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Ahatović Hajro A, Hasanović M, Murtić S, Kalajdžić A, Pojskić N, Durmić-Pašić A. Serpentine environment prevails over geographic distribution in shaping the genetic diversity of Medicago lupulina L. Mol Genet Genomics 2024; 299:28. [PMID: 38472470 DOI: 10.1007/s00438-024-02124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/03/2024] [Indexed: 03/14/2024]
Abstract
Edaphic conditions of serpentine soils, naturally rich in heavy metals, act as a strong selection pressure that shapes specific metal-tolerant ecotypes. Medicago lupulina L. (black medick) is not only a widespread plant species that prefers calcareous and dry soil types but also grows at the borders of serpentine formations. It can also be found in waste and disturbed habitats. This is a species with reported phytoremediation potential, however, there is no published data regarding the impact of the environment on the genetic distribution of this species. The aim of our research was to explore how selection pressure of serpentine soils affects genetic diversity of M. lupulina and to test heavy-metal accumulation capacity of this species. Specimens of 11 M. lupulina populations were collected from serpentine outcrops located in Central and Eastern Bosnia as well as from non-serpentine sites. Soil and plant samples were analyzed for the total contents of heavy metals using air-acetylene flame atomic absorption spectroscopy. Genetic diversity was analyzed using AFLP (Amplified Fragment Length Polymorphism) markers. Serpentine soils showed high nickel, cobalt, chromium and iron concentrations. Nickel and manganese concentrations in soil samples and plant material showed statistically significant correlation. Although plants in two populations show the ability to extract Ni, M. lupulina does not show hyperaccumulating properties. Despite severe selective pressure, genetic diversity in serpentine populations is not reduced. Analyses of intrapopulation and interpopulation genetic diversity showed significant genetic differentiation among populations which is not related to their geographic distance. Population from non-metalliferous soil showed clear separation from all other populations. Diversity data suggest that serpentine populations maintain genetic diversity by undetected mechanisms and that edaphic factors rather than geography influence genetic structure analyzed M. lupulina populations.
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Affiliation(s)
- Anesa Ahatović Hajro
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina.
| | - Mujo Hasanović
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Senad Murtić
- Faculty of Agriculture and Food Sciences, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Abdurahim Kalajdžić
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Naris Pojskić
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Adaleta Durmić-Pašić
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
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Diazgranados M, Barber JC. Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands. PeerJ 2017; 5:e2968. [PMID: 28168124 PMCID: PMC5292030 DOI: 10.7717/peerj.2968] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/09/2017] [Indexed: 12/02/2022] Open
Abstract
Background The páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants. Methods Field expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny. Results Phylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other. Conclusions Our data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.
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Affiliation(s)
- Mauricio Diazgranados
- Natural Capital and Plant Health Department, Wakehurst Place, Royal Botanic Gardens, Kew , Ardingly , West Sussex , United Kingdom
| | - Janet C Barber
- Department of Biology, Saint Louis University, Saint Louis, MO, United States; Missouri Botanical Garden, Saint Louis, MO, United States
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Westberg E, Kadereit JW. Genetic evidence for divergent selection on Oenanthe conioidesand Oe. aquatica(Apiaceae), a candidate case for sympatric speciation. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Erik Westberg
- Institute of Systematic Botany und Botanical Garden; Johannes Gutenberg-University Mainz; D-55099 Mainz Germany
| | - Joachim W. Kadereit
- Institute of Systematic Botany und Botanical Garden; Johannes Gutenberg-University Mainz; D-55099 Mainz Germany
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Genetic architecture of contemporary adaptation to biotic invasions: quantitative trait locus mapping of beak reduction in soapberry bugs. G3-GENES GENOMES GENETICS 2014; 4:255-64. [PMID: 24347624 PMCID: PMC3931560 DOI: 10.1534/g3.113.008334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Biological invasions can result in new selection pressures driven by the establishment of new biotic interactions. The response of exotic and native species to selection depends critically on the genetic architecture of ecologically relevant traits. In the Florida peninsula, the soapberry bug (Jadera haematoloma) has colonized the recently introduced Chinese flametree, Koelreuteria elegans, as a host plant. Driven by feeding efficiency, the populations associated with this new host have differentiated into a new bug ecomorph characterized by short beaks more appropriate for feeding on the flattened pods of the Chinese flametree. In this study, we have generated a three-generation pedigree from crossing the long-beaked and short-beaked ecomorphs to construct a de novo linkage map and to locate putative quantitative trait locus (QTL) controlling beak length and body size in J. haematoloma. Using amplified fragment-length polymorphism markers and a two-way pseudo-testcross design, we have produced two parental maps in six linkage groups, covering the known number of chromosomes. QTL analysis revealed one significant QTL for beak length on a maternal linkage group and the corresponding paternal linkage group. Three QTL were found for body size. Through single marker regression analysis, nine single markers that could not be placed on the map were also found to be significantly associated with one or both of the two traits. Interestingly, the most significant body size QTL co-localized with the beak length QTL, suggesting linkage disequilibrium or pleiotropic effects of related traits. Our results suggest an oligogenic control of beak length.
