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Attikora AJP, Silué S, Yao SDM, De Clerck C, Shumbe L, Diarrassouba N, Fofana IJ, Alabi T, Lassois L. An innovative optimized protocol for high-quality genomic DNA extraction from recalcitrant Shea tree (Vitellaria paradoxa, C.F. Gaertn) plant and its suitability for downstream applications. Mol Biol Rep 2024; 51:171. [PMID: 38252378 DOI: 10.1007/s11033-023-09098-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND It is not always easy to find a universal protocol for the extraction of genomic DNA (gDNA) from plants. Extraction of gDNA from plants such as shea with a lot of polysaccharides in their leaves is done in two steps: a first step to remove the polysaccharides and a second step for the extraction of the gDNA. In this work, we designed a protocol for extracting high-quality gDNA from shea tree and demonstrate its suitability for downstream molecular applications. METHODS Fifty milligrams of leaf and root tissues were used to test the efficiency of our protocol. The quantity of gDNA was measured with the NanoDrop spectrometer and the quality was checked on agarose gel. Its suitability for use in downstream applications was tested with restriction enzymes, SSRs and RAPD polymerase chain reactions and Sanger sequencing. RESULTS The average yield of gDNA was 5.17; 3.96; 2.71 and 2.41 µg for dry leaves, dry roots, fresh leaves and fresh roots respectively per 100 mg of tissue. Variance analysis of the yield showed significant difference between all tissue types. Leaf gDNA quality was better compared to root gDNA at the absorbance ratio A260/280 and A260/230. The minimum amplifiable concentration of leaf gDNA was 1 pg/µl while root gDNA remained amplifiable at 10 pg/µl. Genomic DNA obtained was also suitable for sequencing. CONCLUSION This protocol provides an efficient, convenient and cost effective DNA extraction method suitable for use in various vitellaria paradoxa genomic studies.
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Affiliation(s)
- Affi Jean Paul Attikora
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium.
| | - Souleymane Silué
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Saraka Didier Martial Yao
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro Bio-Tech, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Leonard Shumbe
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Nafan Diarrassouba
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Inza Jésus Fofana
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Taofic Alabi
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
- Functional and Evolutive Entomology, Gembloux Agro Bio-Tech, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Ludivine Lassois
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
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Du L, Oduor AMO, Zuo W, Liu H, Li J. Directional and stabilizing selection shaped morphological, reproductive, and physiological traits of the invader Solidago canadensis. Ecol Evol 2023; 13:e10410. [PMID: 37636867 PMCID: PMC10450839 DOI: 10.1002/ece3.10410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Trait evolution in invasive plant species is important because it can impact demographic parameters key to invasion success. Invasive plant species often show phenotypic clines along geographic and climatic gradients. However, the relative contributions of natural selection and neutral evolutionary processes to phenotypic trait variation among populations of invasive plants remain unclear. A common method to assess whether a trait has been shaped by natural selection or neutral evolutionary processes is to compare the geographical pattern for the trait of interest to the divergence in neutral genetic loci (i.e., Q ST -F ST comparisons). Subsequently, a redundancy analysis (RDA) can facilitate identification of putative agents of natural selection on the trait. Here, we employed both a Q ST -F ST comparisons approach and RDA to infer whether natural selection shaped traits of invasive populations of Solidago canadensis in China and identify the potential environmental drivers of natural selection. We addressed two questions: (1) Did natural selection drive phenotypic trait variation among S. canadensis populations? (2) Did climatic, latitudinal, longitudinal, and altitudinal gradients drive patterns of genetic variation among S. canadensis populations? We found significant directional selection for several morphological and reproductive traits (i.e., Q ST > F ST) and stabilizing selection for physiological traits (i.e., Q ST < F ST). The RDA showed that stem biomass of S. canadensis was strongly positively correlated with longitude, while leaf width ratio and specific leaf area were significantly positively correlated with the mean diurnal range. Stem biomass had a strong negative correlation with annual precipitation. Moreover, height of S. canadensis individuals was strongly positively correlated with altitude and precipitation of the wettest quarter. A longitudinal shift in precipitation seasonality likely selected for larger stem biomass in S. canadensis. Overall, these results suggest that longitudinal and altitudinal clines in climate exerted strong selection pressures that shaped the phenotypic traits of S. canadensis.
