Bayesian multi-QTL mapping for growth curve parameters

Background Identification of QTL affecting a phenotype which is measured multiple times on the same experimental unit is not a trivial task because the repeated measures are not independent and in most cases show a trend in time. A complicating factor is that in most cases the mean increases non-linear with time as well as the variance. A two- step approach was used to analyze a simulated data set containing 1000 individuals with 5 measurements each. First the measurements were summarized in latent variables and subsequently a genome wide analysis was performed of these latent variables to identify segregating QTL using a Bayesian algorithm. Results For each individual a logistic growth curve was fitted and three latent variables: asymptote (ASYM), inflection point (XMID) and scaling factor (SCAL) were estimated per individual. Applying an 'animal' model showed heritabilities of approximately 48% for ASYM and SCAL while the heritability for XMID was approximately 24%. The genome wide scan revealed four QTLs affecting ASYM, one QTL affecting XMID and four QTLs affecting SCAL. The size of the QTL differed. QTL with a larger effect could be more precisely located compared to QTL with small effect. The locations of the QTLs for separate parameters were very close in some cases and probably caused the genetic correlation observed between ASYM and XMID and SCAL respectively. None of the QTL appeared on chromosome five. Conclusions Repeated observations on individuals were affected by at least nine QTLs. For most QTL a precise location could be determined. The QTL for the inflection point (XMID) was difficult to pinpoint and might actually exist of two closely linked QTL on chromosome one

Estimates of avian collision with power lines and carcass disappearance across differing environments

Data on collisions of birds with high-voltage electric power lines are scarce and are often gathered without protocols for the correction of carcass disappearance. There is actually growing awareness that it is important to accomplish carcass removal trials in order to develop correction factors for producing adjusted estimates of mortality due to collisions. In this study, we provided for the first time raw counts and estimates of bird collisions across seven Italian areas that largely differ in their habitats. We also carried out carcass removal trials to compute the rate of carcass disappearance and produce better estimates of collision events and of optimal time intervals of carcass searches. Results of 1-year monitoring showed a general low frequency of birds collided with the power lines. Carcass removal trials showed effects of carcass size and season on the carcass disappearance, which varied largely among the study areas. In four areas, both small and large carcasses had more than 50% probability to be removed within 3–5 days from their distribution. Given the high variation among study areas, we suggest that estimates of carcass persistence and optimal time intervals should be conducted concurrently for each new study site

Differentially expressed genes for aggressive pecking behaviour in laying hens

BACKGROUND: Aggressive behaviour is an important aspect in the daily lives of animals living in groups. Aggressive animals have advantages, such as better access to food or territories, and they produce more offspring than low ranking animals. The social hierarchy in chickens is measured using the 'pecking order' concept, which counts the number of aggressive pecks given and received. To date, little is known about the underlying genetics of the 'pecking order'. RESULTS: A total of 60 hens from a high feather pecking selection line were divided into three groups: only receivers (R), only peckers (P) and mixed peckers and receivers (P&R). In comparing the R and P groups, we observed that there were 40 differentially expressed genes [false discovery rate (FDR) P < 0.10]. It was not fully clear how the 40 genes regulated aggressive behaviour; however, gene set analysis detected a number of GO identifiers, which were potentially involved in aggressive behavioural processes. These genes code for synaptosomes (GO:0019797), and proteins involved in the regulation of the excitatory postsynaptic membrane potential (GO:0060079), the regulation of the membrane potential (GO:0042391), and glutamate receptor binding (GO:0035254). CONCLUSION: In conclusion, our study provides new insights into which genes are involved in aggressive behaviours in chickens. Pecking and receiving hens exhibited different gene expression profiles in their brains. Following confirmation, the identification of differentially expressed genes may elucidate how the pecking order forms in laying hens at a molecular level

