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Molecular Clocks and the Origin of Animals. Solomon P. Shimony, and M. Pollution selection of allozyme polymorphisms in barnacles. Experientia Park et al. This study reported several additional QTL and also showed a high degree of co-localization between QTL for the different traits as well as a partial, but not complete, overlap with the previously reported Growth We summarize the findings from these studies in Table 1.
Despite the large population size for an experimental intercross, relatively few genome-wide QTL were, however, reported. The confidence intervals of the initially detected QTL regions were rather broad, partially due to relatively sparse microsatellite map used.
Additional SNP markers were added by Wahlberg et al.
In this study, 6 of the original 13 QTL were confirmed as significant for at least one body-weight trait, and the overall profile of the QTL signal was very consistent with that found by Jacobsson et al. The Virginia lines have, thus, proven to be highly useful for QTL detection and have been key to the mapping of genetic regions involved in growth regulation in chickens. Detection of epistatic interactions.
Beyond the single QTL analysis, the Virginia lines have also been used in several groundbreaking studies on the role of genetic interactions, often referred to as epistasis, in complex trait determination. The prevalence of epistasis in the system was originally shown by Carlborg et al. The results indicated that the genotype at Growth9 had a significant influence on the effects of the other loci: the peripheral loci Growth4 , Growth6 and Growth12 had no or very small effects in individuals homozygous for the allele inherited from the low-weight line at Growth9.
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They did, however, have strong effects in other genetic backgrounds, especially when Growth9 was homozygous for the allele inherited from the high weight line. In the same way, homozygosity for the high-weight alleles at Growth4 , Growth6 and Growth12 releases the genetic effects on growth by Growth9 , whereas the low weight line alleles hides these effects Figure 1.
The founders from the Virginia line F 2 intercross Carlborg et al. This AIL, which is maintained with approximately individuals in each generation, aims to break up the linkage disequilibrium created by crossing the divergently selected Virginia lines and through this reach a population where the stretches of genetic material inherited from each founder line haplotypes are much shorter than in the F 2 population.
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This is valuable for fine-mapping efforts, since shorter haplotypes allows better resolution when determining QTL locations. When this AIL reached the F 8 generation, approximately individuals were hatched and phenotyped more comprehensively to generate a data set to replicate and fine-map the previously reported QTL Jacobsson et al. This data set is currently being investigated Besnier et al.
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Preliminary results indicate that the most of the previously reported loci, as well as the epistatic interactions, were replicated in the AIL. Large-scale genome wide changes. The Virgina lines have also been utilized in studies aiming to determine the genome wide effects of long-term directional selection. Recently, they were included in a massive chicken genome re-sequencing project by Rubin et al. Here, a large number of chicken lines were re-sequenced to approximately 5X genome coverage with the aim to explain the major genetic differences separating layers and broilers - the two major types of commercially grown chickens.
Several regions were found that were likely to have undergone selective sweeps during the differential selection period, as well as a several mutations that are possibly functionally contributing to some of the differences between layers and broilers. The well-documented history of the Virginia lines was highly useful in this study as it allowed a particular sweep, in the gene TBC1D1, to be dated with good precision since it is present in both the high and low body weight lines. In addition to this large-scale study, there is also an ongoing investigation aiming at discovering the genomic changes that have taken place during the Virginia line selection experiment.
For this, a number of birds from both lines and from different time points in the selection process, have been genotyped using a 60k Illumina SNP chip.
concilezu.tk This is a dramatic amount given the short time since the lines were separated. However, even taking drift into account, the results strongly support the hypothesis that the differences between the two lines are caused by a large number of loci rather than a few major ones Johansson et al. In addition to the future prospects described earlier, an effort is in progress to use genomics to identify the functional mutations underlying the identified QTL and selective sweeps. For this, the Virginia lines will be sequenced with high coverage to identify virtually all SNPs differentiating the lines.
A bioinformatics pipeline is being developed that will utilize comparative genomics data to identify the most plausible causative mutations in the selected regions, and thus reveal potential metabolic pathways and other biological systems that have been affected by the differential selection process Marklund et al. One of the most interesting new developments in animal improvement programs is genomic selection, where data on the genome-wide genotype of individuals is utilized in the evaluation of breeders.
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