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Burge DO, Hopkins R, Tsai YHE, Manos PS. Limited hybridization across an edaphic disjunction between the gabbro-endemic shrub Ceanothus roderickii (Rhamnaceae) and the soil-generalist Ceanothus cuneatus. AMERICAN JOURNAL OF BOTANY 2013; 100:1883-1895. [PMID: 24018856 DOI: 10.3732/ajb.1200604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Hybridization is thought to have played an important role in diversification of the speciose shrub genus Ceanothus; putative hybrid species have been described, and data suggest that intrinsic barriers may not exist among closely related species. However, the extent to which hybridization occurs in the wild is not known, and little is understood about how extrinsic factors such as soil chemistry may influence the process. The present research focuses on the gabbro-endemic C. roderickii and the closely related soil-generalist C. cuneatus. Though the species occur peripatrically, they remain distinct across an edaphic disjunction. • METHODS AFLP was used to quantify hybridization and introgression. Biological data and experiments were used to test for prezygotic isolation. Growth trials were used to test for local adaptation and selection against hybrids. • KEY RESULTS Ceanothus cuneatus and C. roderickii were strongly differentiated morphologically and genetically, despite a lack of evidence for prezygotic barriers. Hybrids and back-crosses were present but infrequent. Finally, there was selection against hybrids in nonnative soil. • CONCLUSIONS There is little genetic exchange between the focal species across an edaphic disjunction, despite the absence of prezygotic barriers. This result implies that soil conditions, as well as other extrinsic factors, should be considered as forces that may restrict hybridization and gene flow in Ceanothus, influencing local adaptation and speciation. Findings presented here are significant because they imply that exchange of genetic material between plants may be limited directly by the abiotic environment, rather than by the biology of the plants.
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Affiliation(s)
- Dylan O Burge
- Duke University Department of Biology, Box 90338 Durham, North Carolina 27705, USA
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Westberg E, Ohali S, Shevelevich A, Fine P, Barazani O. Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient. Ecol Evol 2013; 3:2471-84. [PMID: 24567822 PMCID: PMC3930051 DOI: 10.1002/ece3.646] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 02/01/2023] Open
Abstract
In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a steep climatic gradient. In addition to molecular marker data, we made use of phenotypic evaluation from common garden experiments, and a broad GIS based environmental data with edaphic information gathered in the field. This study, among others, lead to the identification of an outlier locus with an association to trichome formation and herbivore defense, and its ecological adaptive value is discussed.
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Affiliation(s)
- Erik Westberg
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität MainzD-55099, Mainz, Germany
| | - Shachar Ohali
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
| | - Anatoly Shevelevich
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem76100, Rehovot, Israel
| | - Pinchas Fine
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization50250, Bet Dagan, Israel
| | - Oz Barazani
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
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Ley AC, Hardy OJ. Improving AFLP analysis of large-scale patterns of genetic variation - a case study with the Central African lianasHaumaniaspp (Marantaceae) showing interspecific gene flow. Mol Ecol 2013; 22:1984-97. [DOI: 10.1111/mec.12214] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 12/06/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Affiliation(s)
- A. C. Ley
- Institut für Geobotanik und Botanischer Garten; University Halle-Wittenberg; 06108 Halle (Saale) Germany
- Evolutionary Biology and Ecology; CP160/12; Faculté des Sciences; Université Libre de Bruxelles; 50 Av. F. Roosevelt 1050 Brussels Belgium
| | - O. J. Hardy
- Evolutionary Biology and Ecology; CP160/12; Faculté des Sciences; Université Libre de Bruxelles; 50 Av. F. Roosevelt 1050 Brussels Belgium
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Beck JB, Allison JR, Pryer KM, Windham MD. Identifying multiple origins of polyploid taxa: a multilocus study of the hybrid cloak fern (Astrolepis integerrima; Pteridaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:1857-1865. [PMID: 23108464 DOI: 10.3732/ajb.1200199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Molecular studies have shown that multiple origins of polyploid taxa are the rule rather than the exception. To understand the distribution and ecology of polyploid species and the evolutionary significance of polyploidy in general, it is important to delineate these independently derived lineages as accurately as possible. Although gene flow among polyploid lineages and backcrossing to their diploid parents often confound this process, such post origin gene flow is very infrequent in asexual polyploids. In this study, we estimate the number of independent origins of the apomictic allopolyploid fern Astrolepis integerrima, a morphologically heterogeneous species most common in the southwestern United States and Mexico, with outlying populations in the southeastern United States and the Caribbean. METHODS Plastid DNA sequence and AFLP data were obtained from 33 A. integerrima individuals. Phylogenetic analysis of the sequence data and multidimensional clustering of the AFLP data were used to identify independently derived lineages. KEY RESULTS Analysis of the two datasets identified 10 genetic groups within the 33 analyzed samples. These groups suggest a minimum of 10 origins of A. integerrima in the northern portion of its range, with both putative parents functioning as maternal donors, both supplying unreduced gametes, and both contributing a significant portion of their genetic diversity to the hybrids. CONCLUSIONS Our results highlight the extreme cryptic genetic diversity and systematic complexity that can underlie a single polyploid taxon.
