| 1. |
- Abrahamsson, Sara, et al.
(författare)
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Maternal heterozygosity and progeny fitness association in an inbred Scots pine population
- 2013
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Ingår i: Genetica. - : Springer Netherlands. - 0016-6707 .- 1573-6857. ; 141:1-3, s. 41-50
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Tidskriftsartikel (refereegranskat)abstract
- Associations between heterozygosity and fitness traits have typically been investigated in populations characterized by low levels of inbreeding. We investigated the associations between standardized multilocus heterozygosity (stMLH) in mother trees (obtained from12 nuclear microsatellite markers) and five fitness traits measured in progenies from an inbred Scots pine population. The traits studied were proportion of sound seed, mean seed weight, germination rate, mean family height of one-year old seedlings under greenhouse conditions (GH) and mean family height of three-year old seedlings under field conditions (FH). The relatively high average inbreeding coefficient (F) in the population under study corresponds to a mixture of trees with different levels of co-ancestry, potentially resulting from a recent bottleneck. We used both frequentist and Bayesian methods of polynomial regression to investigate the presence of linear and non-linear relations between stMLH and each of the fitness traits. No significant associations were found for any of the traits except for GH, which displayed negative linear effect with stMLH. Negative HFC for GH could potentially be explained by the effect of heterosis caused by mating of two inbred mother trees (Lippman and Zamir 2006), or outbreeding depression at the most heterozygote trees and its negative impact on the fitness of the progeny, while their simultaneous action is also possible (Lynch. 1991). However,since this effect wasn’t detected for FH, we cannot either rule out that the greenhouse conditions introduce artificial effects that disappear under more realistic field conditions.
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| 2. |
- Anglart, Dorota, et al.
(författare)
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Modeling cow somatic cell count using sensor data as input to generalized additive models
- 2020
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Ingår i: Journal of Dairy Research. - 0022-0299 .- 1469-7629. ; 87, s. 282-289
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Tidskriftsartikel (refereegranskat)abstract
- This research paper presents a study investigating if sensor data from an automatic milking rotary could be used to model cow somatic cell count (composite milk SCC: CMSCC). CMSCC is valuable for udder health monitoring and individual cow udder health surveillance could be improved by predicting CMSCC between routine samplings. Data regularly recorded in the automatic milking rotary, in one German dairy herd, were collected for analysis. The cows (Holstein-Friesian,n= 372) were milked twice daily and sampled once weekly in afternoon milkings for 8 weeks for CMSCC. From the potential independent variables, including quarter conductivity, milk flow, blood in milk, kick-offs, not milked quarters and incomplete milkings, new variables that combined quarter data were created. Past period records, i.e. lags, of up to seven days before the actual CMSCC sampling event were added in the dataset to investigate if they were of use in modeling the cell count. Univariable generalized additive models (GAM) were used to screen the data to select potential independent variables. Furthermore, several multivariable GAM were fitted in order to compare the importance of the potential independent variables and to explore how the model performance would be affected by using data from various number of days before the CMSCC sampling event. The result of the model selection showed that the best explanation of CMSCC was provided by the model incorporating all significant variables from the variable screening for the seven preceding days, including the day of the CMSCC sampling event. However, using data from only three days before the CMSCC sampling event is suggested to be sufficient to model CMSCC. Variables combining conductivity quarter data, together with quarter conductivity, are suggested to be important in describing CMSCC. We conclude that CMSCC can be modeled with a high degree of explanation using the information routinely recorded by the milking robot.
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| 3. |
- Garcia Gil, Rosario, et al.
(författare)
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Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine
- 2009
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 103, s. 90-96
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the fine-scale spatial genetic structure in a managed Scots pine forest. For this purpose, we perform a Bayesian genetic-cluster analysis of 96 geographically mapped individual seed trees of Swedish Scots pine based on 14 microsatellite loci. The analysis was carried out with the recently developed program GENECLUST (Francois et al., 2006), which provides the facility to jointly incorporate both spatial information from a geographical neighborhood structure through a Potts-Dirichlet model and account for variable degrees of inbreeding within the clusters. To evaluate whether inbreeding and spatial interaction should be included in the best-fitting statistical model for our data, we used the deviance information criterion (DIC), a weighted measure of model fit that accounts for an effective number of free parameters in a model. Analysis shows that a model with a single estimated cluster, with high levels of inbreeding (0.25) and with a moderate amount of spatial dependency within the unique cluster (Psi = 0.2-0.4), best explains the data. We also carried out Bayesian parentage analysis, which enabled us to exclude the possibility that the sample constitutes one single full-sib family. Heredity (2009) 103, 90-96; doi: 10.1038/hdy.2009.33; published online 22 April 2009
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| 4. |
- Hallander, Jon, et al.
