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Thompson KA, Brandvain Y, Coughlan JM, Delmore KE, Justen H, Linnen CR, Ortiz-Barrientos D, Rushworth CA, Schneemann H, Schumer M, Stelkens R. The Ecology of Hybrid Incompatibilities. Cold Spring Harb Perspect Biol 2024; 16:a041440. [PMID: 38151331 PMCID: PMC11368197 DOI: 10.1101/cshperspect.a041440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.
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Affiliation(s)
- Ken A Thompson
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St Paul, Minnesota 55108, USA
| | - Jenn M Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Kira E Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, Queensland 4072, Australia
| | - Catherine A Rushworth
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322, USA
| | - Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., Calnali 43240, Mexico
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
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2
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Meng QL, Qiang CG, Li JL, Geng MF, Ren NN, Cai Z, Wang MX, Jiao ZH, Zhang FM, Song XJ, Ge S. Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara. Mol Ecol 2024; 33:e17268. [PMID: 38230514 DOI: 10.1111/mec.17268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.
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Affiliation(s)
- Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Long Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian-Jun Song
- Key Laboratory of Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Bresadola L, Caseys C, Castiglione S, Buerkle CA, Wegmann D, Lexer C. Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. THE NEW PHYTOLOGIST 2019; 223:2076-2089. [PMID: 31104343 PMCID: PMC6771622 DOI: 10.1111/nph.15930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/06/2019] [Indexed: 05/03/2023]
Abstract
The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.
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Affiliation(s)
- Luisa Bresadola
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
| | - Céline Caseys
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Plant SciencesUniversity of California DavisOne Shields AvenueDavisCA95616USA
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’University of SalernoVia Giovanni Paolo II 13284084Fisciano, SalernoItaly
| | - C. Alex Buerkle
- Department of BotanyUniversity of Wyoming1000 E. University Ave.LaramieWY82071USA
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Swiss Institute of Bioinformatics1700FribourgSwitzerland
| | - Christian Lexer
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Botany and Biodiversity ResearchFaculty of Life SciencesUniversity of ViennaRennweg 12A‐1030ViennaAustria
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4
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Oppenheim SJ, Gould F, Hopper KR. The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens. Heredity (Edinb) 2017; 120:234-250. [PMID: 29238078 DOI: 10.1038/s41437-017-0016-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022] Open
Abstract
Intraspecific variation in ecologically important traits is a cornerstone of Darwin's theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant use in the Lepidopteran subfamily Heliothinae suggest that architecture may not constrain ecological adaptation in this group. Here we investigate the response of Chloridea virescens, a generalist that feeds on diverse plant species, to selection for performance on a novel host, Physalis angulata (Solanaceae). P. angulata is the preferred host of Chloridea subflexa, a narrow specialist on the genus Physalis. In previous experiments, we found that the performance of C. subflexa on P. angulata depends on many loci of small effect distributed throughout the genome, but whether the same architecture would be involved in the generalist's adoption of P. angulata was unknown. Here we report a rapid response to selection in C. virescens for performance on P. angulata, and establish that the genetic architecture of intraspecific variation is quite similar to that of the interspecific differences in terms of the number, distribution, and effect sizes of the QTL involved. We discuss the impact of genetic architecture on the ability of Heliothine moths to respond to varying ecological selection pressures.
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Affiliation(s)
- Sara J Oppenheim
- The Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024, USA.
| | - Fred Gould
- Department of Entomology and Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, 27607, USA
| | - Keith R Hopper
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE, 19713, USA
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5
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Cloud-Richardson KM, Smith BR, Macdonald SJ. Genetic dissection of intraspecific variation in a male-specific sexual trait in Drosophila melanogaster. Heredity (Edinb) 2016; 117:417-426. [PMID: 27530909 PMCID: PMC5117841 DOI: 10.1038/hdy.2016.63] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 06/07/2016] [Accepted: 06/22/2016] [Indexed: 01/06/2023] Open
Abstract
An open question in evolutionary biology is the relationship between standing variation for a trait and the variation that leads to interspecific divergence. By identifying loci underlying phenotypic variation in intra- and interspecific crosses we can determine the extent to which polymorphism and divergence are controlled by the same genomic regions. Sexual traits provide abundant examples of morphological and behavioral diversity within and among species, and here we leverage variation in the Drosophila sex comb to address this question. The sex comb is an array of modified bristles or ‘teeth' present on the male forelegs of several Drosophilid species. Males use the comb to grasp females during copulation, and ablation experiments have shown that males lacking comb teeth typically fail to mate. We measured tooth number in >700 genotypes derived from a multiparental advanced-intercross population, mapping three moderate-effect loci contributing to trait heritability. Two quantitative trait loci (QTLs) coincide with previously identified intra- and interspecific sex comb QTL, but such overlap can be explained by chance alone, in part because of the broad swathes of the genome implicated by earlier, low-resolution QTL scans. Our mapped QTL regions encompass 70–124 genes, but do not include those genes known to be involved in developmental specification of the comb. Nonetheless, we identified plausible candidates within all QTL intervals, and used RNA interference to validate effects at four loci. Notably, TweedleS expression knockdown substantially reduces tooth number. The genes we highlight are strong candidates to harbor segregating, functional variants contributing to sex comb tooth number.
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Affiliation(s)
| | - B R Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - S J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA.,Center for Computational Biology, University of Kansas, Lawrence, KS, USA
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6
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Brennan AC, Hiscock SJ, Abbott RJ. Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient. AOB PLANTS 2016; 8:plw022. [PMID: 27083198 PMCID: PMC4887755 DOI: 10.1093/aobpla/plw022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 03/19/2016] [Indexed: 05/03/2023]
Abstract
Knowledge of the genetic basis of phenotypic divergence between species and how such divergence is caused and maintained is crucial to an understanding of speciation and the generation of biodiversity. The hybrid zone between Senecio aethnensis and S. chrysanthemifolius on Mount Etna, Sicily, provides a well-studied example of species divergence in response to conditions at different elevations, despite hybridization and gene flow. Here, we investigate the genetic architecture of divergence between these two species using a combination of quantitative trait locus (QTL) mapping and genetic differentiation measures based on genetic marker analysis. A QTL architecture characterized by physical QTL clustering, epistatic interactions between QTLs, and pleiotropy was identified, and is consistent with the presence of divergent QTL complexes resistant to gene flow. A role for divergent selection between species was indicated by significant negative associations between levels of interspecific genetic differentiation at mapped marker gene loci and map distance from QTLs and hybrid incompatibility loci. Within-species selection contributing to interspecific differentiation was evidenced by negative associations between interspecific genetic differentiation and genetic diversity within species. These results show that the two Senecio species, while subject to gene flow, maintain divergent genomic regions consistent with local selection within species and selection against hybrids between species which, in turn, contribute to the maintenance of their distinct phenotypic differences.
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Affiliation(s)
- Adrian C Brennan
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife KY16 9TH, UK Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio s/n, 41092 Sevilla, Spain Present address: School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
| | - Simon J Hiscock
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife KY16 9TH, UK
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7
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Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. THE NEW PHYTOLOGIST 2015; 205:402-14. [PMID: 25252269 PMCID: PMC4265272 DOI: 10.1111/nph.13027] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/31/2014] [Indexed: 05/08/2023]
Abstract
The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as a result of genetic colocalization either by pleiotropy or genetic linkage. The self-fertilizing C4 grass species Panicum hallii includes two major ecotypes found in xeric (var. hallii) or mesic (var. filipes) habitats. We constructed the first linkage map for P. hallii by genotyping a reduced representation genomic library of an F2 population derived from an intercross of var. hallii and filipes. We then evaluated the genetic architecture of divergence between these ecotypes through quantitative trait locus (QTL) mapping. Overall, we mapped QTLs for nine morphological traits that are involved in the divergence between the ecotypes. QTLs for five key ecotype-differentiating traits all colocalized to the same region of linkage group five. Leaf physiological traits were less divergent between ecotypes, but we still mapped five physiological QTLs. We also discovered a two-locus Dobzhansky-Muller hybrid incompatibility. Our study suggests that ecotype-differentiating traits may evolve in tandem as a result of genetic colocalization.
