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Stephan A, Graca FA, Hunt LC, Demontis F. Electroporation of Small Interfering RNAs into Tibialis Anterior Muscles of Mice. Bio Protoc 2022; 12:e4428. [PMID: 35799907 PMCID: PMC9244496 DOI: 10.21769/bioprotoc.4428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
Aging and wasting of skeletal muscle reduce organismal fitness. Regrettably, only limited interventions are currently available to address this unmet medical need. Many methods have been developed to study this condition, including the intramuscular electroporation of DNA plasmids. However, this technique requires surgery and high electrical fields, which cause tissue damage. Here, we report an optimized protocol for the electroporation of small interfering RNAs (siRNAs) into the tibialis anterior muscle of mice. This protocol does not require surgery and, because of the small siRNA size, mild electroporation conditions are utilized. By inducing target mRNA knockdown, this method can be used to interrogate gene function in muscles of mice from different strains, genotypes, and ages. Moreover, a complementary method for siRNA transfection into differentiated myotubes can be used for testing siRNA efficacy before in vivo use. Altogether, this streamlined protocol is instrumental for basic science and translational studies in muscles of mice and other animal models.
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Affiliation(s)
- Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Flavia A. Graca
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liam C. Hunt
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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*For correspondence:
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Pegot-Espagnet P, Guillaume O, Desprez B, Devaux B, Devaux P, Henry K, Henry N, Willems G, Goudemand E, Mangin B. Discovery of interesting new polymorphisms in a sugar beet (elite [Formula: see text] exotic) progeny by comparison with an elite panel. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3063-3078. [PMID: 31485698 PMCID: PMC6791908 DOI: 10.1007/s00122-019-03406-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE The comparison of QTL detection performed on an elite panel and an (elite [Formula: see text] exotic) progeny shows that introducing exotic germplasm into breeding programs can bring new interesting allelic diversity. Selection of stable varieties producing the highest amount of extractable sugar per hectare (ha), resistant to diseases, and respecting environmental criteria is undoubtedly the main target for sugar beet breeding. As sodium, potassium, and [Formula: see text]-amino nitrogen in sugar beets are the impurities that have the biggest negative impact on white sugar extraction, it is interesting to reduce their concentration in further varieties. However, domestication history and strong selection pressures have affected the genetic diversity needed to achieve this goal. In this study, quantitative trait locus (QTL) detection was performed on two populations, an (elite [Formula: see text] exotic) sugar beet progeny and an elite panel, to find potentially new interesting regions brought by the exotic accession. The three traits linked with impurities content were studied. Some QTLs were detected in both populations, the majority in the elite panel because of most statistical power. Some of the QTLs were colocated and had favorable effect in the progeny since the exotic allele was linked with a decrease in the impurity content. A few number of favorable QTLs were detected in the progeny, only. Consequently, introgressing exotic genetic material into sugar beet breeding programs can allow the incorporation of new interesting alleles.
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Affiliation(s)
- Prune Pegot-Espagnet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | | | - Bruno Desprez
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | - Brigitte Devaux
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | - Pierre Devaux
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | - Karine Henry
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | - Nicolas Henry
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | - Glenda Willems
- SESVanderHave, Industriepark Soldatenplein Zone 2/Nr 15, 3300, Tienen, Belgium
| | - Ellen Goudemand
- Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, 59242, Capelle-en-Pévèle, France
| | - Brigitte Mangin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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3
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Lind PA, Libby E, Herzog J, Rainey PB. Predicting mutational routes to new adaptive phenotypes. eLife 2019; 8:e38822. [PMID: 30616716 PMCID: PMC6324874 DOI: 10.7554/elife.38822] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive 'wrinkly spreader' (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.
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Affiliation(s)
- Peter A Lind
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Molecular BiologyUmeå UniversityUmeåSweden
| | - Eric Libby
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Santa Fe InstituteNew MexicoUnited States
- Department of MathematicsUmeå UniversityUmeåSweden
| | - Jenny Herzog
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, ESPCI Paris-TechCNRS UMR 8231, PSL Research UniversityParisFrance
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4
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Seeb LW, Waples RK, Limborg MT, Warheit KI, Pascal CE, Seeb JE. Parallel signatures of selection in temporally isolated lineages of pink salmon. Mol Ecol 2014; 23:2473-85. [PMID: 24762204 DOI: 10.1111/mec.12769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 12/12/2022]
Abstract
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly abundant and widely ranging salmonid, provide a naturally occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life history. The species is composed of two reproductively isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction-site-associated DNA (RAD) sequencing to discover and genotype approximately 8000 SNP loci in three population pairs of even- and odd-year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd-year than within the even-year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation-based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment.