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Affiliation(s)
- Leshan Du
- State Key Laboratory of Environmental Criteria and Risk AssessmentChinese Research Academy of Environmental SciencesBeijingChina
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
| | - Ayub M. O. Oduor
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
- Department of Applied BiologyTechnical University of KenyaNairobiKenya
| | - Wei Zuo
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
- Sanofi (Hangzhou) Pharmaceuticals Co. Ltd.HangzhouChina
| | - Haiyan Liu
- State Key Laboratory of Environmental Criteria and Risk AssessmentChinese Research Academy of Environmental SciencesBeijingChina
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
| | - Jun‐Min Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
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Hale I, Ma X, Melo ATO, Padi FK, Hendre PS, Kingan SB, Sullivan ST, Chen S, Boffa JM, Muchugi A, Danquah A, Barnor MT, Jamnadass R, Van de Peer Y, Van Deynze A. Genomic Resources to Guide Improvement of the Shea Tree. FRONTIERS IN PLANT SCIENCE 2021; 12:720670. [PMID: 34567033 PMCID: PMC8459026 DOI: 10.3389/fpls.2021.720670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2021] [Indexed: 05/25/2023]
Abstract
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.
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Affiliation(s)
- Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Arthur T. O. Melo
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Francis Kwame Padi
- Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana
| | - Prasad S. Hendre
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | | | | | - Shiyu Chen
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
| | - Jean-Marc Boffa
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | - Alice Muchugi
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- The Forage Genebank, Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Agyemang Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Michael Teye Barnor
- Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana
| | - Ramni Jamnadass
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Allen Van Deynze
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
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Bondé L, Ouédraogo O, Traoré S, Thiombiano A, Boussim JI. Impact of environmental conditions on fruit production patterns of shea tree (
Vitellaria paradoxa
C.F.Gaertn) in West Africa. Afr J Ecol 2019. [DOI: 10.1111/aje.12621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Loyapin Bondé
- Laboratory of Plant Biology and Ecology University Ouaga 1 Pr Joseph KI‐ZERBO Ouagadougou Burkina Faso
| | - Oumarou Ouédraogo
- Laboratory of Plant Biology and Ecology University Ouaga 1 Pr Joseph KI‐ZERBO Ouagadougou Burkina Faso
| | - Salifou Traoré
- Laboratory of Plant Biology and Ecology University Ouaga 1 Pr Joseph KI‐ZERBO Ouagadougou Burkina Faso
| | - Adjima Thiombiano
- Laboratory of Plant Biology and Ecology University Ouaga 1 Pr Joseph KI‐ZERBO Ouagadougou Burkina Faso
| | - Joseph I. Boussim
- Laboratory of Plant Biology and Ecology University Ouaga 1 Pr Joseph KI‐ZERBO Ouagadougou Burkina Faso
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Wei Y, Ji B, Siewers V, Xu D, Halkier BA, Nielsen J. Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression. Appl Microbiol Biotechnol 2019; 103:3727-3736. [PMID: 30915502 PMCID: PMC6469615 DOI: 10.1007/s00253-019-09720-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 11/23/2022]
Abstract
Shea tree (Vitellaria paradoxa) is one economically important plant species that mainly distributes in West Africa. Shea butter extracted from shea fruit kernels can be used as valuable products in the food and cosmetic industries. The most valuable composition in shea butter was one kind of triacylglycerol (TAG), 1,3-distearoyl-2-oleoyl-glycerol (SOS, C18:0–C18:1–C18:0). However, shea butter production is limited and little is known about the genetic information of shea tree. In this study, we tried to reveal genetic information of shea tree and identified shea TAG biosynthetic genes for future shea butter production in yeast cell factories. First, we measured lipid content, lipid composition, and TAG composition of seven shea fruits at different ripe stages. Then, we performed transcriptome analysis on two shea fruits containing obviously different levels of SOS and revealed a list of TAG biosynthetic genes potentially involved in TAG biosynthesis. In total, 4 glycerol-3-phosphate acyltransferase (GPAT) genes, 8 lysophospholipid acyltransferase (LPAT) genes, and 11 diacylglycerol acyltransferase (DGAT) genes in TAG biosynthetic pathway were predicted from the assembled transcriptome and 14 of them were cloned from shea fruit cDNA. Furthermore, the heterologous expression of these 14 potential GPAT, LPAT, and DGAT genes in Saccharomyces cerevisiae changed yeast fatty acid and lipid profiles, suggesting that they functioned in S. cerevisiae. Moreover, two shea DGAT genes, VpDGAT1 and VpDGAT7, were identified as functional DGATs in shea tree, showing they might be useful for shea butter (SOS) production in yeast cell factories.