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Affiliation(s)
- David B Lowry
- Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA; Division of Science and Environmental Policy, California State University, Monterey Bay, 100 Campus Center, Seaside, CA, 93955, USA
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8
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Kenney AM, McKay JK, Richards JH, Juenger TE. Direct and indirect selection on flowering time, water-use efficiency (WUE, δ (13)C), and WUE plasticity to drought in Arabidopsis thaliana. Ecol Evol 2014; 4:4505-21. [PMID: 25512847 PMCID: PMC4264900 DOI: 10.1002/ece3.1270] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 07/15/2014] [Accepted: 08/19/2014] [Indexed: 11/09/2022] Open
Abstract
Flowering time and water-use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time, WUE, and WUE plasticity to drought in Arabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genetically correlated within and between different soil moisture environments? (2) Does terminal drought select for early flowering and drought escape? (3) Is WUE plasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions of A. thaliana grown in well-watered and season-ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment. WUE and flowering time were consistently positively genetically correlated. WUE was correlated with WUE plasticity, but the direction changed between treatments. Selection generally favored early flowering and low WUE, with drought favoring earlier flowering significantly more than well-watered conditions. Selection for lower WUE was marginally stronger under drought. There were no net fitness costs of WUE plasticity. WUE plasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation between WUE and flowering time may facilitate the evolution of drought escape, or constrain independent evolution of these traits. Terminal drought favored drought escape in these spring flowering accessions of A. thaliana. WUE plasticity may be favored over completely fixed development in environments with periodic drought.
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Affiliation(s)
- Amanda M Kenney
- Department of Biological Sciences, St. Edward's University Austin, Texas
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University Fort Collins, Colorado
| | - James H Richards
- Land, Air and Water Resources, University of California, Davis Davis, California
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin Austin, Texas
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9
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Lindtke D, González-Martínez SC, Macaya-Sanz D, Lexer C. Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations. Heredity (Edinb) 2013; 111:474-85. [PMID: 23860234 PMCID: PMC3833683 DOI: 10.1038/hdy.2013.69] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 06/06/2013] [Accepted: 06/12/2013] [Indexed: 01/30/2023] Open
Abstract
Uncovering the genetic architecture of species differences is of central importance for understanding the origin and maintenance of biological diversity. Admixture mapping can be used to identify the number and effect sizes of genes that contribute to the divergence of ecologically important traits, even in taxa that are not amenable to laboratory crosses because of their long generation time or other limitations. Here, we apply admixture mapping to naturally occurring hybrids between two ecologically divergent Populus species. We map quantitative trait loci for eight leaf morphological traits using 77 mapped microsatellite markers from all 19 chromosomes of Populus. We apply multivariate linear regression analysis allowing the modeling of additive and non-additive gene action and identify several candidate genomic regions associated with leaf morphology using an information-theoretic approach. We perform simulation studies to assess the power and limitations of admixture mapping of quantitative traits in natural hybrid populations for a variety of genetic architectures and modes of gene action. Our results indicate that (1) admixture mapping has considerable power to identify the genetic architecture of species differences if sample sizes and marker densities are sufficiently high, (2) modeling of non-additive gene action can help to elucidate the discrepancy between genotype and phenotype sometimes seen in interspecific hybrids, and (3) the genetic architecture of leaf morphological traits in the studied Populus species involves complementary and overdominant gene action, providing the basis for rapid adaptation of these ecologically important forest trees.
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Affiliation(s)
- D Lindtke
- Unit of Ecology and Evolution, Department of
Biology, University of Fribourg, Fribourg,
Switzerland
| | - S C González-Martínez
- INIA, Forest Research Centre, Department of
Forest Ecology and Genetics, Madrid, Spain
| | - D Macaya-Sanz
- INIA, Forest Research Centre, Department of
Forest Ecology and Genetics, Madrid, Spain
- Technical University of Madrid, ETS Forestry
Engineering, Department of Silviculture, Madrid, Spain
| | - C Lexer
- Unit of Ecology and Evolution, Department of
Biology, University of Fribourg, Fribourg,
Switzerland
- Jodrell Laboratory, Royal Botanic
Gardens, Kew, Richmond, Surrey, UK
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10
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Andrew RL, Rieseberg LH. DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES. Evolution 2013; 67:2468-82. [DOI: 10.1111/evo.12106] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/20/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany, University of British Columbia, 3529-6270 University Blvd; Vancouver; British Columbia; V6T 1Z4; Canada
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11
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Gompert Z, Lucas LK, Nice CC, Buerkle CA. GENOME DIVERGENCE AND THE GENETIC ARCHITECTURE OF BARRIERS TO GENE FLOW BETWEENLYCAEIDES IDASANDL. MELISSA. Evolution 2012; 67:2498-514. [DOI: 10.1111/evo.12021] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/30/2012] [Indexed: 01/28/2023]
Affiliation(s)
| | - Lauren K. Lucas
- Department of Biology; Texas State University; San Marcos; Texas
| | - Chris C. Nice
- Department of Biology; Texas State University; San Marcos; Texas
| | - C. Alex Buerkle
- Department of Botany; University of Wyoming; Laramie; Wyoming
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12
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Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size. G3-GENES GENOMES GENETICS 2012; 2:905-11. [PMID: 22908039 PMCID: PMC3411246 DOI: 10.1534/g3.112.003228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 06/11/2012] [Indexed: 11/18/2022]
Abstract
Allelic effects at quantitative trait loci (QTL) between lineages are potentially informative for indicating the action of natural selection. The QTL Sign Test uses the number of + and − alleles observed in a QTL study to infer a history of selection. This test has been constructed to condition on the phenotypic difference between the two lines in question. By applying the test to QTL data simulated under selection, we demonstrate that conditioning on the phenotypic difference results in a loss of power to reject the neutral hypothesis and marked sensitivity to variation in locus effect magnitude.
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13
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Oppenheim SJ, Gould F, Hopper KR. The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa. Evolution 2012; 66:3336-51. [PMID: 23106701 DOI: 10.1111/j.1558-5646.2012.01712.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We used genetic mapping to examine the genetic architecture of differences in host plant use between two species of noctuid moths, Heliothis subflexa, a specialist on Physalis spp., and its close relative, the broad generalist H. virescens. We introgressed H. subflexa chromosomes into the H. virescens background and analyzed 1462 backcross insects. The effects of H. subflexa-origin chromosomes were small when measured as the percent variation explained in backcross populations (0.2-5%), but were larger when considered in relation to the interspecific difference explained (1.5-165%). Most significant chromosomes had effects on more than one trait, and their effects varied between years, sexes, and genetic backgrounds. Different chromosomes could produce similar phenotypes, suggesting that the same trait might be controlled by different chromosomes in different backcross populations. It appears that many loci of small effect contribute to the use of Physalis by H. subflexa. We hypothesize that behavioral changes may have paved the way for physiological adaptation to Physalis by the generalist ancestor of H. subflexa and H. virescens.
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Affiliation(s)
- Sara J Oppenheim
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA.