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Affiliation(s)
- L W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
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5
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Schielzeth H, Husby A. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Ann N Y Acad Sci 2014; 1320:35-57. [PMID: 24689944 DOI: 10.1111/nyas.12397] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.
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Affiliation(s)
- Holger Schielzeth
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
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6
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Vijendravarma RK, Kawecki TJ. Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila. J Evol Biol 2013; 26:2566-80. [PMID: 24118120 DOI: 10.1111/jeb.12248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 11/30/2022]
Abstract
Based on ecological and metabolic arguments, some authors predict that adaptation to novel, harsh environments should involve alleles showing negative (diminishing return) epistasis and/or that it should be mediated in part by evolution of maternal effects. Although the first prediction has been supported in microbes, there has been little experimental support for either prediction in multicellular eukaryotes. Here we use a line-cross design to study the genetic architecture of adaptation to chronic larval malnutrition in a population of Drosophila melanogaster that evolved on an extremely nutrient-poor larval food for 84 generations. We assayed three fitness-related traits (developmental rate, adult female weight and egg-to-adult viability) under the malnutrition conditions in 14 crosses between this selected population and a nonadapted control population originally derived from the same base population. All traits showed a pattern of negative epistasis between alleles improving performance under malnutrition. Furthermore, evolutionary changes in maternal traits accounted for half of the 68% increase in viability and for the whole of 8% reduction in adult female body weight in the selected population (relative to unselected controls). These results thus support both of the above predictions and point to the importance of nonadditive effects in adaptive microevolution.
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Affiliation(s)
- R K Vijendravarma
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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7
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Hansen TF. Why epistasis is important for selection and adaptation. Evolution 2013; 67:3501-11. [PMID: 24299403 DOI: 10.1111/evo.12214] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/04/2013] [Indexed: 12/16/2022]
Abstract
Organisms are built from thousands of genes that interact in complex ways. Still, the mathematical theory of evolution is dominated by a gene-by-gene perspective in which genes are assumed to have the same effects regardless of genetic background. Gene interaction, or epistasis, plays a role in some theoretical developments such as the evolution of recombination, reproductive isolation, and canalization, but is strikingly missing from our standard accounts of phenotypic adaptation. This absence is most puzzling within the field of quantitative genetics, which, despite its polygenic perspective and elaborate statistical representation of epistasis, has not found a single important role for gene interaction in evolution. To the contrary, there is a widespread consensus that epistasis is evolutionary inert, and that all we need to know to predict evolutionary dynamics is the additive component of the genetic variance. This view may have roots in convenience, but also in theoretical results showing that the response to selection derived from epistatic variance components is not permanent and will decay when selection is relaxed. I show that these results are tied to a conceptual confusion, and are misleading as general statements about the significance of epistasis for the selection response and adaptation.
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Affiliation(s)
- Thomas F Hansen
- Department of Biology, University of Oslo, CEES, P.O. Box 1066, Blindern, N-0316 Oslo, Norway.
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8
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Little evidence for a selective advantage of armour-reduced threespined stickleback individuals in an invertebrate predation experiment. Evol Ecol 2012. [DOI: 10.1007/s10682-012-9566-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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9
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Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. PLANT PHYSIOLOGY 2012; 158:2-22. [PMID: 22147517 PMCID: PMC3252104 DOI: 10.1104/pp.111.189845] [Citation(s) in RCA: 242] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/05/2011] [Indexed: 05/18/2023]
Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany.
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10
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Barrett RDH, Hoekstra HE. Molecular spandrels: tests of adaptation at the genetic level. Nat Rev Genet 2011; 12:767-80. [PMID: 22005986 DOI: 10.1038/nrg3015] [Citation(s) in RCA: 363] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness. Nonetheless, genes are commonly labelled as 'adaptive' if an allele has been shown to affect a phenotype with known or suspected functional importance or if patterns of nucleotide variation at the locus are consistent with positive selection. In these cases, the 'adaptive' designation may be premature and may lead to incorrect conclusions about the relationships between gene function and fitness. Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles.
