| 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. |
- Andersson, Leif
(författare)
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Genome-wide association analysis in domestic animals : a powerful approach for genetic dissection of trait loci
- 2009
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Ingår i: Genetica. - : Springer. - 0016-6707 .- 1573-6857. ; 136:2, s. 341-349
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Tidskriftsartikel (refereegranskat)abstract
- Domestic animals have a sufficiently old history (thousands of generations) to allow evolution of phenotypes, but also a sufficiently young history (approximately 10,000 years) to allow powerful genetic dissection of phenotypic diversity. Domestic animals are therefore a unique resource for exploring genotype-phenotype relationships. Quantitative Trait Locus (QTL) mapping has been very successful in domestic animals but the identification of Quantitative Trait Mutations (QTMs) has been hard although a few prominent success histories have been reported. Genome-wide association analysis is now emerging as a powerful method for high-resolution mapping of loci controlling phenotypic traits in domestic animals. In two recent proof-of-principle studies we have used this approach to identify the mutations underlying two monogenic trait loci in dogs, white spotting and the hair ridge in Ridgeback dogs. In each case, we used only about 10 cases and 10 controls and mapped the locus to a region of about one mega base pair. In both cases the underlying mutations were non-coding underscoring the significance of regulatory mutations as a source for phenotypic diversity. Furthermore, we were able to shed light on the evolution of the allelic series at the white spotting (S) locus in dogs which encodes the microphthalmia-associated transcription factor (MITF). Our data showed that the three variant alleles described at this locus (Irish spotting, piebald and extreme white) do not represent three independent mutations but rather different combinations of a set of regulatory mutations affecting MITF expression. This is an excellent illustration of how the characterization of alleles selected during animal domestication contributes to an improved understanding of genotype-phenotype relationships.
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| 3. |
- Ardalan, Arman, et al.
(författare)
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Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry.
- 2012
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 1573-6857 .- 0016-6707. ; 140:1-3, s. 65-73
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Tidskriftsartikel (refereegranskat)abstract
- The dingo (Canis lupus dingo) is an iconic animal in the native culture of Australia, but archaeological and molecular records indicate a relatively recent history on the continent. Studies of mitochondrial DNA (mtDNA) imply that the current dingo population was founded by a small population of already tamed dogs from Southeast Asia. However, the maternal genetic data might give a unilateral picture, and the gene pool has yet to be screened for paternal ancestry. We sequenced 14,437bp of the Y-chromosome (Y-chr) from two dingoes and one New Guinea Singing Dog (NGSD). This positioned dingo and NGSD within the domestic dog Y-chr phylogeny, and produced one haplotype not detected before. With this data, we characterized 47 male dingoes in 30 Y-chr single-nucleotide polymorphism sites using protease-mediated allele-specific extension technology. Only two haplotypes, H3 and H60, were found among the dingoes, at frequencies of 68.1 and 31.9%, respectively, compared to 27 haplotypes previously established in the domestic dog. While H3 is common among Southeast Asian dogs, H60 was specifically found in dingoes and the NGSD, but was related to Southeast Asian dog Y-chr haplotypes. H3 and H60 were observed exclusively in the western and eastern parts of Australia, respectively, but had a common range in Southeast. Thus, the Y-chr diversity was very low, similar to previous observations for d-loop mtDNA. Overall genetic evidence suggests a very restricted introduction of the first dingoes into Australia, possibly from New Guinea. This study further confirms the dingo as an isolated feral dog.
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| 4. |
- Chevin, Luis Miguel, et al.
(författare)
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Using phenotypic plasticity to understand the structure and evolution of the genotype–phenotype map
- 2021
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857.
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Tidskriftsartikel (refereegranskat)abstract
- Deciphering the genotype–phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype–phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype–environment–phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.
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| 5. |
- Demakov, Sergei, et al.