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14
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ANDREW ROSEL, OSTEVIK KATHERINEL, EBERT DANIELP, RIESEBERG LORENH. Adaptation with gene flow across the landscape in a dune sunflower. Mol Ecol 2012; 21:2078-91. [DOI: 10.1111/j.1365-294x.2012.05454.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Christensen AR, Malcomber ST. Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales. EvoDevo 2012; 3:4. [PMID: 22340849 PMCID: PMC3305426 DOI: 10.1186/2041-9139-3-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/17/2012] [Indexed: 11/10/2022] Open
Abstract
Background Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The LEAFY HULL STERILE1 (LHS1) SEPALLATA (SEP) genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1) when the duplication event that produced the LHS1 clade and its paralogous lineage Oryza sativa MADS5 (OSM5) occurred, and 2) how changes in gene structure and/or expression might have contributed to subfunctionalization and/or neofunctionalization in the two lineages. Methods Phylogenetic relationships among 84 SEP genes were estimated using Bayesian methods. RNA expression patterns were inferred using in situ hybridization. The patterns of protein sequence and RNA expression evolution were reconstructed using maximum parsimony (MP) and maximum likelihood (ML) methods, respectively. Results Phylogenetic analyses mapped the LHS1/OSM5 duplication event to the base of the grass family. MP character reconstructions estimated a change from cytosine to thymine in the first codon position of the first amino acid after the Zea mays MADS3 (ZMM3) domain converted a glutamine to a stop codon in the OSM5 ancestor following the LHS1/OSM5 duplication event. RNA expression analyses of OSM5 co-orthologs in Avena sativa, Chasmanthium latifolium, Hordeum vulgare, Pennisetum glaucum, and Sorghum bicolor followed by ML reconstructions of these data and previously published analyses estimated a complex pattern of gain and loss of LHS1 and OSM5 expression in different floral organs and different flowers within the spikelet or inflorescence. Conclusions Previous authors have reported that rice OSM5 and LHS1 proteins have different interaction partners indicating that the truncation of OSM5 following the LHS1/OSM5 duplication event has resulted in both partitioned and potentially novel gene functions. The complex pattern of OSM5 and LHS1 expression evolution is not consistent with a simple subfunctionalization model following the gene duplication event, but there is evidence of recent partitioning of OSM5 and LHS1 expression within different floral organs of A. sativa, C. latifolium, P. glaucum and S. bicolor, and between the upper and lower florets of the two-flowered maize spikelet.
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Affiliation(s)
- Ashley R Christensen
- Department of Biological Sciences, California State University - Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840, USA.
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16
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A test for selection employing quantitative trait locus and mutation accumulation data. Genetics 2012; 190:1533-45. [PMID: 22298701 DOI: 10.1534/genetics.111.137075] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolutionary biologists attribute much of the phenotypic diversity observed in nature to the action of natural selection. However, for many phenotypic traits, especially quantitative phenotypic traits, it has been challenging to test for the historical action of selection. An important challenge for biologists studying quantitative traits, therefore, is to distinguish between traits that have evolved under the influence of strong selection and those that have evolved neutrally. Most existing tests for selection employ molecular data, but selection also leaves a mark on the genetic architecture underlying a trait. In particular, the distribution of quantitative trait locus (QTL) effect sizes and the distribution of mutational effects together provide information regarding the history of selection. Despite the increasing availability of QTL and mutation accumulation data, such data have not yet been effectively exploited for this purpose. We present a model of the evolution of QTL and employ it to formulate a test for historical selection. To provide a baseline for neutral evolution of the trait, we estimate the distribution of mutational effects from mutation accumulation experiments. We then apply a maximum-likelihood-based method of inference to estimate the range of selection strengths under which such a distribution of mutations could generate the observed QTL. Our test thus represents the first integration of population genetic theory and QTL data to measure the historical influence of selection.
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Kim SC. Mapping unexplored genomes II: genetic architecture of species differences in the woody Sonchus alliance (Asteraceae) in the Macaronesian Islands. JOURNAL OF PLANT RESEARCH 2012; 125:125-136. [PMID: 21505946 DOI: 10.1007/s10265-011-0424-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 03/23/2011] [Indexed: 05/30/2023]
Abstract
Despite numerous, well-documented evolutionary histories of plant groups which underwent rapid radiation in various oceanic archipelagos, very little is known about the genetic basis of species differences and adaptive radiation. This paper represents the first such study in the Macaronesian Islands using non-model endemic plants, the woody Sonchus alliance. Here I inferred the genetic basis of species differences between two Canary Island endemics, the herbaceous perennial, shade tolerant Lactucosonchus webbii and the woody, coastal desert perennial Sonchus radicatus by quantitative trait locus (QTL) mapping using AFLP markers. A total of 23 QTL (7.3-23.8% PVE; phenotypic variance explained) for 11 morphological traits were found, one for flowering time (31% PVE), and five QTL (7-10.7% PVE) for two physiological traits (intrinsic water use efficiency and stomatal conductance). Interpreted cautiously, these results suggest that major morphological and some physiological differences between the two species are controlled by numerous genes with small to moderate effect. This implies that major morphological changes in island plants can be more complex than suggested by other studies, such as in Tetramolopium in the Hawaiian Islands. The genetic basis of arborescence on islands, one of the most spectacular convergent features of plants across different lineages and archipelagos, is also discussed.
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Affiliation(s)
- Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 300 Cheoncheon-dong, Jangan-gu, Suwon, Gyeonggi-do, 440-746, Korea.
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18
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Abstract
Local adaptation is considered to be the result of fitness trade-offs for particular phenotypes across different habitats. However, it is unclear whether such phenotypic trade-offs exist at the level of individual genetic loci. Local adaptation could arise from trade-offs of alternative alleles at individual loci or by complementary sets of loci with different fitness effects of alleles in one habitat but selective neutrality in the alternative habitat. To evaluate the genome-wide basis of local adaptation, we performed a field-based quantitative trait locus (QTL) mapping experiment on recombinant inbred lines (RILs) created from coastal perennial and inland annual races of the yellow monkeyflower (Mimulus guttatus) grown reciprocally in native parental habitats. Overall, we detected 19 QTLs affecting one or more of 16 traits measured in two environments, most of small effect. We identified 15 additional QTL effects at two previously identified candidate QTLs [DIVERGENCE (DIV)]. Significant QTL by environment interactions were detected at the DIV loci, which was largely attributable to genotypic differences at a single field site. We found no detectable evidence for trade-offs for any one component of fitness, although DIV2 showed a trade-off involving different fitness traits between sites, suggesting that local adaptation is largely controlled by non-overlapping loci. This is surprising for an outcrosser, implying that reduced gene flow prevents the evolution of individuals adapted to multiple environments. We also determined that native genotypes were not uniformly adaptive, possibly reflecting fixed mutational load in one of the populations.
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Affiliation(s)
- M C Hall
- Department of Molecular and Cell Biology, Energy Biosciences Institute, 545 Life Sciences Addition, University of California-Berkeley, Berkeley, CA 94720-3200, USA.
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19
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Linnen CR, Hoekstra HE. Measuring natural selection on genotypes and phenotypes in the wild. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2010; 74:155-68. [PMID: 20413707 DOI: 10.1101/sqb.2009.74.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A complete understanding of the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting in the wild. Accordingly, several approaches using a variety of data-including patterns of DNA variability, spatial and temporal changes in allele frequencies, and fitness estimates-have been developed to identify and quantify selection on both genotypes and phenotypes. Here, we review these approaches, drawing on both recent and classic examples to illustrate their utility and limitations. We then argue that by combining estimates of selection at multiple levels-from individual mutations to phenotypes-and at multiple timescales-from ecological to evolutionary-with experiments that demonstrate why traits are under selection, we can gain a much more complete picture of the adaptive process.