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Affiliation(s)
- Rowan D H Barrett
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.
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Dalziel AC, Rogers SM, Schulte PM. Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology. Mol Ecol 2009; 18:4997-5017. [PMID: 19912534 DOI: 10.1111/j.1365-294x.2009.04427.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The accessibility of new genomic resources, high-throughput molecular technologies and analytical approaches such as genome scans have made finding genes contributing to fitness variation in natural populations an increasingly feasible task. Once candidate genes are identified, we argue that it is necessary to take a mechanistic approach and work up through the levels of biological organization to fully understand the impacts of genetic variation at these candidate genes. We demonstrate how this approach provides testable hypotheses about the causal links among levels of biological organization, and assists in designing relevant experiments to test the effects of genetic variation on phenotype, whole-organism performance capabilities and fitness. We review some of the research programs that have incorporated mechanistic approaches when examining naturally occurring genetic and phenotypic variation and use these examples to highlight the value of developing a comprehensive understanding of the relationship between genotype and fitness. We give suggestions to guide future research aimed at uncovering and understanding the genetic basis of adaptation and argue that further integration of mechanistic approaches will help molecular ecologists better understand the evolution of natural populations.
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Affiliation(s)
- Anne C Dalziel
- Department of Zoology, University of British Columbia, Vancouver, Canada.
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Marchinko KB. PREDATION'S ROLE IN REPEATED PHENOTYPIC AND GENETIC DIVERGENCE OF ARMOR IN THREESPINE STICKLEBACK. Evolution 2009; 63:127-38. [PMID: 18803682 DOI: 10.1111/j.1558-5646.2008.00529.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paris M, Roux F, Bérard A, Reboud X. The effects of the genetic background on herbicide resistance fitness cost and its associated dominance in Arabidopsis thaliana. Heredity (Edinb) 2008; 101:499-506. [PMID: 18766202 DOI: 10.1038/hdy.2008.92] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The advantage of the resistance conferred by a mutation can sometimes be offset by a high fitness-cost penalty. This balance will affect possible fate of the resistance allele. Few studies have explored the impact of the genetic background on the expression of the resistance fitness cost and none has attempted to measure the variation in fitness-cost dominance. However, both the fitness penalty and its dominance may modify evolutionary trajectory and outcome. Here the impact of Arabidopsis thaliana intraspecific genetic diversity on fitness cost and its associated dominance was investigated by analysing 12 quantitative traits in crosses between a mutant conferring resistance to the herbicide 2,4-D and nine different natural genetic backgrounds. Fitness cost values were found to be more affected by intraspecific genetic diversity than fitness cost dominance, even though this effect depends on the quantitative trait measured. This observation has implications for the choice of the best strategy for preventing herbicide resistance development. In addition, our results pinpoint a potential compensatory improvement of the resistance fitness cost and its associated dominance by the genetic diversity locally present within a species.
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Affiliation(s)
- M Paris
- UMR1210 Biologie et Gestion des Adventices, INRA, Dijon, France
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De Luca M, Chambers MM, Casazza K, Lok KH, Hunter GR, Gower BA, Fernández JR. Genetic variation in a member of the laminin gene family affects variation in body composition in Drosophila and humans. BMC Genet 2008; 9:52. [PMID: 18694491 PMCID: PMC2533007 DOI: 10.1186/1471-2156-9-52] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 08/11/2008] [Indexed: 11/23/2022] Open
Abstract
Background The objective of the present study was to map candidate loci influencing naturally occurring variation in triacylglycerol (TAG) storage using quantitative complementation procedures in Drosophila melanogaster. Based on our results from Drosophila, we performed a human population-based association study to investigate the effect of natural variation in LAMA5 gene on body composition in humans. Results We identified four candidate genes that contributed to differences in TAG storage between two strains of D. melanogaster, including Laminin A (LanA), which is a member of the α subfamily of laminin chains. We confirmed the effects of this gene using a viable LanA mutant and showed that female flies homozygous for the mutation had significantly lower TAG storage, body weight, and total protein content than control flies. Drosophila LanA is closely related to human LAMA5 gene, which maps to the well-replicated obesity-linkage region on chromosome 20q13.2-q13.3. We tested for association between three common single nucleotide polymorphisms (SNPs) in the human LAMA5 gene and variation in body composition and lipid profile traits in a cohort of unrelated women of European American (EA) and African American (AA) descent. In both ethnic groups, we found that SNP rs659822 was associated with weight (EA: P = 0.008; AA: P = 0.05) and lean mass (EA: P= 0.003; AA: P = 0.03). We also found this SNP to be associated with height (P = 0.01), total fat mass (P = 0.01), and HDL-cholesterol (P = 0.003) but only in EA women. Finally, significant associations of SNP rs944895 with serum TAG levels (P = 0.02) and HDL-cholesterol (P = 0.03) were observed in AA women. Conclusion Our results suggest an evolutionarily conserved role of a member of the laminin gene family in contributing to variation in weight and body composition.