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Affiliation(s)
- Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of State Ministry of Education, Key Laboratory of Henan province for Drug Quality Control and Evaluation, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Deyang Xu
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs., DK-2800, Lyngby, Denmark.
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Gallagher DE, Dueppen SA, Walsh R. The Archaeology of Shea Butter (Vitellaria paradoxa) in Burkina Faso, West Africa. J ETHNOBIOL 2016. [DOI: 10.2993/0278-0771-36.1.150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Gaoue OG, Lemes MR, Ticktin T, Sinsin B, Eyog-Matig O. Non-timber Forest Product Harvest does not Affect the Genetic Diversity of a Tropical Tree Despite Negative Effects on Population Fitness. Biotropica 2014. [DOI: 10.1111/btp.12145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Orou G. Gaoue
- Department of Botany; University of Hawaii at Manoa; Honolulu HI 96822 U.S.A
- Laboratoire d'Ecologie Appliquée; Université d'Abomey Calavi; Cotonou Benin
| | - Maristerra R. Lemes
- Laboratório de Genética e Biologia Reprodutiva de Plantas; Instituto Nacional de Pesquisas da Amazônia; Manaus-AM Brazil
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Jardim Botânico; Rio de Janeiro RJ Brazil
| | - Tamara Ticktin
- Department of Botany; University of Hawaii at Manoa; Honolulu HI 96822 U.S.A
| | - Brice Sinsin
- Laboratoire d'Ecologie Appliquée; Université d'Abomey Calavi; Cotonou Benin
| | - Oscar Eyog-Matig
- Bioversity International; c/o CIFOR Regional Office; Yaounde Cameroon
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Tomomatsu Y. Parkia biglobosa-Dominated Cultural Landscape: An Ethnohistory of the Dagomba Political Institution in Farmed Parkland of Northern Ghana. J ETHNOBIOL 2014. [DOI: 10.2993/0278-0771-34.2.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Human impacts on genetic diversity and differentiation in six natural populations of Madhuca hainanensis, an endemic and endangered timber species in China. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Edelaar P, Burraco P, Gomez-Mestre I. Comparisons between Q(ST) and F(ST) --how wrong have we been? Mol Ecol 2011; 20:4830-9. [PMID: 22060729 DOI: 10.1111/j.1365-294x.2011.05333.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The comparison between quantitative genetic divergence (Q(ST) ) and neutral genetic divergence (F(ST) ) among populations has become the standard test for historical signatures of selection on quantitative traits. However, when the mutation rate of neutral markers is relatively high in comparison with gene flow, estimates of F(ST) will decrease, resulting in upwardly biased comparisons of Q(ST) vs. F(ST) . Reviewing empirical studies, the difference between Q(ST) and F(ST) is positively related to marker heterozygosity. After refuting alternative explanations for this pattern, we conclude that marker mutation rate indeed has had a biasing effect on published Q(ST) -F(ST) comparisons. Hence, it is no longer clear that populations have commonly diverged in response to divergent selection. We present and discuss potential solutions to this bias. Comparing Q(ST) with recent indices of neutral divergence that statistically correct for marker heterozygosity (Hedrick's G'st and Jost's D) is not advised, because these indices are not theoretically equivalent to Q(ST) . One valid solution is to estimate F(ST) from neutral markers with mutation rates comparable to those of the loci underlying quantitative traits (e.g. SNPs). Q(ST) can also be compared to Φ(ST) (Phi(ST) ) of amova, as long as the genetic distance among allelic variants used to estimate Φ(ST) reflects evolutionary history: in that case, neutral divergence is independent of mutation rate. In contrast to their common usage in comparisons of Q(ST) and F(ST) , microsatellites typically have high mutation rates and do not evolve according to a simple evolutionary model, so are best avoided in Q(ST) -F(ST) comparisons.