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Affiliation(s)
- C R Linnen
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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20
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Tang S, Okashah RA, Knapp SJ, Arnold ML, Martin NH. Transmission ratio distortion results in asymmetric introgression in Louisiana Iris. BMC PLANT BIOLOGY 2010; 10:48. [PMID: 20298609 PMCID: PMC2923522 DOI: 10.1186/1471-2229-10-48] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 03/18/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Linkage maps are useful tools for examining both the genetic architecture of quantitative traits and the evolution of reproductive incompatibilities. We describe the generation of two genetic maps using reciprocal interspecific backcross 1 (BC1) mapping populations from crosses between Iris brevicaulis and Iris fulva. These maps were constructed using expressed sequence tag (EST)- derived codominant microsatellite markers. Such a codominant marker system allowed for the ability to link the two reciprocal maps, and compare patterns of transmission ratio distortion observed between the two. RESULTS Linkage mapping resulted in markers that coalesced into 21 linkage groups for each of the reciprocal backcross maps, presumably corresponding to the 21 haploid chromosomes of I. brevicaulis and I. fulva. The composite map was 1190.0-cM long, spanned 81% of the I. brevicaulis and I. fulva genomes, and had a mean density of 4.5 cM per locus. Transmission ratio distortion (TRD) was observed in 138 (48.5%) loci distributed in 19 of the 21 LGs in BCIB, BCIF, or both BC1 mapping populations. Of the distorted markers identified, I. fulva alleles were detected at consistently higher-than-expected frequencies in both mapping populations. CONCLUSIONS The observation that I. fulva alleles are overrepresented in both mapping populations suggests that I. fulva alleles are favored to introgress into I. brevicaulis genetic backgrounds, while I. brevicaulis alleles would tend to be prevented from introgressing into I. fulva. These data are consistent with the previously observed patterns of introgression in natural hybrid zones, where I. fulva alleles have been consistently shown to introgress across species boundaries.
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Affiliation(s)
- Shunxue Tang
- Center for Applied Genetic Technologies, The University of Georgia, Athens, GA 30602, USA
- Dow AgroSciences LLC, Indianapolis, IN 46268, USA
| | - Rebecca A Okashah
- Center for Applied Genetic Technologies, The University of Georgia, Athens, GA 30602, USA
| | - Steven J Knapp
- Center for Applied Genetic Technologies, The University of Georgia, Athens, GA 30602, USA
| | - Michael L Arnold
- Department of Genetics, The University of Georgia, Athens, GA 30602, USA
| | - Noland H Martin
- Department of Biology, Texas State University - San Marcos, San Marcos, TX 78666, USA
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21
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Bachlava E, Tang S, Pizarro G, Schuppert GF, Brunick RK, Draeger D, Leon A, Hahn V, Knapp SJ. Pleiotropy of the branching locus (B) masks linked and unlinked quantitative trait loci affecting seed traits in sunflower. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:829-42. [PMID: 19921140 DOI: 10.1007/s00122-009-1212-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 10/27/2009] [Indexed: 05/20/2023]
Abstract
The discovery of unbranched, monocephalic natural variants was pivotal for the domestication of sunflower (Helianthus annuus L.). The branching locus (B), one of several loci apparently targeted by aboriginal selection for monocephaly, pleiotropically affects plant, seed and capitula morphology and, when segregating, confounds the discovery of favorable alleles for seed yield and other traits. The present study was undertaken to gain deeper insights into the genetics of branching and seed traits affected by branching. We produced an unbranched hybrid testcross recombinant inbred line (TC-RIL) population by crossing branched (bb) and unbranched (BB) RILs to an unbranched (BB) tester. The elimination of branching concomitantly eliminated a cluster of B-linked seed trait quantitative trait loci (QTL) identified by RIL per se testing. We identified a seed oil content QTL linked in repulsion and a 100-seed weight QTL linked in coupling to the B locus and additional unlinked QTL, previously masked by B-locus pleiotropy. Genomic segments flanking the B locus harbor multiple loci for domestication and post-domestication traits, the effects of which are masked by B-locus pleiotropy in populations segregating for branching and can only be disentangled by genetic analyses in unbranched populations. QTL analyses of NILs carrying wild B alleles substantiated the pleiotropic effects of the B locus. The effect of the B locus on branching was masked by the effects of wild alleles at independent branching loci in hybrids between monocephalic domesticated lines and polycephalic wild ecotypes; hence, the B locus appears to be necessary, but not sufficient, for monocephaly in domesticated sunflower.
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Affiliation(s)
- Eleni Bachlava
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
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22
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Gailing O, Vornam B, Leinemann L, Finkeldey R. Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model. PHYSIOLOGIA PLANTARUM 2009; 137:509-19. [PMID: 19627554 DOI: 10.1111/j.1399-3054.2009.01263.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the increasing availability of sequence information at putatively important genes or regulatory regions, the characterization of adaptive genetic diversity and their association with phenotypic trait variation becomes feasible for many non-model organisms such as forest trees. Especially in predominantly outcrossing forest tree populations with large effective size, a high genetic variation in relevant genes is maintained, that is the raw material for the adaptation to changing and variable environments, and likewise for plant breeding. Oaks (Quercus spp.) are excellent model species to study the adaptation of forest trees to changing environments. They show a wide geographic distribution in Europe as dominant tree species in many forests and grow under a wide range of climatic and edaphic conditions. With the availability of a growing amount of functional and expressional candidate genes, we are now able to test the functional importance of single nucleotide polymorphisms (SNPs) by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in segregating or natural populations. Here, we report on quantitative trait locus (QTL), candidate gene and association mapping approaches that are applicable to characterize gene markers and SNPs associated with variation in adaptive traits, such as bud burst, drought resistance and other traits showing selective responses to environmental change and stress. Because genome-wide association mapping studies are not feasible because of the enormous amount of SNP markers required in outcrossing trees with high recombination rates, the success of such an approach depends largely on the reasonable selection of candidate genes.
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Affiliation(s)
- Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Germany.
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23
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Muir CD, Moyle LC. Antagonistic epistasis for ecophysiological trait differences between Solanum species. THE NEW PHYTOLOGIST 2009; 183:789-802. [PMID: 19659589 DOI: 10.1111/j.1469-8137.2009.02949.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Epistasis, the nonadditive interaction between loci, is thought to play a role in many fundamental evolutionary processes, including adaptive differentiation and speciation. Focusing on species differences in ecophysiological traits, we examined the strength and direction of pairwise epistatic interactions between target chromosomal regions from one species, when co-introgressed into the genetic background of a foreign species. A full diallel cross was performed using 15 near-isogenic lines (NILs) constructed between two tomato species (Solanum habrochaites and Solanum lycopersicum) to compare the phenotypic effects of each chromosomal region singly and in combination with each other region. We detected main effect quantitative trait loci (QTLs) for two of our three focal traits. Epistatic effects accounted for c. 25% of detected effects on trait means, depending on the trait. Strikingly, all but two interactions were antagonistic, with the combined effect of chromosomal regions acting in the opposite direction from that of one or both individual chromosomal regions. Our study is one of the few to systematically examine pairwise epistatic effects in a nonmicrobial system. Our results suggest that epistatic interactions can contribute substantially to the genetic basis of traits involved in adaptive species differentiation, especially highly complex, multivariate traits.