(författare)
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Bayesian Inference of Genetic Parameters Based on Conditional Decompositions of Multivariate Normal Distributions
- 2010
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 185, s. 645-654
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Tidskriftsartikel (refereegranskat)abstract
- It is widely recognized that the mixed linear model is an important tool for parameter estimation in the analysis of complex pedigrees, which includes both pedigree and genomic information, and where mutually dependent genetic factors are often assumed to follow multivariate normal distributions of high dimension. We have developed a Bayesian statistical method based on the decomposition of the multivariate normal prior distribution into products of conditional univariate distributions. This procedure permits computationally demanding genetic evaluations of complex pedigrees, within the user-friendly computer package WinBUGS. To demonstrate and evaluate the flexibility of the method, we analyzed two example pedigrees: a large noninbred pedigree of Scots pine (Pinus sylvestris L.) that includes additive and dominance polygenic relationships and a simulated pedigree where genomic relationships have been calculated on the basis of a dense marker map. The analysis showed that our method was fast and provided accurate estimates and that it should therefore be a helpful tool for estimating genetic parameters of complex pedigrees quickly and reliably.
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| 5. |
- Hallander, Jon, et al.
(författare)
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Optimization of selection contribution and mate allocations in monoecious tree breeding populations
- 2009
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Conclusion: The main reason why MCM schemes yielded higher genetic gains was the improvement in managing the long term genetic contribution of founders in the population; this was achieved by connecting unrelated families. In addition, the accumulation of inbreeding was reduced by MCM schemes since the variance in long term genetic contributions of founders was smaller than in the other schemes. Consequently, by combining an MCM scheme with an algorithm that optimizes contributions of the selected individuals, a higher long term response is obtained while reducing the risk within the breeding program.
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| 6. |
- Hallander, Jon, et al.
(författare)
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Optimum contribution selection in large general tree breeding populations with an application to Scots pine
- 2009
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Ingår i: TAG Theoretical and Applied Genetics. - : Springer Science and Business Media LLC. - 0040-5752 .- 1432-2242. ; 118, s. 1133-1142
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Tidskriftsartikel (refereegranskat)abstract
- Development of selection methods that optimises selection differential subject to a constraint on the increase of inbreeding (or coancestry) in a population is an important part of breeding programmes. One such method that has received much attention in animal breeding is the optimum contribution (OC) dynamic selection method. We implemented the OC algorithm and applied it to a diallel progeny trial of Pinus sylvestris L. (Scots pine) focussing on two traits (total tree height and stem diameter). The OC method resulted in a higher increase in genetic gain (8-30%) compared to the genetic gain achieved using standard restricted selection method at the same level of coancestry constraint. Genetic merit obtained at two different levels of restriction on coancestry showed that the benefit of OC was highest when restriction was strict. At the same level of genetic merit, OC decreased coancestry with 56 and 39% for diameter and height, respectively, compared to the level of coancestry obtained using unrestricted truncation selection. Inclusion of a dominance term in the statistical model resulted in changes in contribution rank of trees with 7 and 13% for diameter and height, respectively, compared to results achieved by using a pure additive model. However, the genetic gain was higher for the pure additive model than for the model including dominance for both traits.
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| 7. |
- Mészáros, Gábor, et al.
(författare)
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A genome wide association study for longevity in cattle
- 2014
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Ingår i: Open Journal of Genetics. - : Scientific Research Publishing. - 2162-4453 .- 2162-4461. ; 4:1, s. 46-55
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Tidskriftsartikel (refereegranskat)abstract
- Longevity is regarded as the most important functional trait in cattle breeding with high economic value yet low heritability. In order to identify genomic regions associated with longevity, a genome wise association study was performed using data from 4887 Fleckvieh bulls and 33,556 SNPs after quality control. Single SNP regression was used for identification of important SNPs including eigenvectors as a means of correction for population structure. SNPs selected with a false discovery rate threshold of 0.05 and with local false discovery rate identified genomic regions associated with longevity which were subsequently cross checked with the National Center for Biotechnology Information (NCBI) database. This, to identify interesting genes in cattle and their homologue forms in other species. The most notable genes were SYT10 located on chromosome 5, ADAMTS3 on chromosome 6, NTRK2 on chromosome 8 and SNTG1 on chromosome 14 of the cattle genome. Several of the genes found have previously been associated with cattle fertility. Poor fertility is an important culling reason and thereby affects longevity in cattle. Several signals were located in regions sparse with described genes, which suggest that there might be several other non-identified genetic pathways for this important trait.