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Affiliation(s)
- Pim Edelaar
- Estación Biológica de Doñana (EBD-CSIC). Avda. Américo Vespucio s/n, Sevilla E-41092, Spain.
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Logossa ZA, Camus-Kulandaivelu L, Allal F, Vaillant A, Sanou H, Kokou K, Bouvet JM. Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa. Mol Ecol 2011; 20:4009-27. [PMID: 21914014 DOI: 10.1111/j.1365-294x.2011.05249.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano-Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within-population diversity: allelic richness ranged from R(nuc) = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (F(STnuc) = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub-set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (R(cp) = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (G(STcp) = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10,000 bp) have probably enhanced gene flow and population expansion.
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Allal F, Sanou H, Millet L, Vaillant A, Camus-Kulandaivelu L, Logossa ZA, Lefèvre F, Bouvet JM. Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa. Heredity (Edinb) 2011; 107:174-86. [PMID: 21407253 DOI: 10.1038/hdy.2011.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (F(ST) = 0.21; R(ST) = 0.28; R(ST) > R(ST) (permuted)) and chloroplast simple sequence repeats (SSRs) (G(ST) = 0.81; N(ST) = 0.90; N(ST) > N(ST) (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa.
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Affiliation(s)
- F Allal
- Cirad-Bios Department, Research Unit, Genetic Diversity and Breeding of Forest Tree Species, International Campus of Baillarguet, Montpellier, France.
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Chun YJ, LE Corre V, Bretagnolle F. Adaptive divergence for a fitness-related trait among invasive Ambrosia artemisiifolia populations in France. Mol Ecol 2011; 20:1378-88. [PMID: 21306459 DOI: 10.1111/j.1365-294x.2011.05013.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The impact of natural selection on the adaptive divergence of invasive populations can be assessed by testing the null hypothesis that the extent of quantitative genetic differentiation (Q(ST) ) would be similar to that of neutral molecular differentiation (F(ST) ). Using eight microsatellite loci and a common garden approach, we compared Q(ST) and F(ST) among ten populations of an invasive species Ambrosia artemisiifolia (common ragweed) in France. In a common garden study with varying water and nutrient levels, we measured Q(ST) for five traits (height, total biomass, reproductive allocation, above- to belowground biomass ratio, and days to flowering). Although low F(ST) indicated weak genetic structure and strong gene flow among populations, we found significant diversifying selection (Q(ST) > F(ST) ) for reproductive allocation that may be closely related to fitness. It suggests that abiotic conditions may have exerted selection pressure on A. artemisiifolia populations to differentiate adaptively, such that populations at higher altitude or latitude evolved greater reproductive allocation. As previous studies indicate multiple introductions from various source populations of A. artemisiifolia in North America, our results suggest that the admixture of introduced populations may have increased genetic diversity and additive genetic variance, and in turn, promoted the rapid evolution and adaptation of this invasive species.
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Affiliation(s)
- Young Jin Chun
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Korea.
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Ekué MRM, Gailing O, Vornam B, Finkeldey R. Assessment of the domestication state of ackee (Blighia sapida K.D. Koenig) in Benin based on AFLP and microsatellite markers. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0155-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kyndt T, Assogbadjo AE, Hardy OJ, Glele Kakaï R, Sinsin B, Van Damme P, Gheysen G. Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa. AMERICAN JOURNAL OF BOTANY 2009; 96:950-957. [PMID: 21628247 DOI: 10.3732/ajb.0800266] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.