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Affiliation(s)
- Christopher D Muir
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47401, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47401, USA
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24
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Cooley AM, Willis JH. Genetic divergence causes parallel evolution of flower color in Chilean Mimulus. THE NEW PHYTOLOGIST 2009; 183:729-739. [PMID: 19453433 DOI: 10.1111/j.1469-8137.2009.02858.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Deciphering the genetic architecture of phenotypic change provides a framework for understanding how evolution proceeds at a genetic level, and paves the way for work at the molecular level. A series of intra- and interspecific crosses were used to investigate the genetic control of recently evolved floral pigmentation phenotypes in a group of closely related Mimulus species from central Chile. An intraspecific polymorphism was found to be controlled by a single Mendelian locus. Differences between species, by contrast, were composed of multiple independent patterning elements, including both Mendelian and polygenic traits. The most striking phenotypic novelty in this group, anthocyanin pigmentation in the petal lobes, has evolved three times independently. The results illustrate how genetically simple modular elements can interact with polygenic or quantitative traits to create complex new phenotypes. The repeated evolution of petal lobe anthocyanins suggests that natural selection may have played a role in the evolution of red coloration in the Chilean Mimulus, and shows that red coloration has been achieved via different genetic pathways in these closely related species.
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Affiliation(s)
| | - John H Willis
- Department of Biology, Duke University, Durham, NC 27708, USA
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25
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Strasburg JL, Scotti-Saintagne C, Scotti I, Lai Z, Rieseberg LH. Genomic patterns of adaptive divergence between chromosomally differentiated sunflower species. Mol Biol Evol 2009; 26:1341-55. [PMID: 19276154 PMCID: PMC2727376 DOI: 10.1093/molbev/msp043] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2009] [Indexed: 01/13/2023] Open
Abstract
Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
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Affiliation(s)
- Jared L Strasburg
- Department of Biology, Indiana University, Bloomington, Indiana, USA.
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26
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Grillo MA, Li C, Fowlkes AM, Briggeman TM, Zhou A, Schemske DW, Sang T. GENETIC ARCHITECTURE FOR THE ADAPTIVE ORIGIN OF ANNUAL WILD RICE,ORYZA NIVARA. Evolution 2009; 63:870-83. [DOI: 10.1111/j.1558-5646.2008.00602.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kliebenstein D. Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. ANNUAL REVIEW OF PLANT BIOLOGY 2009; 60:93-114. [PMID: 19012536 DOI: 10.1146/annurev.arplant.043008.092114] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Scientific inquiries in fields ranging from ecology to plant breeding assess phenotypic variation within a plant species either to explain its presence or utilize its consequences. Frequently this natural genetic variation is studied via mapping quantitative trait loci (QTLs); however, elucidation of the underlying molecular mechanisms is a continuing bottleneck. The genomic analysis of transcripts as individual phenotypes has led to the emerging field of expression QTL analysis. This field has begun both to delve into the ecological/evolutionary significance of this transcript variation as well as to use specific eQTLs to speed up our analysis of the molecular basis of quantitative traits. This review introduces eQTL analysis and begins to illustrate how these data can be applied to multiple research fields.
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Affiliation(s)
- Dan Kliebenstein
- Plant Sciences, University of California, Davis, California 95616, USA.
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28
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Lexer C, Widmer A. Review. The genic view of plant speciation: recent progress and emerging questions. Philos Trans R Soc Lond B Biol Sci 2008; 363:3023-36. [PMID: 18579476 DOI: 10.1098/rstb.2008.0078] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The genic view of the process of speciation is based on the notion that species isolation may be achieved by a modest number of genes. Although great strides have been made to characterize 'speciation genes' in some groups of animals, little is known about the nature of genic barriers to gene flow in plants. We review recent progress in the characterization of genic species barriers in plants with a focus on five 'model' genera: Mimulus (monkey flowers); Iris (irises); Helianthus (sunflowers); Silene (campions); and Populus (poplars, aspens, cottonwoods). The study species in all five genera are diploid in terms of meiotic behaviour, and chromosomal rearrangements are assumed to play a minor role in species isolation, with the exception of Helianthus for which data on the relative roles of chromosomal and genic isolation factors are available. Our review identifies the following key topics as being of special interest for future research: the role of intraspecific variation in speciation; the detection of balancing versus directional selection in speciation genetic studies; the timing of fixation of alleles of major versus minor effects during plant speciation; the likelihood of adaptive trait introgression; and the identification and characterization of speciation genes and speciation gene networks.
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Affiliation(s)
- Christian Lexer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
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Baxter SW, Johnston SE, Jiggins CD. Butterfly speciation and the distribution of gene effect sizes fixed during adaptation. Heredity (Edinb) 2008; 102:57-65. [DOI: 10.1038/hdy.2008.109] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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30
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Gailing O. QTL analysis of leaf morphological characters in a Quercus robur full-sib family (Q. robur x Q. robur ssp. slavonica). PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10:624-34. [PMID: 18761500 DOI: 10.1111/j.1438-8677.2008.00063.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The distinction between white oak species (section Quercus sensu stricto) is largely based on leaf morphological characters. There is, however, considerable within-species variation and no single species-diagnostic character, possibly due to phenotypic plasticity and/or underlying genetic variation. The aim of the present study was to identify quantitative trait loci (QTL) underlying the high within-species variation for leaf morphological characters in an F(1) full-sib family derived from a cross between Q. robur and Q. robur ssp. slavonica. In accordance with an earlier QTL mapping study in an intraspecific Q. robur full-sib family, polygenic inheritance was detected for leaf morphological characters that are used to discriminate between the species Quercus robur and Q. petraea. QTLs were distributed over ten linkage groups, showed a moderate effect in terms of phenotypic variance explained (PVE) in the mapping pedigree (3.6-9.6%), but accounted for a considerable amount of the parental differences. Co-localisation of QTLs on the same linkage group in different genetic backgrounds was found for the number and percentage of intercalary veins (NV, PV) on linkage group 3 and for NV on linkage group 5, revealing a high congruence in the relative QTL positions. The generally low correspondence of the other QTLs in the different mapping pedigrees may be an effect of the genetic background and of the environment. In conclusion, leaf morphological characters were found to be under polygenic control, and a comparison to earlier published results led to the identification of two QTLs that were stable across different genetic backgrounds.
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Affiliation(s)
- O Gailing
- Institute of Forest Genetics and Forest Tree Breeding, Georg-August University Göttingen, Göttingen, Germany.
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31
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Rowe HC, Hansen BG, Halkier BA, Kliebenstein DJ. Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome. THE PLANT CELL 2008; 20:1199-216. [PMID: 18515501 PMCID: PMC2438456 DOI: 10.1105/tpc.108.058131] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 05/05/2008] [Accepted: 05/12/2008] [Indexed: 05/18/2023]
Abstract
Genomic approaches have accelerated the study of the quantitative genetics that underlie phenotypic variation. These approaches associate genome-scale analyses such as transcript profiling with targeted phenotypes such as measurements of specific metabolites. Additionally, these approaches can help identify uncharacterized networks or pathways. However, little is known about the genomic architecture underlying data sets such as metabolomics or the potential of such data sets to reveal networks. To describe the genetic regulation of variation in the Arabidopsis thaliana metabolome and test our ability to integrate unknown metabolites into biochemical networks, we conducted a replicated metabolomic analysis on 210 lines of an Arabidopsis population that was previously used for targeted metabolite quantitative trait locus (QTL) and global expression QTL analysis. Metabolic traits were less heritable than the average transcript trait, suggesting that there are differences in the power to detect QTLs between transcript and metabolite traits. We used statistical analysis to identify a large number of metabolite QTLs with moderate phenotypic effects and found frequent epistatic interactions controlling a majority of the variation. The distribution of metabolite QTLs across the genome included 11 QTL clusters; 8 of these clusters were associated in an epistatic network that regulated plant central metabolism. We also generated two de novo biochemical network models from the available data, one of unknown function and the other associated with central plant metabolism.