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Affiliation(s)
- Maria De Luca
- Department of Nutrition Sciences, School of Health Professions, University of Alabama at Birmingham, 3rd Avenue South, Birmingham, AL 35294-3360, USA.
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15
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Schlichting CD. Hidden Reaction Norms, Cryptic Genetic Variation, and Evolvability. Ann N Y Acad Sci 2008; 1133:187-203. [DOI: 10.1196/annals.1438.010] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Le Rouzic A, Siegel PB, Carlborg O. Phenotypic evolution from genetic polymorphisms in a radial network architecture. BMC Biol 2007; 5:50. [PMID: 18001473 PMCID: PMC2194667 DOI: 10.1186/1741-7007-5-50] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 11/14/2007] [Indexed: 11/12/2022] Open
Abstract
Background The genetic architecture of a quantitative trait influences the phenotypic response to natural or artificial selection. One of the main objectives of genetic mapping studies is to identify the genetic factors underlying complex traits and understand how they contribute to phenotypic expression. Presently, we are good at identifying and locating individual loci with large effects, but there is a void in describing more complex genetic architectures. Although large networks of connected genes have been reported, there is an almost complete lack of information on how polymorphisms in these networks contribute to phenotypic variation and change. To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support. Results A previous study provided evidence that nearly half of the difference in eight-week body weight between two divergently selected lines of chickens was a result of four loci organized in a 'radial' network (one central locus interacting with three 'radial' loci that, in turn, only interacted with the central locus). Here, we study the relationship between phenotypic change and genetic polymorphism in this empirically detected network. We use a model-free approach to study, through individual-based simulations, the dynamic properties of this polymorphic and epistatic genetic architecture. The study provides new insights to how epistasis can modify the selection response, buffer and reveal effects of major loci leading to a progressive release of genetic variation. We also illustrate the difficulty of predicting genetic architecture from observed selection response, and discuss mechanisms that might lead to misleading conclusions on underlying genetic architectures from quantitative trait locus (QTL) experiments in selected populations. Conclusion Considering both molecular (QTL) and phenotypic (selection response) data, as suggested in this work, provides additional insights into the genetic mechanisms involved in the response to selection. Such dissection of genetic architectures and in-depth studies of their ability to contribute to short- or long-term selection response represents an important step towards a better understanding of the genetic bases of complex traits and, consequently, of the evolutionary properties of populations.
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Affiliation(s)
- Arnaud Le Rouzic
- Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden.
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Gao YM, Zhu J. Mapping QTLs with digenic epistasis under multiple environments and predicting heterosis based on QTL effects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:325-33. [PMID: 17534594 DOI: 10.1007/s00122-007-0564-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 04/23/2007] [Indexed: 05/15/2023]
Abstract
Mixed linear model approach was proposed for mapping QTLs with the digenic epistasis and QTL by environment (QE) interaction as well as additive and dominant effects. Monte Carlo simulations indicated that the proposed method could provide unbiased estimations for both positions and genetic main effects of QTLs, as well as unbiased predictions for QE interaction effects. A method was suggested for predicting heterosis based on individual QTL effects. The immortalized F(2) (IF(2)) population constructed by random mating among RI or DH lines is appropriate for mapping QTLs with epistasis and their QE interaction. Based on the models and methodology proposed, we developed a QTL mapping software, QTLMapper 2.0 on the basis of QTLmapper 1.0, which is suitable for analyzing populations of DH, RIL, F(2) and IF(2). Data of thousand grain weight of IF(2) population with 240 lines derived from elite hybrid rice Shanyou 63 were analyzed as a worked example.