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MESH Headings
- Amplified Fragment Length Polymorphism Analysis
- DNA, Intergenic/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Evolution, Molecular
- Genes, Plant/genetics
- Geography
- Mexico
- Molecular Sequence Data
- Phylogeny
- Polyploidy
- Pteridaceae/classification
- Pteridaceae/genetics
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Gly/genetics
- Sequence Analysis, DNA
- United States
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Affiliation(s)
- James B Beck
- Department of Biological Sciences, Wichita State University, 537 Hubbard Hall, Wichita, Kansas 67260, USA.
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Keller I, Schuler J, Bezault E, Seehausen O. Parallel divergent adaptation along replicated altitudinal gradients in Alpine trout. BMC Evol Biol 2012; 12:210. [PMID: 23102191 PMCID: PMC3552777 DOI: 10.1186/1471-2148-12-210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 10/12/2012] [Indexed: 12/05/2022] Open
Abstract
Background The European trout (Salmo trutta species complex) occurs across a very wide altitudinal range from lowland rivers to alpine streams. Historically, the major European river systems contained different, evolutionarily distinct trout lineages, and some of this genetic diversity has persisted in spite of extensive human-mediated translocations. We used AFLP-based genome scans to investigate the extent of potentially adaptive divergence among major drainages and along altitudinal gradients replicated in several rivers. Results The proportion of loci showing evidence of divergent selection was larger between drainages than along altitudinal transects within drainages. This suggests divergent selection is stronger between drainages, or adaptive divergence is constrained by gene flow among populations within drainages, although the latter could not be confirmed at a more local scale. Still, altitudinal divergence occurred and, at approximately 2% of the markers, parallel changes of the AFLP band frequencies with altitude were observed suggesting that altitude may well be an important source of divergent selection within rivers. Conclusions Our results indicate that adaptive genetic divergence is common both between major European river systems and along altitudinal gradients within drainages. Alpine trout appear to be a promising model system to investigate the relative roles of divergent selection and gene flow in promoting or preventing adaptation to climate gradients.
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Affiliation(s)
- Irene Keller
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, Seestrasse 79, Kastanienbaum, Switzerland.
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VALTUEÑA FRANCISCOJ, PRESTON CHRISD, KADEREIT JOACHIMW. Evolutionary significance of the invasion of introduced populations into the native range of Meconopsis cambrica. Mol Ecol 2011; 20:4318-31. [DOI: 10.1111/j.1365-294x.2011.05273.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Oberle B, Schaal BA. Responses to historical climate change identify contemporary threats to diversity in Dodecatheon. Proc Natl Acad Sci U S A 2011; 108:5655-60. [PMID: 21402919 PMCID: PMC3078354 DOI: 10.1073/pnas.1012302108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic climate change may threaten many species with extinction. However, species at risk today survived global climate change in recent geological history. Describing how habitat tracking and adaptation allowed species to survive warming since the end of the Pleistocene can indicate the relative importance of dispersal and natural selection during climate change. By taking this historical perspective, we can identify how contemporary climate change could interfere with these mechanisms and threaten the most vulnerable species. We focused on a group of closely related plant species in the genus Dodecatheon (Primulaceae) in eastern North America. Two rare species (Dodecatheon amethystinum and Dodecatheon frenchii) that are endemic to patchy cool cliffs may be glacial relicts whose ranges constricted following the last glacial maximum. Alternatively, these species may be extreme ecotypes of a single widespread species (Dodecatheon meadia) that quickly adapted to microclimatic differences among habitats. We test support for these alternative scenarios by combining ecophysiological and population genetic data at a regional scale. An important ecophysiological trait distinguishes rare species from D. meadia, but only a few northern populations of D. amethystinum are genetically distinctive. These relict populations indicate that habitat tracking did occur with historical climate change. However, relatively stronger evidence for isolation by distance and admixture suggests that local adaptation and genetic introgression have been at least as important. The complex response of Dodecatheon to historical climate change suggests that contemporary conservation efforts should accommodate evolutionary processes, in some cases by restoring genetic connectivity between ecologically differentiated populations.