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Affiliation(s)
- Heather C Rowe
- Genetics Graduate Group and Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
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Albert AYK, Sawaya S, Vines TH, Knecht AK, Miller CT, Summers BR, Balabhadra S, Kingsley DM, Schluter D. The genetics of adaptive shape shift in stickleback: pleiotropy and effect size. Evolution 2007; 62:76-85. [PMID: 18005154 DOI: 10.1111/j.1558-5646.2007.00259.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The distribution of effect sizes of genes underlying adaptation is unknown (Orr 2005). Are suites of traits that diverged under natural selection controlled by a few pleiotropic genes of large effect (major genes model), by many independently acting genes of small effect (infinitesimal model), or by a combination, with frequency inversely related to effect size (geometric model)? To address this we carried out a quantitative trait loci (QTL) study of a suite of 54 position traits describing body shapes of two threespine stickleback species: an ancestral Pacific marine form and a highly derived benthic species inhabiting a geologically young lake. About half of the 26 detected QTL affected just one coordinate and had small net effects, but several genomic regions affected multiple aspects of shape and had large net effects. The distribution of effect sizes followed the gamma distribution, as predicted by the geometric model of adaptation when detection limits are taken into account. The sex-determining chromosome region had the largest effect of any QTL. Ancestral sexual dimorphism was similar to the direction of divergence, and was largely eliminated during freshwater adaptation, suggesting that sex differences may provide variation upon which selection can act. Several shape QTL are linked to Eda, a major gene responsible for reduction of lateral body armor in freshwater. Our results are consistent with predictions of the geometric model of adaptation. Shape evolution in stickleback results from a few genes with large and possibly widespread effects and multiple genes of smaller effect.
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Affiliation(s)
- Arianne Y K Albert
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Abstract
The formation of hybrid zones between nascent species is a widespread phenomenon. The evolutionary consequences of hybridization are influenced by numerous factors, including the action of natural selection on quantitative trait variation. Here we examine how the genetic basis of floral traits of two species of Louisiana Irises affects the extent of quantitative trait variation in their hybrids. Quantitative trait locus (QTL) mapping was used to assess the size (magnitude) of phenotypic effects of individual QTL, the degree to which QTL for different floral traits are colocalized, and the occurrence of mixed QTL effects. These aspects of quantitative genetic variation would be expected to influence (1) the number of genetic steps (in terms of QTL substitutions) separating the parental species phenotypes; (2) trait correlations; and (3) the potential for transgressive segregation in hybrid populations. Results indicate that some Louisiana Iris floral trait QTL have large effects and QTL for different traits tend to colocalize. Transgressive variation was observed for six of nine traits, despite the fact that mixed QTL effects influence few traits. Overall, our QTL results imply that the genetic basis of floral morphology and color traits might facilitate the maintenance of phenotypic divergence between Iris fulva and Iris brevicaulis, although a great deal of phenotypic variation was observed among hybrids.
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Affiliation(s)
- Amy Bouck
- Department of Genetics, The University of Georgia, Athens, GA 30602, USA.
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Abstract
The distribution of fitness effects (DFE) of new mutations is a fundamental entity in genetics that has implications ranging from the genetic basis of complex disease to the stability of the molecular clock. It has been studied by two different approaches: mutation accumulation and mutagenesis experiments, and the analysis of DNA sequence data. The proportion of mutations that are advantageous, effectively neutral and deleterious varies between species, and the DFE differs between coding and non-coding DNA. Despite these differences between species and genomic regions, some general principles have emerged: advantageous mutations are rare, and those that are strongly selected are exponentially distributed; and the DFE of deleterious mutations is complex and multi-modal.
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Affiliation(s)
- Adam Eyre-Walker
- Centre for the Study of Evolution, University of Sussex, Brighton, BN1 9QG, UK.
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Wentzell AM, Rowe HC, Hansen BG, Ticconi C, Halkier BA, Kliebenstein DJ. Linking metabolic QTLs with network and cis-eQTLs controlling biosynthetic pathways. PLoS Genet 2007; 3:1687-701. [PMID: 17941713 PMCID: PMC1976331 DOI: 10.1371/journal.pgen.0030162] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 08/01/2007] [Indexed: 11/18/2022] Open
Abstract
Phenotypic variation between individuals of a species is often under quantitative genetic control. Genomic analysis of gene expression polymorphisms between individuals is rapidly gaining popularity as a way to query the underlying mechanistic causes of variation between individuals. However, there is little direct evidence of a linkage between global gene expression polymorphisms and phenotypic consequences. In this report, we have mapped quantitative trait loci (QTLs)-controlling glucosinolate content in a population of 403 Arabidopsis Bay x Sha recombinant inbred lines, 211 of which were previously used to identify expression QTLs controlling the transcript levels of biosynthetic genes. In a comparative study, we have directly tested two plant biosynthetic pathways for association between polymorphisms controlling biosynthetic gene transcripts and the resulting metabolites within the Arabidopsis Bay x Sha recombinant inbred line population. In this analysis, all loci controlling expression variation also affected the accumulation of the resulting metabolites. In addition, epistasis was detected more frequently for metabolic traits compared to transcript traits, even when both traits showed similar distributions. An analysis of candidate genes for QTL-controlling networks of transcripts and metabolites suggested that the controlling factors are a mix of enzymes and regulatory factors. This analysis showed that regulatory connections can feedback from metabolism to transcripts. Surprisingly, the most likely major regulator of both transcript level for nearly the entire pathway and aliphatic glucosinolate accumulation is variation in the last enzyme in the biosynthetic pathway, AOP2. This suggests that natural variation in transcripts may significantly impact phenotypic variation, but that natural variation in metabolites or their enzymatic loci can feed back to affect the transcripts.
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Affiliation(s)
- Adam M Wentzell
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Genetics Graduate Group, University of California Davis, Davis, California, United States of America
| | - Heather C Rowe
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Genetics Graduate Group, University of California Davis, Davis, California, United States of America
| | - Bjarne Gram Hansen
- Plant Biochemistry Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carla Ticconi
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Barbara Ann Halkier
- Plant Biochemistry Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Genetics Graduate Group, University of California Davis, Davis, California, United States of America
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36
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Graze RM, Barmina O, Tufts D, Naderi E, Harmon KL, Persianinova M, Nuzhdin SV. New candidate genes for sex-comb divergence between Drosophila mauritiana and Drosophila simulans. Genetics 2007; 176:2561-76. [PMID: 17565959 PMCID: PMC1950655 DOI: 10.1534/genetics.106.067686] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A large-effect QTL for divergence in sex-comb tooth number between Drosophila simulans and D. mauritiana was previously mapped to 73A-84AB. Here we identify genes that are likely contributors to this divergence. We first improved the mapping resolution in the 73A-84AB region using 12 introgression lines and 62 recombinant nearly isogenic lines. To further narrow the list of candidate genes, we assayed leg-specific expression and identified genes with transcript-level evolution consistent with a potential role in sex-comb divergence. Sex combs are formed on the prothoracic (front) legs, but not on the mesothoracic (middle) legs of Drosophila males. We extracted RNA from the prothoracic and mesothoracic pupal legs of two species to determine which of the genes expressed differently between leg types were also divergent for gene expression. Two good functional candidate genes, Scr and dsx, are located in one of our fine-scale QTL regions. In addition, three previously uncharacterized genes (CG15186, CG2016, and CG2791) emerged as new candidates. These genes are located in regions strongly associated with sex-comb tooth number differences and are expressed differently between leg tissues and between species. Further supporting the potential involvement of these genes in sex-comb divergence, we found a significant difference in sex-comb tooth number between co-isogenic D. melanogaster lines with and without P-element insertions at CG2791.