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Affiliation(s)
- Yong-Ming Gao
- Department of Agronomy, Zhejiang University, Hangzhou 310029, People's Republic of China.
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18
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Abstract
Quantitative genetics is at or is fast approaching its centennial. In this perspective I consider five current issues pertinent to the application of quantitative genetics to evolutionary theory. First, I discuss the utility of a quantitative genetic perspective in describing genetic variation at two very different levels of resolution, (1) in natural, free-ranging populations and (2) to describe variation at the level of DNA transcription. Whereas quantitative genetics can serve as a very useful descriptor of genetic variation, its greater usefulness is in predicting evolutionary change, particularly when used in the first instance (wild populations). Second, I review the contributions of Quantitative trait loci (QLT) analysis in determining the number of loci and distribution of their genetic effects, the possible importance of identifying specific genes, and the ability of the multivariate breeder's equation to predict the results of bivariate selection experiments. QLT analyses appear to indicate that genetic effects are skewed, that at least 20 loci are generally involved, with an unknown number of alleles, and that a few loci have major effects. However, epistatic effects are common, which means that such loci might not have population-wide major effects: this question waits upon (QTL) analyses conducted on more than a few inbred lines. Third, I examine the importance of research into the action of specific genes on traits. Although great progress has been made in identifying specific genes contributing to trait variation, the high level of gene interactions underlying quantitative traits makes it unlikely that in the near future we will have mechanistic models for such traits, or that these would have greater predictive power than quantitative genetic models. In the fourth section I present evidence that the results of bivariate selection experiments when selection is antagonistic to the genetic covariance are frequently not well predicted by the multivariate breeder's equation. Bivariate experiments that combine both selection and functional analyses are urgently needed. Finally, I discuss the importance of gaining more insight, both theoretical and empirical, on the evolution of the G and P matrices.
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Affiliation(s)
- Derek A Roff
- Department of Biology, University of California, Riverside, California 92521, USA.
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Abstract
Life-history theory seeks to understand the factors that produce variation in life histories that are found both among and within species. At the organismal level there is a well developed mathematical framework, and an important focus of the current research is determining the biological underpinnings of this framework, with particular attention to the causal mechanisms that underlie trade-offs. Genomic approaches are proving useful in addressing this issue.
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Affiliation(s)
- Derek A Roff
- Department of Biology, University of California, Riverside, California 92521, USA.
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Kane NC, Rieseberg LH. Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus. Genetics 2007; 175:1823-34. [PMID: 17237516 PMCID: PMC1855101 DOI: 10.1534/genetics.106.067728] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Here we report the results of an analysis of variation at 128 EST-based microsatellites in wild Helianthus annuus, using populations from the species' typical plains habitat in Kansas and Colorado, as well as two arid desert and two distinct brackish marsh areas in Utah. The test statistics lnRV and lnRH were used to find regions of the genome that were significantly less variable in one population relative to the others and thus are likely to contain genes under selection. A small but detectable percentage (1.5-6%) of genes showed evidence for selection from both statistics in any particular environment, and a total of 17 loci showed evidence of selection in at least one environment. Distance-based measures provided additional evidence of selection for 15 of the 17 loci. Global F(ST)-values were significantly higher for candidate loci, as expected under divergent selection. However, pairwise F(ST)-values were lower for populations that shared a selective sweep. Moreover, while spatially separated populations undergoing similar selective pressures showed evidence of divergence at some loci, they evolved in concert at other loci. Thus, this study illustrates how selective sweeps might contribute both to the integration of conspecific populations and to the differentiation of races or species.
