increased by 14%. A significant (p = 0.04), favourable effect of SBV was found on both the number of pigs with ear lesions in the group and the mean number of ear lesions per pig. For a 1 unit increase in mean SBV, the mean number of lesions per pig decreased by 0.06 from a mean of 0.98. Individual severity of ear lesions conditional upon the number of ear lesions was also significantly affected (p = 0.05) by the mean SBV in the group. In groups for which the mean SBV increased by 1 unit, the proportion of pigs that were observed with a lower severity score was increased by 20% on a three-level scale. Most pigs received no tail biting injuries and no effect of SBV was observed on the tail injury score. CONCLUSIONS: After 7 weeks in the finisher unit, crossbred progeny with high SBV were calmer in the weighing crate and had fewer ear lesions. These results indicate that selection of purebred parents for SBV for growth rate will increase welfare in their crossbred progeny by decreasing the number of ear lesions and making them easier to handle.


Assuntos
Comportamento Animal , Mordeduras e Picadas , Suínos/genética , Animais , Feminino , Masculino , Cauda/lesões
3.
Genet Sel Evol ; 54(1): 25, 2022 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-35387581

RESUMO

BACKGROUND: In livestock breeding, selection for some traits can be improved with direct selection for crossbred performance. However, genetic analyses with phenotypes from crossbred animals require methods for multibreed relationship matrices; especially when some animals are rotationally crossbred. Multiple methods for multibreed relationship matrices exist, but there is a lack of knowledge on how these methods compare for prediction of breeding values with phenotypes from rotationally crossbred animals. Therefore, the objective of this study was to compare models that use different multibreed relationship matrices in terms of ability to predict accurate and unbiased breeding values with phenotypes from two-way rotationally crossbred animals. METHODS: We compared four methods for multibreed relationship matrices: numerator relationship matrices (NRM), García-Cortés and Toro's partial relationship matrices (GT), Strandén and Mäntysaari's approximation to the GT method (SM), and one NRM with metafounders (MF). The methods were compared using simulated data. We simulated two phenotypes; one with and one without dominance effects. Only crossbred animals were phenotyped and only purebred animals were genotyped. RESULTS: The MF and GT methods were the most accurate and least biased methods for prediction of breeding values in rotationally crossbred animals. Without genomic information, all methods were almost equally accurate for prediction of breeding values in purebred animals; however, with genomic information, the MF and GT methods were the most accurate. The GT, MF, and SM methods were the least biased methods for prediction of breeding values in purebred animals. CONCLUSIONS: For prediction of breeding values with phenotypes from rotationally crossbred animals, models using the MF method or the GT method were generally more accurate and less biased than models using the SM method or the NRM method.


Assuntos
Hibridização Genética , Modelos Genéticos , Animais , Genoma , Genótipo , Modelos Animais , Fenótipo
4.
Heredity (Edinb) ; 126(1): 206-217, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32665691

RESUMO

Records on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.


Assuntos
Cruzamento , Genômica , Animais , Suínos
5.
Genet Sel Evol ; 53(1): 15, 2021 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-33579188

RESUMO

BACKGROUND: Average daily gain (ADG) in pigs is affected by both direct and social genetic effects (SGE). However, selection for SGE in purebreds has not conclusively been shown to improve ADG in crossbreds, and it is unknown whether SGE in purebreds are equal to those in crossbreds. Moreover, SGE may reflect dominance related behaviour, which is affected by the variation in body weight within a group. Therefore, we hypothesized that (a) there is a positive effect of parent average SGE estimated in purebred pigs on phenotypic ADG in crossbred offspring, and (b) there is an interaction between SGE on ADG and standard deviation in starting weight of pigs within the group. We also hypothesized that (c) social genetic variance for ADG exists in crossbred pigs, and (d) there is a favourable genetic correlation between SGE on ADG in purebred and crossbred pigs. RESULTS: We found a statistically significant interaction between the standard deviation in starting weight and SGE within groups, and conditioning on the mean standard deviation in starting weight, we found a favourable regression coefficient (0.37 ± 0.21) of ADG in crossbreds on SGE in purebreds. Variances for SGE were small in both Landrace (L) and Yorkshire (Y), and higher for SGE in both the dam and sire component of crossbred YL. The genetic correlations between SGE in purebreds and the dam or sire component of SGE in crossbreds were also favourable (0.52 ± 0.48 and 0.34 ± 0.42, respectively), although not significantly different from 0. CONCLUSIONS: We confirmed that there is a positive effect of SGE estimated using purebred information on phenotypic ADG in crossbreds, and that the largest effect is achieved when the within-group variation in starting weight is small. Our results indicate that social genetic variance in crossbreds exists and that there is a favourable genetic correlation between social genetic effects in purebreds and crossbreds. Collectively, our results indicate that selection for SGE on ADG in purebreds in a nucleus farm environment with little competition for resources can improve ADG in crossbreds in a commercial environment.