Bayesian genomic selection: the effect of haplotype length and priors

Breeding values for animals with marker data are estimated using a genomic selection approach where data is analyzed using Bayesian multi-marker association models. Fourteen model scenarios with varying haplotype lengths, hyper parameter and prior distributions were compared to find the scenario expected to give the most correct genomic estimated breeding values for animals with marker information only. Five-fold cross validation was performed to assess the ability of models to estimate breeding values for animals in generation 3. In each of the five subsets, 20% of phenotypic records in generation 3 were left out. Correlations between breeding values estimated on full data and on subsets for the "leave-out" animals varied between 0.77–0.99. Regression coefficients of breeding values from full data on breeding values from subsets ranged from 0.78–1.01. Single-SNP marker models didn't perform well. Correlations were 0.77–0.89 and predicted breeding values were biased. In addition the models seemed to over fit the genomic part of the variation. Highest correlations and most unbiased results were obtained when SNP markers were joined into haplotypes. Especially the scenarios with 5-SNP haplotypes gave promising results (distance between adjacent SNPs is 0.1 cM evenly over the genome). All correlations were 0.99 and regression coefficients were 0.99–1.01. Models with 5-SNP markers seemed robust to hyper parameter and prior changes. Haplotypes up to 40 SNPs also gave good results. However, longer haplotypes are expected to have less predictive ability over several generations and therefore the 5-SNP haplotypes are expected to give the best predictions for generations 4–6

From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding

This article reviews methods of integration of transcriptomics (and equally proteomics and metabolomics), genetics, and genomics in the form of systems genetics into existing genome analyses and their potential use in animal breeding and quantitative genomic modeling of complex traits. Genetical genomics or the expression quantitative trait loci (eQTL) mapping method and key findings in this research are reviewed. Various procedures and potential uses of eQTL mapping, global linkage clustering, and systems genetics are illustrated using actual analysis on recombinant inbred lines of mice with data on gene expression (for diabetes- and obesity-related genes), pathway, and single nucleotide polymorphism (SNP) linkage maps. Experimental and bioinformatics difficulties and possible solutions are discussed. The main uses of this systems genetics approach in quantitative genomics were shown to be in refinement of the identified QTL, candidate gene and SNP discovery, understanding gene-environment and gene-gene interactions, detection of candidate regulator genes/eQTL, discriminating multiple QTL/eQTL, and detection of pleiotropic QTL/eQTL, in addition to its use in reconstructing regulatory networks. The potential uses in animal breeding are direct selection on heritable gene expression measures, termed "expression assisted selection,” and genetical genomic selection of both QTL and eQTL based on breeding values of the respective genes, termed "expression-assisted evaluation.

Identification of a major gene in F1 and F2 data when alleles are assumed fixed in the parental lines

International audienc

A bird and small mammal BACI and IG design studies in a wind farm in Malpica (Spain)

Wind farms have shown a spectacular growth during the last 10 years. As far as we know, this study is the first where the relationship between wind power and birds and small mammals have been considered. Before-after control impact (BACI) study design to birds and Impact Gradient (IG) study design to small mammals to test the null hypothesis of no impact of a wind farm were used. In the BACI model Windfarm Area and a Reference Area were considered. Distance from turbines was considered in the IG model. Windfarm installations did not clearly affect bird and small mammal populations. Flight height of nesting and no nesting birds did not show a clear tendency. Small mammals populations suffered high variations in numbers through times by intrinsic population factors. There are many practical problems of detection of human influence on abundances of populations so sampling in the long run can be suggested. © Springer 2005.Peer Reviewe

Producción agropecuaria y desarrollo local en los cantones Cayambe y Pedro Moncayo

Estas investigaciones de la carrera de Ingeniería Agropecuaria que la Universidad Politécnica Salesiana oferta en Cayambe, son resultado de una apuesta por el desarrollo local y hoy salen a la luz gracias al aporte de Ayuda en Acción, Ecuador. Se trata de diez trabajos que van desde el valor en la alimentación de las especies andinas como la mashua, el melloco, la oca, a la producción de bioinsumos pasando por la correlación de métodos en el laboratorio para el control de la mastitis, mejoramiento sanitario del queso fresco y propuestas de cambios en la producción agropecuaria. Su lectura dará fe del resultado académico y de la aplicabilidad de las investigaciones. Más allá de la satisfacción por el éxito de una iniciativa fraguada al calor de las discusiones sobre el modelo de desarrollo y el papel del agente externo, está el sentirse privilegiado de la confianza brindada por las comunidades indígenas de Cayambe y Pedro Moncayo para poner en juego sus capacidades y posibilidades para lograr metas y diseñar nuevos futuros