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Affiliation(s)
- Nolan C Kane
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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21
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Kawecki TJ, Mery F. Genetically idiosyncratic responses of Drosophila melanogaster populations to selection for improved learning ability. J Evol Biol 2006; 19:1265-74. [PMID: 16780527 DOI: 10.1111/j.1420-9101.2005.01071.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To what extent is adaptive evolution over short timescales repeatable? To address this question, we studied the performance of crosses between replicate Drosophila melanogaster lines previously subject to selection for improved learning response in the context of oviposition substrate choice. Of the 10 pairwise F1 crosses among the five selection lines, four performed in the original learning assay similarly to the parental lines, whereas the remaining six showed learning scores significantly below the average of the parental lines. In particular, four F1 crosses (three involving the same line) showed no detectable learning, on a par with unselected control lines. This indicates that the response to selection in some lines involved allelic substitutions at different loci. Additional assays of crosses between two selection lines indicated that the loss of performance in hybrids generalized to another type of learning assay, and held for both short- and long-term memory. Joint analysis of first- and second-generation crosses between these two lines supported the hypothesis that the response to selection in these different lines was based on the spread of recessive alleles at different loci. These results show that the evolutionary trajectories of populations of the same origin subject to uniform selection may sometimes diverge over very short evolutionary timescales.
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Affiliation(s)
- T J Kawecki
- Section of Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland.
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22
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Le Corre V. Variation at two flowering time genes within and among populations of Arabidopsis thaliana: comparison with markers and traits. Mol Ecol 2006; 14:4181-92. [PMID: 16262868 DOI: 10.1111/j.1365-294x.2005.02722.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Flowering Locus C (FLC) and Frigida are two interacting genes controlling flowering time variation in Arabidopsis thaliana. Variation at these genes was surveyed in 12 A. thaliana populations sampled in France. These populations were also screened for variation at molecular markers [12 microsatellites and 19 cleaved amplified polymorphic sequence (CAPS) markers] and at seven quantitative traits measured with and without vernalization. Seven populations were highly polymorphic at markers (H(S) = 0.57 at microsatellites, 0.24 at CAPS) and showed heritable variation for bolting time and some other traits. Five populations were genetically fixed or nearly fixed. Q(ST) for bolting time without vernalization was significantly higher than F(ST), suggesting local divergent selection. One of the two haplotype groups at FLC (FLC(A)) was very predominant (frequency of 99%). The first exon of Frigida showed elevated nonsynonymous variation, and nine loss-of-function mutations were found throughout the gene. The association between loss-of-function and earlier bolting was confirmed. Overall, 18 Frigida haplotypes were detected. The pattern of variation at Frigida was largely similar to that found at markers and traits, with the same populations being fixed or highly diverse. Metapopulation dynamics is thus probably the main factor shaping genetic variation in A. thaliana. However, F(ST) for functional (FRI) vs. nonfunctional (FRI(Delta)) haplotypes was significantly higher than F(ST) at markers. This suggested that loss-of-function at Frigida is under local selection for flowering time.
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Affiliation(s)
- V Le Corre
- UMR Biologie et Gestion des Adventices, INRA, BP 86510, 21065 Dijon cedex, France.
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Carlborg O, Jacobsson L, Ahgren P, Siegel P, Andersson L. Epistasis and the release of genetic variation during long-term selection. Nat Genet 2006; 38:418-20. [PMID: 16532011 DOI: 10.1038/ng1761] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 02/06/2006] [Indexed: 11/08/2022]
Abstract
It is an enigma how long-term selection in model organisms and agricultural species can lead to marked phenotypic changes without exhausting genetic variation for the selected trait. Here, we show that the genetic architecture of an apparently major locus for growth in chicken dissects into a genetic network of four interacting loci. The interactions in this radial network mediate a considerably larger selection response than predicted by a single-locus model.
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Affiliation(s)
- Orjan Carlborg
- Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden.
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Kwitek AE, Jacob HJ, Baker JE, Dwinell MR, Forster HV, Greene AS, Kunert MP, Lombard JH, Mattson DL, Pritchard KA, Roman RJ, Tonellato PJ, Cowley AW. BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat. Physiol Genomics 2006; 25:303-13. [PMID: 16478827 DOI: 10.1152/physiolgenomics.00288.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The postgenome era has provided resources to link disease phenotypes to the genomic sequence, i.e., creating a disease "phenome." Our detailed characterization of the sequenced BN rat strain (BN/NHsdMcwi) provides the first concerted effort in creating a direct link between a sequenced genome and its resulting biology. For the BN sequence to be of broad value to investigators, these measures need to be put into the context of the spectrum of the laboratory rats, so that their physiology can be benchmarked against the sequenced BN. As a major step in generating a comprehensive cardiovascular and pulmonary disease phenome, we measured 281 traits related to diseases of the heart, lung, and blood (http://pga.mcw.edu) in the sequenced BN. We compared these data with those of the same traits measured across multiple genetic backgrounds, both genders, and differing environments. We show that no single strain, inbred or outbred, can be considered a physiological control strain; what is normal depends on what trait is being measured and the strains' genome backgrounds. We find vast differences between the genders, also dependent on genome background. By combining the values across all strains studied, we generated a "population" mean and normal range of values for each of these traits, which are more genetically representative than the measured values in any single inbred or outbred strain. These data provide a baseline for physiological comparison of traits related to cardiovascular, lung, blood, and renal function in the sequenced BN rats relative to the major strains of rats studied in biomedical research.