Assuntos
Interação Gene-Ambiente , Seleção Artificial , Meio Social , Suínos/genética , Aumento de Peso , Animais , Feminino , Hibridização Genética , Endogamia , Masculino , Seleção Genética , Suínos/fisiologia
6.
Genet Sel Evol ; 53(1): 33, 2021 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-33832423

RESUMO

BACKGROUND: In breeding programs, recording large-scale feed intake (FI) data routinely at the individual level is costly and difficult compared with other production traits. An alternative approach could be to record FI at the group level since animals such as pigs are normally housed in groups and fed by a shared feeder. However, to date there have been few investigations about the difference between group- and individual-level FI recorded in different environments. We hypothesized that group- and individual-level FI are genetically correlated but different traits. This study, based on the experiment undertaken in purebred DanBred Landrace (L) boars, was set out to estimate the genetic variances and correlations between group- and individual-level FI using a bivariate random regression model, and to examine to what extent prediction accuracy can be improved by adding information of individual-level FI to group-level FI for animals recorded in groups. For both bivariate and univariate models, single-step genomic best linear unbiased prediction (ssGBLUP) and pedigree-based BLUP (PBLUP) were implemented and compared. RESULTS: The variance components from group-level records and from individual-level records were similar. Heritabilities estimated from group-level FI were lower than those from individual-level FI over the test period. The estimated genetic correlations between group- and individual-level FI based on each test day were on average equal to 0.32 (SD = 0.07), and the estimated genetic correlation for the whole test period was equal to 0.23. Our results demonstrate that by adding information from individual-level FI records to group-level FI records, prediction accuracy increased by 0.018 and 0.032 compared with using group-level FI records only (bivariate vs. univariate model) for PBLUP and ssGBLUP, respectively. CONCLUSIONS: Based on the current dataset, our findings support the hypothesis that group- and individual-level FI are different traits. Thus, the differences in FI traits under these two feeding systems need to be taken into consideration in pig breeding programs. Overall, adding information from individual records can improve prediction accuracy for animals with group records.


Assuntos
Fenômenos Fisiológicos da Nutrição Animal/genética , Peso Corporal , Cruzamento/métodos , Característica Quantitativa Herdável , Suínos/genética , Animais , Ingestão de Alimentos , Linhagem , Suínos/fisiologia
7.
Genet Sel Evol ; 52(1): 23, 2020 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-32375639

RESUMO

An amendment to this paper has been published and can be accessed via the original article.