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Affiliation(s)
- Rita M Graze
- Genetics Graduate Group, Center for Genetics and Development, University of California-Davis, 1 Shields Avenue, Davis, CA 95616.
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Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 2007; 175:1883-93. [PMID: 17277373 PMCID: PMC1855124 DOI: 10.1534/genetics.106.064469] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant species may remain morphologically distinct despite gene exchange with congeners, yet little is known about the genomewide pattern of introgression among species. Here we analyze the effects of persistent gene flow on genomic differentiation between the sympatric sunflower species Helianthus annuus and H. petiolaris. While the species are strongly isolated in testcrosses, genetic distances at 108 microsatellite loci and 14 sequenced genes are highly variable and much lower (on average) than for more closely related but historically allopatric congeners. Our analyses failed to detect a positive association between levels of genetic differentiation and chromosomal rearrangements (as reported in a prior publication) or proximity to QTL for morphological differences or hybrid sterility. However, a significant increase in differentiation was observed for markers within 5 cM of chromosomal breakpoints. Together, these results suggest that islands of differentiation between these two species are small, except in areas of low recombination. Furthermore, only microsatellites associated with ESTs were identified as outlier loci in tests for selection, which might indicate that the ESTs themselves are the targets of selection rather than linked genes (or that coding regions are not randomly distributed). In general, these results indicate that even strong and genetically complex reproductive barriers cannot prevent widespread introgression.
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Affiliation(s)
- Yoko Yatabe
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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38
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Brouillette LC, Rosenthal DM, Rieseberg LH, Lexer C, Malmberg RL, Donovan LA. Genetic architecture of leaf ecophysiological traits in Helianthus. ACTA ACUST UNITED AC 2007; 98:142-6. [PMID: 17208933 PMCID: PMC2442921 DOI: 10.1093/jhered/esl063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We investigated quantitative trait loci (QTLs) for several leaf chemistry traits in early-generation hybrids between Helianthus annuus and Helianthus petiolaris, the parental species of the ancient diploid hybrid sunflower species Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus. We grew individuals of a second-generation backcross (BC(2)) toward H. petiolaris under optimum conditions in a glass house experiment. Trait values were measured once for each individual. In addition, genotypic data previously determined for each individual were employed for composite interval mapping of QTLs. We detected QTLs for leaf carbon concentration, leaf nitrogen concentration, leaf nitrogen per unit area, and photosynthetic nitrogen use efficiency. Leaf carbon isotope discrimination (delta(13)C) and leaf nitrogen isotopic composition (delta(15)N) were analyzed, but no significant QTLs were found for these traits. Interestingly, two neighboring loci explained a relatively large percentage of the variation in leaf nitrogen per unit area. This was notable because leaf nitrogen has been shown to strongly affect the fitness of early-generation sunflower hybrids in the H. anomalus habitat, and QTLs of large effect are expected to respond relatively quickly to selection. We speculate that the genetic architecture underlying leaf nitrogen may have facilitated the colonization of active desert sand dunes by H. anomalus.
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Rogers SM, Isabel N, Bernatchez L. Linkage maps of the dwarf and Normal lake whitefish (Coregonus clupeaformis) species complex and their hybrids reveal the genetic architecture of population divergence. Genetics 2007; 175:375-98. [PMID: 17110497 PMCID: PMC1774998 DOI: 10.1534/genetics.106.061457] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 10/24/2006] [Indexed: 01/22/2023] Open
Abstract
Elucidating the genetic architecture of population divergence may reveal the evolution of reproductive barriers and the genomic regions implicated in the process. We assembled genetic linkage maps for the dwarf and Normal lake whitefish species complex and their hybrids. A total of 877 AFLP loci and 30 microsatellites were positioned. The homology of mapped loci between families supported the existence of 34 linkage groups (of 40n expected) exhibiting 83% colinearity among linked loci between these two families. Classes of AFLP markers were not randomly distributed among linkage groups. Both AFLP and microsatellites exhibited deviations from Mendelian expectations, with 30.4% exhibiting significant segregation distortion across 28 linkage groups of the four linkage maps in both families (P < 0.00001). Eight loci distributed over seven homologous linkage groups were significantly distorted in both families and the level of distortion, when comparing homologous loci of the same phase between families, was correlated (Spearman R = 0.378, P = 0.0021). These results suggest that substantial divergence incurred during allopatric glacial separation and subsequent sympatric ecological specialization has resulted in several genomic regions that are no longer complementary between dwarf and Normal populations issued from different evolutionary glacial lineages.
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Affiliation(s)
- S M Rogers
- Québec Océan, Département de Biologie, Université Laval, Sainte-Foy, Québec G1K 7P4, Canada.
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40
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Willi Y, Van Buskirk J, Hoffmann AA. Limits to the Adaptive Potential of Small Populations. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2006. [DOI: 10.1146/annurev.ecolsys.37.091305.110145] [Citation(s) in RCA: 593] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yvonne Willi
- Centre for Environmental Stress and Adaptation Research, Department of Zoology and Department of Genetics, University of Melbourne, Parkville, VIC 3010 Australia; ,
| | - Josh Van Buskirk
- Department of Zoology, University of Melbourne, Parkville, VIC 3010 Australia; and Institute of Zoology, University of Zürich, CH-8057 Zürich, Switzerland;
| | - Ary A. Hoffmann
- Centre for Environmental Stress and Adaptation Research, Department of Zoology and Department of Genetics, University of Melbourne, Parkville, VIC 3010 Australia; ,
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Tian B, Chen Y, Li D, Yan Y. Cloning and characterization of a bamboo LEAFY HULL STERILE1 homologous gene. ACTA ACUST UNITED AC 2006; 17:143-51. [PMID: 17076257 DOI: 10.1080/10425170600699877] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A cDNA named DlMADS8 was isolated from the young spikelets of the sweet bamboo, Dendrocalamus latiflorus by rapid amplification of cDNA end (RACE). DNA sequence analysis showed that DlMADS8 was composed of full ORF and 3'UTR, but without 5'UTR. The cDNA contained 1059 nucleotides and encoded a putative protein of 244 amino acid residues. The gene displayed the structure of a typical plant MADS-box gene, which consisted of a MADS domain, K domain, a short I region, and the C-terminal region. Phylogenetic analysis of plant MADS-box genes based on amino acid sequences revealed that DlMADS8 was grouped into the AGAMOUS-LIKE 2 (AGL2)-like subfamily. It was homologous to the LEAFY HULL STERILE1 (LHS1) genes of grasses. To study the functions of it, DlMADS8 cDNA clone driven by the CaMV 35S promoter was transformed into Arabidopsis thaliana. Transgenic plants of DlMADS8 exhibited the phenotypes of curled leaves and early flowering. After bolting, three novel phenotypes related to inflorescence development were observed in different transgenic plants. No obvious homeotic conversions of floral organs were observed in all of the 35S::DllMADS8 transgenic Arabidopsis plants. These results indicated that DlMADS8 probably plays a role in floral meristem determinacy and is involved in controlling the flowering time of D. latiflorus.
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Affiliation(s)
- Bo Tian
- Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, People's Republic of China.