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Affiliation(s)
- Tina Kyndt
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000 Ghent, Belgium
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Gay L, Neubauer G, Zagalska-Neubauer M, Pons JM, Bell DA, Crochet PA. Speciation with gene flow in the large white-headed gulls: does selection counterbalance introgression? Heredity (Edinb) 2008; 102:133-46. [PMID: 18813326 DOI: 10.1038/hdy.2008.99] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We investigated the role of selection in generating and maintaining species distinctness in spite of ongoing gene flow, using two zones of secondary contact between large gull species in Europe (Larus argentatus and Larus cachinnans) and North America (Larus glaucescens and Larus occidentalis). We used the pattern of neutral genetic differentiation at nine microsatellite loci (F(ST)) as an indicator of expected changes under neutral processes and compared it with phenotypic differentiation (P(ST)) for a large number of traits (size, plumage melanism and coloration of bare parts). Even assuming very low heritability, interspecific divergence between L. glaucescens and L. occidentalis in plumage melanism and orbital ring colour clearly exceeded neutral differentiation. Similarly, melanism of the central primaries was highly divergent between L. argentatus and L. cachinnans. Such divergence is unlikely to have arisen randomly and is therefore attributed to spatially varying selection. Variation in plumage melanism in both transects agrees with Gloger's rule, which suggests that latitude (and associated sun and humidity gradients) could be the selective pressure shaping differentiation in plumage melanism. We suggest that strong species differentiation in orbital ring colour results from sexual selection. We conclude that these large gull species, along with other recently diverged species that hybridize after coming into secondary contact, may differ only in restricted regions of the genome that are undergoing strong disruptive selection because of their phenotypic effects.
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Affiliation(s)
- L Gay
- CEFE-CNRS, UMR 5175, Montpellier cedex 5, France.
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Muller F, Voccia M, Bâ A, Bouvet JM. Genetic diversity and gene flow in a Caribbean tree Pterocarpus officinalis Jacq.: a study based on chloroplast and nuclear microsatellites. Genetica 2008; 135:185-98. [DOI: 10.1007/s10709-008-9268-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 04/13/2008] [Indexed: 11/30/2022]
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Leinonen T, O'Hara RB, Cano JM, Merilä J. Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis. J Evol Biol 2007; 21:1-17. [PMID: 18028355 DOI: 10.1111/j.1420-9101.2007.01445.x] [Citation(s) in RCA: 271] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- T Leinonen
- Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - R B O'Hara
- Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - J M Cano
- Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - J Merilä
- Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Bottin L, Isnard C, Lagrange A, Bouvet JM. Comparative Molecular and Phytochemical Study of the Tree SpeciesSantalum austrocaledonicum (Santalaceae) Distributed in the New-Caledonian Archipelago. Chem Biodivers 2007; 4:1541-56. [PMID: 17638336 DOI: 10.1002/cbdv.200790134] [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: 11/07/2022]
Abstract
We have tried to elucidate the origin of phytochemical variation in trees by studying concomitantly the chemical and microsatellite variations in Santalum austrocaledonicum. Eight natural populations were sampled in the New-Caledonian archipelago, a total of 157 individuals being analyzed. The main components, as revealed by gas chromatography (GC), were alpha- and beta-santalol (as in other sandalwood species), although the level of (Z)-lanceol was particularly high. Most of the chemical variation was observed within populations (83.7%). With microsatellites, the variation between populations was more pronounced (32% of the total variation). Although the chemical variation between populations was small, we investigated the effects of genetic drift and migration by comparing the chemical- and molecular-differentiation patterns. The poor congruence between neighbor-joining trees, confirmed by the non-significant Mantel test between the molecular and chemical distance matrices (R=0.26, P=0.12), showed that genetic drift and migration are not the main evolutionary forces acting on chemical differentiation between populations. We could not find any effect of soil and rainfall conditions neither. Although the impact of drift and migration cannot be discounted in rationalizing between-population differentiation, the low variation among populations could result from a stabilizing selection caused by the same phytopathogen charge across the natural range.
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Affiliation(s)
- Lorraine Bottin
- Museum National d'Histoire Naturelle, UMR 5173, Conservation des espèces, restauration et suivi des populations, 61 rue Buffon, F-75005 Paris
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Demographic bottlenecks and low gene flow in remnant populations of the critically endangered Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) inferred from microsatellite markers. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9324-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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