8.
Genet Sel Evol ; 51(1): 45, 2019 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-31426753

RESUMO

BACKGROUND: Crossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content, whereas maternal lines are also bred for reproduction and longevity traits, and the resulting three-way crossbred pigs are used for production of meat. The most important genetic basis for heterosis is dominance effects, e.g. removal of inbreeding depression. The aims of this study were to (1) present a modification of a previously developed model with additive, dominance and inbreeding depression genetic effects for analysis of data from a purebred sire line and three-way crossbred pigs; (2) based on this model, present equations for additive genetic variances, additive genetic covariance, and estimated breeding values (EBV) with associated accuracies for purebred and crossbred performances; (3) use the model to analyse four production traits, i.e. ultra-sound recorded backfat thickness (BF), conformation score (CONF), average daily gain (ADG), and feed conversion ratio (FCR), recorded on Danbred Duroc and Danbred Duroc-Landrace-Yorkshire crossbred pigs reared in the same environment; and (4) obtain estimates of genetic parameters, additive genetic correlations between purebred and crossbred performances, and EBV with associated accuracies for purebred and crossbred performances for this data set. RESULTS: Additive genetic correlations (with associated standard errors) between purebred and crossbred performances were equal to 0.96 (0.07), 0.83 (0.16), 0.75 (0.17), and 0.87 (0.18) for BF, CONF, ADG, and FCR, respectively. For BF, ADG, and FCR, the additive genetic variance was smaller for purebred performance than for crossbred performance, but for CONF the reverse was observed. EBV on Duroc boars were more accurate for purebred performance than for crossbred performance for BF, CONF and FCR, but not for ADG. CONCLUSIONS: Methodological developments led to equations for genetic (co)variances and EBV with associated accuracies for purebred and crossbred performances in a three-way crossbreeding system. As illustrated by the data analysis, these equations may be useful for implementation of genomic selection in this system.


Assuntos
Cruzamento , Depressão por Endogamia , Modelos Genéticos , Modelos Estatísticos , Suínos/genética , Animais , Cruzamentos Genéticos , Feminino , Variação Genética , Hibridização Genética , Masculino
9.
Genet Sel Evol ; 50(1): 42, 2018 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-30107792

RESUMO

BACKGROUND: Records on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake in pigs or beef cattle. Here, we present a model, which handles group records from varying group sizes and involves multiple fixed and random effects, for estimating variance components and predicting BV. Moreover, using simulation, we investigated the efficiency of group records for predicting BV in situations with various group sizes and structures, and factors that affect the trait. RESULTS: The results show that the presented model for group records worked well and that variances estimated from group records with varying group sizes were consistent with those estimated from individual records, but with larger standard errors. Ignoring litter and pen effects had very little or no influence on the accuracy of estimated BV (EBV) obtained from group records. However, ignoring litter effects resulted in biased estimates of additive genetic variance and EBV. The presence of litter and pen effects on phenotypes decreased the accuracy of EBV although the prediction model fitted both effects. Having more littermates in the same pen led to a higher accuracy of EBV. The decay of EBV accuracy with increasing group size was more marked for scenarios with litter and pen effects than without. When litters of six individuals were divided into two pens, accuracies of EBV obtained from group records with a size up to 12 (average 9.6) and up to 24 (average 19.2) were 66.6 and 57.6% of those estimated from individual records in the scenario with litter and pen effects on phenotypes. These percentages reached 77.0 and 68.4% in the scenario without litter and pen effects on phenotypes. CONCLUSIONS: Our results indicate that the model works appropriately for the analysis of group records from varying group sizes. Using group records for genetic evaluation of traits such as feed intake in pig is feasible and the efficiency of the resulting estimates depends on the size and structure of the groups and on the magnitude of the variances for litter and pen effects.


Assuntos
Cruzamento/métodos , Variação Genética , Modelos Genéticos , Registros , Criação de Animais Domésticos/métodos , Animais , Característica Quantitativa Herdável , Tamanho da Amostra , Suínos/genética
10.
Org Biomol Chem ; 15(13): 2784-2790, 2017 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-28272644

RESUMO

We introduce bis-aryl croconamides as a new member in the family of dual hydrogen bonding anion receptors. In this study a series of croconamides are synthesised, and the selectivity for anion binding is investigated (Cl- > Br- > I- in CH2Cl2). The croconamides exhibit different structures in the crystal phase depending on the substituents on the aromatic rings, and furthermore, the crystal structure revealed the presence of tautomers. DFT calculations elucidated the complex structures formed upon addition of anion to the croconamides, confirming the order of association constants towards the halogen anions. The use of croconamides as organocatalysts in a proof-of-concept study is demonstrated in the formation of THP ethers. In addition to this, construction of a Hammet plot further elucidates the mechanism in action on formation of THP ethers.