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Affiliation(s)
- Brad Oberle
- Department of Biology, Washington University, St Louis, MO 63130, USA.
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Avolio ML, Chang CC, Smith MD. Assessing Fine-Scale Genotypic Structure of a Dominant Species in Native Grasslands. AMERICAN MIDLAND NATURALIST 2011. [DOI: 10.1674/0003-0031-165.2.211] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Karp A, Hanley SJ, Trybush SO, Macalpine W, Pei M, Shield I. Genetic improvement of willow for bioenergy and biofuels. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:151-65. [PMID: 21205181 DOI: 10.1111/j.1744-7909.2010.01015.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Willows (Salix spp.) are a very diverse group of catkin-bearing trees and shrubs that are widely distributed across temperate regions of the globe. Some species respond well to being grown in short rotation coppice (SRC) cycles, which are much shorter than conventional forestry. Coppicing reinvigorates growth and the biomass rapidly accumulated can be used as a source of renewable carbon for bioenergy and biofuels. As SRC willows re-distribute nutrients during the perennial cycle they require only minimal nitrogen fertilizer for growth. This results in fuel chains with potentially high greenhouse gas reductions. To exploit their potential for renewable energy, willows need to be kept free of pests and diseases and yields need to be improved without significantly increasing the requirements for fertilizers and water. The biomass composition needs to be optimized for different end-uses. Yields also need to be sustainable on land less productive for food crops to reduce conflicts over land use. Advances in understanding the physiology and growth of willow, and in the identification of genes underlying key traits, are now at the stage where they can start to be used in breeding programs to help achieve these goals.
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Affiliation(s)
- Angela Karp
- Centre for Bioenergy and Climate Change, Plant and Invertebrate Ecology Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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WALL WADEA, DOUGLAS NORMANA, XIANG QIUYUNJENNY, HOFFMANN WILLIAMA, WENTWORTH THOMASR, HOHMANN MATTHEWG. Evidence for range stasis during the latter Pleistocene for the Atlantic Coastal Plain endemic genus, Pyxidanthera Michaux. Mol Ecol 2010; 19:4302-14. [DOI: 10.1111/j.1365-294x.2010.04793.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Herrmann D, Poncet BN, Manel S, Rioux D, Gielly L, Taberlet P, Gugerli F. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome 2010; 53:302-10. [DOI: 10.1139/g10-006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.
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Affiliation(s)
- Doris Herrmann
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Bénédicte N. Poncet
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Stéphanie Manel
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Delphine Rioux
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Ludovic Gielly
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Pierre Taberlet
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Felix Gugerli
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
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Grimmer MK, Bean KMR, Asher MJC. Mapping of five resistance genes to sugar-beet powdery mildew using AFLP and anchored SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:67-75. [PMID: 17426954 DOI: 10.1007/s00122-007-0541-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 03/17/2007] [Indexed: 05/14/2023]
Abstract
Sugar-beet powdery mildew, caused by the fungus Erysiphe betae, now occurs in all sugar-beet growing areas and can reduce sugar yield by up to 30%. Powdery mildew resistant plants from three novel sources were crossed with sugar beet to generate segregating populations. Evaluation of resistance was carried out in artificially inoculated field and controlled environment tests. The resistance level in two of the sources was found to be significantly higher than that in currently available sugar-beet cultivars. AFLP analysis was used in combination with bulked segregant analysis to develop markers linked to the resistant phenotype in each population. Five dominant major resistance genes were identified and assigned the proposed symbols Pm2 to Pm6. Pm3 conferred complete resistance to powdery mildew; the other genes conferred high levels of partial resistance. From the use of anchoring SNP markers, two genes were located to chromosome II and three to chromosome IV. Two of the genes on chromosome IV mapped to the same location and one of the genes on chromosome II mapped to the same region as the previously identified Pm1 gene. With the availability of these genes there is now excellent potential for achieving durable resistance to sugar-beet powdery mildew, thus reducing or obviating the need for chemical control.
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Affiliation(s)
- M K Grimmer
- Broom's Barn Research Station, Higham, Bury St Edmunds, IP28 6NP, UK.
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