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42
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Rieseberg LH, Kim SC, Randell RA, Whitney KD, Gross BL, Lexer C, Clay K. Hybridization and the colonization of novel habitats by annual sunflowers. Genetica 2006; 129:149-65. [PMID: 16955330 PMCID: PMC2442915 DOI: 10.1007/s10709-006-9011-y] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Accepted: 09/25/2005] [Indexed: 11/26/2022]
Abstract
Although invasive plant species often have a hybrid ancestry, unambiguous evidence that hybridization has stimulated the evolution of invasive behaviors has been difficult to come by. Here, we briefly review how hybridization might contribute to the colonization of novel habitats, range expansions, and invasiveness and then describe work on hybrid sunflowers that forges a direct link between hybridization and ecological divergence. We first discuss the invasion of Texas by the common sunflower and show that the introgression of chromosomal segments from a locally adapted species may have facilitated range expansion. We then present evidence that the colonization of sand dune, desert floor, and salt marsh habitats by three hybrid sunflower species was made possible by selection on extreme or "transgressive" phenotypes generated by hybridization. This body of work corroborates earlier claims regarding the role of hybridization in adaptive evolution and provides an experimental and conceptual framework for ongoing studies in this area.
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Affiliation(s)
- Loren H. Rieseberg
- Department of Biology, Indiana University, Bloomington, IN 47405, USA, e-mail:
| | - Seung-Chul Kim
- Department of Botany and Plant Science, University of California, Riverside, CA 92521, USA
| | - Rebecca A. Randell
- Department of Biology, Indiana University, Bloomington, IN 47405, USA, e-mail:
| | - Kenneth D. Whitney
- Department of Biology, Indiana University, Bloomington, IN 47405, USA, e-mail:
| | - Briana L. Gross
- Department of Biology, Indiana University, Bloomington, IN 47405, USA, e-mail:
| | - Christian Lexer
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3DS, UK
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, IN 47405, USA, e-mail:
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BRATTELER MARTIN, BALTISBERGER MATTHIAS, WIDMER ALEX. QTL analysis of intraspecific differences between two Silene vulgaris ecotypes. ANNALS OF BOTANY 2006; 98:411-9. [PMID: 16757498 PMCID: PMC2803471 DOI: 10.1093/aob/mcl113] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Serpentine soils provide a highly selective substrate for plant colonization and growth and represent an ideal system for studying the evolution of plant-ecotypes. In the present study the aim was to identify the genetic architecture of morphological traits distinguishing serpentine and non-serpentine ecotypes of Silene vulgaris. METHODS Using an F(2) mapping population derived from an intraspecific cross between a serpentine and a non-serpentine ecotype of S. vulgaris, the genetic architecture of 12 morphological traits was explored using a quantitative trait locus (QTL) analysis. KEY RESULTS The QTL analysis identified a total of 49 QTLs, of which 24 were classified as major QTLs. The mean number of QTLs per trait category was found to correspond well with numbers reported in the literature for similar crosses. Clustering of QTLs for different traits was found on several linkage groups. CONCLUSIONS Morphological traits that differentiate the two ecotypes are strongly correlated, presumably as a consequence of the joint effects of extensive linkage of QTLs for different traits and directional selection. The signature of consistent directional selection was found for leaf and shoot trait divergence. Intraspecific ecotype differences in S. vulgaris were found to be distributed across the entire genome. The study shows that QTL analyses on non-model organisms can provide novel insights into the genetic basis of plant diversification.
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Lai Z, Gross BL, Zou Y, Andrews J, Rieseberg LH. Microarray analysis reveals differential gene expression in hybrid sunflower species. Mol Ecol 2006; 15:1213-27. [PMID: 16626449 DOI: 10.1111/j.1365-294x.2006.02775.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes the creation of a cDNA microarray for annual sunflowers and its use to elucidate patterns of gene expression in Helianthus annuus, Helianthus petiolaris, and the homoploid hybrid species Helianthus deserticola. The array comprises 3743 ESTs (expressed sequence tags) representing approximately 2897 unique genes. It has an average clone/EST identity rate of 91%, is applicable across species boundaries within the annual sunflowers, and shows patterns of gene expression that are highly reproducible according to real-time RT-PCR (reverse transcription-polymerase chain reaction) results. Overall, 12.8% of genes on the array showed statistically significant differential expression across the three species. Helianthus deserticola displayed transgressive, or extreme, expression for 58 genes, with roughly equal numbers exhibiting up- or down-regulation relative to both parental species. Transport-related proteins were strongly over-represented among the transgressively expressed genes, which makes functional sense given the extreme desert floor habitat of H. deserticola. The potential adaptive value of differential gene expression was evaluated for five genes in two populations of early generation (BC2) hybrids between the parental species grown in the H. deserticola habitat. One gene (a G protein-coupled receptor) had a significant association with fitness and maps close to a QTL controlling traits that may be adaptive in the desert habitat.
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Affiliation(s)
- Zhao Lai
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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45
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Hall MC, Basten CJ, Willis JH. Pleiotropic quantitative trait loci contribute to population divergence in traits associated with life-history variation in Mimulus guttatus. Genetics 2005; 172:1829-44. [PMID: 16361232 PMCID: PMC1456280 DOI: 10.1534/genetics.105.051227] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evolutionary biologists seek to understand the genetic basis for multivariate phenotypic divergence. We constructed an F2 mapping population (N = 539) between two distinct populations of Mimulus guttatus. We measured 20 floral, vegetative, and life-history characters on parents and F1 and F2 hybrids in a common garden experiment. We employed multitrait composite interval mapping to determine the number, effect, and degree of pleiotropy in quantitative trait loci (QTL) affecting divergence in floral, vegetative, and life-history characters. We detected 16 QTL affecting floral traits; 7 affecting vegetative traits; and 5 affecting selected floral, vegetative, and life-history traits. Floral and vegetative traits are clearly polygenic. We detected a few major QTL, with all remaining QTL of small effect. Most detected QTL are pleiotropic, implying that the evolutionary shift between these annual and perennial populations is constrained. We also compared the genetic architecture controlling floral trait divergence both within (our intraspecific study) and between species, on the basis of a previously published analysis of M. guttatus and M. nasutus. Eleven of our 16 floral QTL map to approximately the same location in the interspecific map based on shared, collinear markers, implying that there may be a shared genetic basis for floral divergence within and among species of Mimulus.
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Affiliation(s)
- Megan C Hall
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.
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Städler T, Roselius K, Stephan W. GENEALOGICAL FOOTPRINTS OF SPECIATION PROCESSES IN WILD TOMATOES: DEMOGRAPHY AND EVIDENCE FOR HISTORICAL GENE FLOW. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01777.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Städler T, Roselius K, Stephan W. GENEALOGICAL FOOTPRINTS OF SPECIATION PROCESSES IN WILD TOMATOES: DEMOGRAPHY AND EVIDENCE FOR HISTORICAL GENE FLOW. Evolution 2005. [DOI: 10.1554/04-722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Our understanding of homoploid hybrid speciation has advanced substantially since this mechanism of species formation was codified 50 years ago. Early theory and research focused almost exclusively on the importance of chromosomal rearrangements, but it later became evident that natural selection, specifically ecological selection, might play a major role as well. In light of this recent shift, we present an evaluation of ecology's role in homoploid hybrid speciation, with an emphasis on the genetics underlying ecological components of the speciation process. We briefly review new theoretical developments related to the ecology of homoploid hybrid speciation; propose a set of explicit, testable questions that must be answered to verify the role of ecological selection in homoploid hybrid speciation; discuss published work with reference to these questions; and also report new data supporting the importance of ecological selection in the origin of the homoploid hybrid sunflower species Helianthus deserticola. Overall, theory and empirical evidence gathered to date suggest that ecological selection is a major factor promoting homoploid hybrid speciation, with the strongest evidence coming from genetic studies.
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Affiliation(s)
- B L Gross
- Department of Biology, 1001 E. 3rd Street, Jordan Hall 142, Indiana University, Bloomington, IN 47405, USA.
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