11.
Genet Sel Evol ; 49(1): 12, 2017 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-28118822

RESUMO

BACKGROUND: Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses. METHODS: Data on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses. Estimated effects of single nucleotide polymorphisms (SNPs) from single-trait association analyses were combined in two meta-analyses: (1) a within-breed meta-analysis for multiple traits to examine if there are pleiotropic genetic variants within a breed; and (2) an across-breed meta-analysis for a single trait to examine if the same quantitative trait loci (QTL) segregate across breeds. SNP annotation was implemented through Sus scrofa Build 10.2 on Ensembl to search for candidate genes. RESULTS: Among the 14, 12 and 13 QTL that were detected in the single-trait association analyses for the three breeds, the most significant SNPs explained 2, 2.3 and 11.4% of genetic variance for back quality in Landrace, overall conformation in Yorkshire and back quality in Duroc, respectively. Several candidate genes for these QTL were also identified, i.e. LRPPRC, WRAP73, VRTN and PPARD likely control conformation traits through the regulation of bone and muscle development, and IGF2BP2, GH1, CCND2 and MSH2 can have an influence through growth-related processes. Meta-analyses not only confirmed many significant SNPs from single-trait analyses with higher significance levels, but also detected several additional associated SNPs and suggested QTL with possible pleiotropic effects. CONCLUSIONS: Our results imply that conformation traits are complex and may be partly controlled by genes that are involved in bone and skeleton development, muscle and fat metabolism, and growth processes. A reliable list of QTL and candidate genes was provided that can be used in fine-mapping and marker assisted selection to improve conformation traits in pigs.


Assuntos
Estudo de Associação Genômica Ampla , Genoma , Genômica , Característica Quantitativa Herdável , Suínos/genética , Animais , Cruzamento , Genômica/métodos , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Seleção Genética
13.
Inorg Chem ; 54(15): 7600-6, 2015 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-26201004

RESUMO

Determination of the electronic energy spectrum of a trigonal-symmetry mononuclear Yb(3+) single-molecule magnet (SMM) by high-resolution absorption and luminescence spectroscopies reveals that the first excited electronic doublet is placed nearly 500 cm(-1) above the ground one. Fitting of the paramagnetic relaxation times of this SMM to a thermally activated (Orbach) model {τ = τ0 × exp[ΔOrbach/(kBT)]} affords an activation barrier, ΔOrbach, of only 38 cm(-1). This result is incompatible with the spectroscopic observations. Thus, we unambiguously demonstrate, solely on the basis of experimental data, that Orbach relaxation cannot a priori be considered as the main mechanism determining the spin dynamics of SMMs. This study highlights the fact that the general synthetic approach of optimizing SMM behavior by maximization of the anisotropy barrier, intimately linked to the ligand field, as the sole parameter to be tuned, is insufficient because of the complete neglect of the interaction of the magnetic moment of the molecule with its environment. The Orbach mechanism is expected dominant only in the cases in which the energy of the excited ligand field state is below the Debye temperature, which is typically low for molecular crystals and, thus, prevents the use of the anisotropy barrier as a design criterion for the realization of high-temperature SMMs. Therefore, consideration of additional design criteria that address the presence of alternative relaxation processes beyond the traditional double-well picture is required.

14.
Org Biomol Chem ; 13(2): 369-73, 2015 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-25407665

RESUMO

In this contribution we show that the newly discovered 6 + 6 biotin-formaldehyde macrocycle Biotin[6]uril binds a variety of anionic guest molecules in water. We discuss how and why the anions are bound based on data obtained using NMR spectroscopy, mass spectrometry, isothermal titration calorimetry (ITC), computational calculations and single crystal X-ray crystallography.