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Affiliation(s)
- Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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Malmberg RL, Held S, Waits A, Mauricio R. Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and in the greenhouse. Genetics 2005; 171:2013-27. [PMID: 16157670 PMCID: PMC1456117 DOI: 10.1534/genetics.105.046078] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 08/29/2005] [Indexed: 11/18/2022] Open
Abstract
The extent to which epistasis contributes to adaptation, population differentiation, and speciation is a long-standing and important problem in evolutionary genetics. Using recombinant inbred (RI) lines of Arabidopsis thaliana grown under natural field conditions, we have examined the genetic architecture of fitness-correlated traits with respect to epistasis; we identified both single-locus additive and two-locus epistatic QTL for natural variation in fruit number, germination, and seed length and width. For fruit number, we found seven significant epistatic interactions, but only two additive QTL. For seed germination, length, and width, there were from two to four additive QTL and from five to eight epistatic interactions. The epistatic interactions were both positive and negative. In each case, the magnitude of the epistatic effects was roughly double that of the effects of the additive QTL, varying from -41% to +29% for fruit number and from -5% to +4% for seed germination, length, and width. A number of the QTL that we describe participate in more than one epistatic interaction, and some loci identified as additive also may participate in an epistatic interaction; the genetic architecture for fitness traits may be a network of additive and epistatic effects. We compared the map positions of the additive and epistatic QTL for germination, seed width, and seed length from plants grown in both the field and the greenhouse. While the total number of significant additive and epistatic QTL was similar under the two growth conditions, the map locations were largely different. We found a small number of significant epistatic QTL x environment effects when we tested directly for them. Our results support the idea that epistatic interactions are an important part of natural genetic variation and reinforce the need for caution in comparing results from greenhouse-grown and field-grown plants.
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Affiliation(s)
- Russell L Malmberg
- Department of Plant Biology, 2502 Plant Sciences Building, University of Georgia, Athens, GA 30602, USA.
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Abstract
Recent results of evolutionary genomics and other research programmes indicate an important role for environment-dependent selection in speciation, but the conceptual frameworks of speciation genetics and environmental stress physiology have not been fully integrated. Only a small number of model systems have been established for cross-disciplinary studies of this type in animals and plants. In these taxa (e.g. Drosophila and Arabidopsis/Arabis), studies of the mechanistic basis of various stress responses are increasingly combined with attempts to understand their evolutionary consequences. Our understanding of the role of environmental stress in speciation would benefit from studies of a larger variety of taxa. We pinpoint areas for future study and predict that in many taxa 'broad' hybrid zones maintained by ecological selection will be valuable venues for addressing the link between environmental stress, adaptation, and speciation.
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Affiliation(s)
- C Lexer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
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Spencer CC, Promislow DEL. Age-specific changes in epistatic effects on mortality rate in Drosophila melanogaster. ACTA ACUST UNITED AC 2005; 96:513-21. [PMID: 15958798 DOI: 10.1093/jhered/esi071] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Models for the evolution of senescence assume that genes with age-specific effects act independently of one another. Although recent empirical data show that longevity is influenced in part by interactions between genes, there are currently few data on whether epistasis influences age-specific components of mortality. To gauge if and how interactions affect age-specific traits, we incorporated the Drosophila visible marker mutations ebony, forked, and purple into seven wild-caught strains of D. melanogaster to examine gene x genetic background interactions. We found significant natural genetic variation for longevity and baseline mortality rates. Gene x genetic background interactions were prevalent not only for longevity but also for baseline mortality rates and age-specific mortality rates. We conclude that gene x genetic background epistasis is prevalent for aging-related traits and could play a significant role in the evolution of aging. These results suggest that future genetic models for the evolution of aging should incorporate the effects of epistasis.