(författare)
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Molecular and genetic organization of Drosophila melanogaster polytene chromosomes : evidence for two types of interband regions
- 2004
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Ingår i: Genetica. - 0016-6707 .- 1573-6857. ; 122:3, s. 311-324
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Tidskriftsartikel (refereegranskat)abstract
- The 3A and 60E regions of Drosophila melanogaster polytene chromosomes containing inserted copies of the P[1ArB] transposon have been subjected to an electron microscopic (EM) analysis. We show that both inserts led to formation of new bands within the interband regions 3A4/A6 and 60E8-9/E10. This allowed us to clone DNA of these interbands. Their sequences, as well as those of DNA from other four interbands described earlier, have been analyzed. We have found that, with the exception of 60E8-9/E10 interband, all other five regions under study corresponded to 5' or 3' ends of genes. We have further obtained the evidence for 60E8-9/E10 interband to harbor the 'housekeeping' RpL19 gene, which is transcribed in many tissues, including salivary glands. Based upon the genetic heterogeneity of the interbands observed a revised model of polytene chromosome organization is discussed.
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| 6. |
- den Tex, Robert-Jan, et al.
(författare)
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Nuclear copies of mitochondrial genes : another problem for ancient DNA
- 2010
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857. ; 138:9-10, s. 979-984
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Tidskriftsartikel (refereegranskat)abstract
- The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.
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| 7. |
- Ekblom, Robert, et al.
(författare)
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Balancing selection, sexual selection and geographic structure in MHC genes of Great Snipe
- 2010
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857. ; 138:4, s. 453-461
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Tidskriftsartikel (refereegranskat)abstract
- Signatures of balancing selection are often found when investigating the extremely polymorphic regions of major histocompatibility complex (MHC) genes, and it is generally accepted that selective forces maintain this polymorphism. However, the exact nature of the selection is controversial. Theoretical studies have mainly focused on overdominance and/or frequency dependent selection while laboratory studies have emphasised the role of mate choice. Empirical field data, on the other hand, have been relatively scarce. Previously we have found that geographic structure in MHC class II genes of the Great Snipe (Gallinago media) is too pronounced to be explained by neutral forces alone. Here we test the hypothesis that sexual selection on MHC alleles may be influencing this geographic structure between mountain and lowland populations. We found evidence of balancing selection acting on MHC genes in the form of a higher rate of amino-acid changing substitutions compared to silent substitutions in the peptide binding regions. Not only natural selection but also sexual selection may influence MHC polymorphism in this bird because certain MHC alleles have been found to be associated with higher male mating success. Contrary to predictions from negative frequency dependent selection, males carrying locally rare alleles did not have a mating advantage. Instead, the mating success of alleles in a mountain population was positively correlated to their relative frequency in the mountains compared to the lowlands, implying that locally adapted MHC alleles may also be favoured by sexual selection.
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| 8. |
- Frank, A. Carolin, et al.
(författare)
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Genome deterioration : Loss of repeated sequences and accumulation of junk DNA
- 2002
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Ingår i: Genetica. - 0016-6707 .- 1573-6857. ; 115:1, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and 'junk' DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.
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| 9. |
- Kan, Tatiana, et al.
(författare)
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[Model genetic system for analysis of attachment of HeT-A elements to terminal deletions in Drosophila melanogaster].
- 2000
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Ingår i: Genetica. - 0016-6707 .- 1573-6857.
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Tidskriftsartikel (refereegranskat)abstract
- Telomeres of Drosophila consist of multiple copies of LINE-like transposable elements. These elements are assigned to two classes, HeT-A and TART. They are attached to terminal deletions at their 3' end, thus compensating for the absence of telomerase in Drosophila cells. The attachment of HeT-A elements to the X-chromosome terminal deletions of the regulatory region of the yellow gene was studied. It was shown that, in the case of degradation of the yellow promoter sequence (chromosome underreplication), the Het-A promoter located at the 3' end of this element can activate transcription of the gene. The minimal size of the 3'-end HeT-A element sequence sufficient for the yellow expression was shown to be 400 bp. Since the yellow mutation is expressed phenotypically and the gene impairment is not lethal, we created a convenient model genetic system based on this effect. Using this system, the frequency of attachments of the HeT-A elements to the chromosome end can be visually recorded. This frequency varied in a wide range (from 0.2 x 10(-4) to 2 x 10(-3)) and was strain-specific.
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| 10. |
- Lundin, KE, et al.
(författare)
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Nanotechnology approaches for gene transfer
- 2009
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 1573-6857 .- 0016-6707. ; 137:1, s. 47-56
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Tidskriftsartikel (refereegranskat)
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