15.
Org Biomol Chem ; 13(21): 5937-43, 2015 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-25925233

RESUMO

Insights to the subtle reactivity patterns of hydroxy-substituted carbazoles allows the precise synthesis of unsymmetrical azatrioxa[8]circulenes by the reaction of N-benzyl-2,7-di-tert-butyl-3,6-dihydroxycarbazole with two different 1,4-benzoquinones in the presence of an oxidant (chloranil) and a Lewis acid (BF3OEt2). The unique synthetic control obtained originates from the selectivity obtained upon reacting N-benzyl-2,7-di-tert-butyl-3,6-dihydroxycarbazole with an electron-rich benzoquinone to give first the C-C bond formation and then subsequently the dibenzofuran formation with high regioselectivity. Herein the first synthesis of unsymmetrical antiaromatic azatrioxa[8]circulenes and the full characterization using NMR spectroscopy, optical spectroscopy, electrochemistry, computational techniques and single crystal X-ray crystallography is reported. The controlled stepwise condensation of N-benzyl-2,7-di-tert-butyl-3,6-dihydroxycarbazole with two different 1,4-benzoquinones gives selectively the unsymmetrical azatrioxa[8]circulenes.

16.
Genet Sel Evol ; 46: 23, 2014 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-24666469

RESUMO

BACKGROUND: For a two-breed crossbreeding system, Wei and van der Werf presented a model for genetic evaluation using information from both purebred and crossbred animals. The model provides breeding values for both purebred and crossbred performances. Genomic evaluation incorporates marker genotypes into a genetic evaluation system. Among popular methods are the so-called single-step methods, in which marker genotypes are incorporated into a traditional animal model by using a combined relationship matrix that extends the marker-based relationship matrix to non-genotyped animals. However, a single-step method for genomic evaluation of both purebred and crossbred performances has not been developed yet. RESULTS: An extension of the Wei and van der Werf model that incorporates genomic information is presented. The extension consists of four steps: (1) the Wei van der Werf model is reformulated using two partial relationship matrices for the two breeds; (2) marker-based partial relationship matrices are constructed; (3) marker-based partial relationship matrices are adjusted to be compatible to pedigree-based partial relationship matrices and (4) combined partial relationship matrices are constructed using information from both pedigree and marker genotypes. The extension of the Wei van der Werf model can be implemented using software that allows inverse covariance matrices in sparse format as input. CONCLUSIONS: A method for genomic evaluation of both purebred and crossbred performances was developed for a two-breed crossbreeding system. The method allows information from crossbred animals to be incorporated in a coherent manner for such crossbreeding systems.


Assuntos
Cruzamento , Genoma , Hibridização Genética , Modelos Genéticos , Animais , Genótipo , Fenótipo
17.
Chemistry ; 19(50): 17097-102, 2013 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-24194455

RESUMO

In this paper we describe a new class of antiaromatic planar cyclooctatetraenes: the diazadioxa[8]circulenes. The synthesis was achieved by means of a new acid-mediated oxidative dimerization of 3,6-dihydroxycarbazoles to yield the diazadioxa[8]circulenes in high yields. The synthetic protocol appears to be general, and is a one-pot transformation in which two C-C bonds and two C-O bonds are formed with the loss of two molecules of water. We also present a detailed characterization of the optical and electrochemical properties of this new class of stable planar cyclooctatetraenes. The properties of the diazadioxa[8]circulenes are compared with the properties of isoelectronic tetraoxa[8]circulenes and azatrioxa[8]circulenes. We discuss the antiaromatic nature of the planar central cyclooctatetraene moiety. The antiaromatic nature of the planar cyclooctatetraenes was studied by using computational methods (NICS calculations), and these calculations reveal that the central eight-membered ring has antiaromatic character.