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Affiliation(s)
- C C Spencer
- Department of Genetics, Life Sciences, University of Georgia, Athens, GA 30602-7223, USA.
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Abstract
Over the last 15 years quantitative trait locus (QTL) mapping has become a popular method for understanding the genetic basis of continuous variation in a variety of systems. For example, the technique is now an integral tool in medical genetics, livestock production, plant breeding and population genetics of model organisms. Ten years ago, it was suggested that the method could be used to understand continuous variation in natural populations. In this review I: (i) clarify what is meant by natural population in the QTL context, (ii) discuss whether evolutionary biologists have successfully mapped QTL in natural populations, (iii) highlight some of the questions that have been addressed by QTL mapping in natural populations, (iv) describe how QTL mapping can be conducted in unmanipulated natural populations, (v) highlight some of the limitations of QTL mapping and (vi) try to predict some future directions for QTL mapping in natural populations.
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Affiliation(s)
- Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, UK.
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29
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Abstract
Theoretical models of the accumulation of Dobzhansky-Muller incompatibilities (DMIs) are studied, and in particular, the framework introduced by Orr (1995) and a verbal model introduced by Kondrashov et al. (2002). These models embody very different assumptions about the relationship between the substitution process underlying evolutionary divergence and the formation of incompatibilities. These differences have implications for our ability to make inferences about the divergence from patterns in the relevant data. With this in mind, the models are investigated for their ability to account for three patterns evident in this data: (1) the asymmetrical nature of incompatibilities under reciprocal introgression; (2) the finding that multiple concurrent introgressions may be necessary for an incompatibility to form; and (3) the finding that the probability of obtaining an incompatibility by introgressing a single amino acid remains roughly constant over a wide range of genetic distances. None of the models available in the literature can account for all of the empirical patterns. However, modified versions of the models can do so. Ways of discriminating between the different models are then discussed.
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Affiliation(s)
- John J Welch
- Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton BN1 9QG, Sussex, United Kingdom.
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Abstract
The genomics tools available for studying Arabidopsis thaliana are a great resource for researchers trying to characterize and understand the genetic basis of natural variation. Abundant polymorphic markers aid quantitative trait locus (QTL) mapping, the fully sequenced genome provides rapid identification of candidate loci, and extensive knockout collections allow those candidate loci to be tested. Combining QTL mapping of classic phenotypic traits with biochemical or expression analysis is providing mechanistic insight into the traits of interest. Conversely, natural variation studies are now being done on genomic traits such as methylation or chiasma frequency.
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Affiliation(s)
- Julin N Maloof
- Division of Biological Sciences, One Shields Ave, University of California, Davis, CA 95616, USA.
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Welch JJ. ACCUMULATING DOBZHANSKY-MULLER INCOMPATIBILITIES: RECONCILING THEORY AND DATA. Evolution 2004. [DOI: 10.1554/03-502] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 2003; 4:981-94. [PMID: 14631358 DOI: 10.1038/nrg1226] [Citation(s) in RCA: 750] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Population genomics has the potential to improve studies of evolutionary genetics, molecular ecology and conservation biology, by facilitating the identification of adaptive molecular variation and by improving the estimation of important parameters such as population size, migration rates and phylogenetic relationships. There has been much excitement in the recent literature about the identification of adaptive molecular variation using the population-genomic approach. However, the most useful contribution of the genomics model to population genetics will be improving inferences about population demography and evolutionary history.
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Affiliation(s)
- Gordon Luikart
- Laboratoire d'Ecologie Alpine, Génomique des Populations et Biodiversit, CNRS UMR 5553, Université Joseph Fourier, B.P. 53, F-38041 Grenoble, Cedex 9, France.
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Abstract
Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life-history and fitness-related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map-based population genetic data to study how selection acts on standing genetic variation in populations.
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Affiliation(s)
- Mark C Ungerer
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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Ungerer MC, Rieseberg LH. GENETIC ARCHITECTURE OF A SELECTION RESPONSE IN ARABIDOPSIS THALIANA. Evolution 2003. [DOI: 10.1554/03-117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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