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| 8. |
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| 9. |
- Pathak, Surajit, et al.
(författare)
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Radiation and SN38 treatments modulate the expression of microRNAs, cytokines and chemokines in colon cancer cells in a p53-directed manner
- 2015
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Ingår i: Oncotarget. - : IMPACT JOURNALS LLC. - 1949-2553. ; 6:42, s. 44758-44780
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Tidskriftsartikel (refereegranskat)abstract
- Aberrant expression of miRNAs, cytokines and chemokines are involved in pathogenesis of colon cancer. However, the expression of p53 mediated miRNAs, cyto- and chemokines after radiation and SN38 treatment in colon cancer remains elusive. Here, human colon cancer cells, HCT116 with wild-type, heterozygous and a functionally null p53, were treated by radiation and SN38. The expression of 384 miRNAs was determined by using the TaqMan (R) miRNA array, and the expression of cyto- and chemokines was analyzed by Meso-Scale-Discovery instrument. Up- or down-regulations of miRNAs after radiation and SN38 treatments were largely dependent on p53 status of the cells. Cytokines, IL-6, TNF-alpha, IL-1 beta, Il-4, IL-10, VEGF, and chemokines, IL-8, MIP-1 alpha were increased, and IFN-gamma expression was decreased after radiation, whereas, IL-6, IFN-gamma, TNF-alpha, IL-1 beta, Il-4, IL-10, IL-8 were decreased, and VEGF and MIP-1 alpha were increased after SN38 treatment. Bioinformatic analysis pointed out that the highly up-regulated miRNAs, let-7f-5p, miR-455-3p, miR-98, miR-155-5p and the down-regulated miRNAs, miR-1, miR-127-5p, miR-142-5p, miR-202-5p were associated with colon cancer pathways and correlated with cyto- or chemokine expression. These miRNAs have the potential for use in colon cancer therapy as they are related to p53, pro- or anti-inflammatory cyto- or chemokines after the radiation and SN38 treatment.
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| 10. |
- Quilot-Turion, Bénédicte, et al.
(författare)
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Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata
- 2013
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Ingår i: Annals of Botany. - : Oxford University Press. - 0305-7364 .- 1095-8290. ; 111:5, s. 957-968
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims The adaptive plastic reactions of plant populations to changing climatic factors, such as winter temperatures and photoperiod, have changed during range shifts after the last glaciation. Timing of flowering is an adaptive trait regulated by environmental cues. Its genetics has been intensively studied in annual plants, but in perennials it is currently not well characterized. This study examined the genetic basis of differentiation in flowering time, morphology, and their plastic responses to vernalization in two locally adapted populations of the perennial Arabidopsis lyrata: (1) to determine whether the two populations differ in their vernalization responses for flowering phenology and morphology; and (2) to determine the genomic areas governing differentiation and vernalization responses.Methods Two A. lyrata populations, from central Europe and Scandinavia, were grown in growth-chamber conditions with and without cold treatment. A QTL analysis was performed to find genomic regions that interact with vernalization.Key Results The population from central Europe flowered more rapidly and invested more in inflorescence growth than the population from alpine Scandinavia, especially after vernalization. The alpine population had consistently a low number of inflorescences and few flowers, suggesting strong constraints due to a short growing season, but instead had longer leaves and higher leaf rosettes. QTL mapping in the F2 population revealed genomic regions governing differentiation in flowering time and morphology and, in some cases, the allelic effects from the two populations on a trait were influenced by vernalization (QTL × vernalization interactions).Conclusions The results indicate that many potentially adaptive genetic changes have occurred during colonization; the two populations have diverged in their plastic responses to vernalization in traits closely connected to fitness through changes in many genomic areas.
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