18.
J Anim Sci Biotechnol ; 14(1): 1, 2023 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-36593522

RESUMO

BACKGROUND: Survival from birth to slaughter is an important economic trait in commercial pig productions. Increasing survival can improve both economic efficiency and animal welfare. The aim of this study is to explore the impact of genotyping strategies and statistical models on the accuracy of genomic prediction for survival in pigs during the total growing period from birth to slaughter.  RESULTS: We simulated pig populations with different direct and maternal heritabilities and used a linear mixed model, a logit model, and a probit model to predict genomic breeding values of pig survival based on data of individual survival records with binary outcomes (0, 1). The results show that in the case of only alive animals having genotype data, unbiased genomic predictions can be achieved when using variances estimated from pedigree-based model. Models using genomic information achieved up to 59.2% higher accuracy of estimated breeding value compared to pedigree-based model, dependent on genotyping scenarios. The scenario of genotyping all individuals, both dead and alive individuals, obtained the highest accuracy. When an equal number of individuals (80%) were genotyped, random sample of individuals with genotypes achieved higher accuracy than only alive individuals with genotypes. The linear model, logit model and probit model achieved similar accuracy. CONCLUSIONS: Our conclusion is that genomic prediction of pig survival is feasible in the situation that only alive pigs have genotypes, but genomic information of dead individuals can increase accuracy of genomic prediction by 2.06% to 6.04%.

19.
Genet Sel Evol ; 43: 38, 2011 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-22070746

RESUMO

BACKGROUND: Genomic selection can be implemented by a multi-step procedure, which requires a response variable and a statistical method. For pure-bred pigs, it was hypothesised that deregressed estimated breeding values (EBV) with the parent average removed as the response variable generate higher reliabilities of genomic breeding values than EBV, and that the normal, thick-tailed and mixture-distribution models yield similar reliabilities. METHODS: Reliabilities of genomic breeding values were estimated with EBV and deregressed EBV as response variables and under the three statistical methods, genomic BLUP, Bayesian Lasso and MIXTURE. The methods were examined by splitting data into a reference data set of 1375 genotyped animals that were performance tested before October 2008, and 536 genotyped validation animals that were performance tested after October 2008. The traits examined were daily gain and feed conversion ratio. RESULTS: Using deregressed EBV as the response variable yielded 18 to 39% higher reliabilities of the genomic breeding values than using EBV as the response variable. For daily gain, the increase in reliability due to deregression was significant and approximately 35%, whereas for feed conversion ratio it ranged between 18 and 39% and was significant only when MIXTURE was used. Genomic BLUP, Bayesian Lasso and MIXTURE had similar reliabilities. CONCLUSIONS: Deregressed EBV is the preferred response variable, whereas the choice of statistical method is less critical for pure-bred pigs. The increase of 18 to 39% in reliability is worthwhile, since the reliabilities of the genomic breeding values directly affect the returns from genomic selection.


Assuntos
Cruzamento , Genômica/métodos , Sus scrofa/genética , Animais , Feminino , Genótipo , Masculino , Modelos Genéticos , Modelos Estatísticos , Linhagem , Fenótipo , Sus scrofa/crescimento & desenvolvimento
20.
PLoS One ; 16(5): e0249476, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33979332

RESUMO

Changes in funerary practices are key to the understanding of social transformations of past societies. Over the course of the Nordic Bronze Age, funerary practices changed from inhumation to cremation. The aim of this study is to shed light on this fundamental change through a cross-examination of archaeometric provenance data and archaeological discussions of the context and layouts of early cremation graves. To this end, we conducted 19 new provenance analyses of strontium isotopes from Early Nordic Bronze age contexts in Thisted County and Zealand and Late Bronze Age contexts from Thisted County and Vesthimmerland (Denmark). These data are subsequently compared with data from other extant relevant studies, including those from Late Bronze Age Fraugde on the Danish island of Fyn. Overall, the variations within our provenience data suggest that the integration and establishment of cremation may not have had a one-to-one relationship with in-migration to Nordic Bronze Age Denmark. Moreover, there seems to be no single blanket scenario which dictated the uptake of cremation as a practice within this part of Southern Scandinavia. By addressing habitus in relation to the deposition of cremations as juxtaposed with these provenance data¸ we hypothesize several potential pathways for the uptake of cremation as a new cultural practice within the Danish Nordic Bronze Age and suggest that this may have been a highly individual process, whose tempo may have been dictated by the specificities of the region(s) concerned.


Assuntos
Arqueologia/métodos , Cremação , Isótopos de Estrôncio/análise , Dinamarca , Países Escandinavos e Nórdicos
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