AFLP analysis of the pseudometallophyte Cistus ladanifer: comparison with cpSSRs and exploratory genome scan to investigate loci associated to soil variables
详细信息    查看全文
  • 作者:Celestino Quintela-Sabarís (1) tino.quintela.sabaris@gmail.com
    Maria Margarida Ribeiro (2)
    Bénédicte Poncet (3)
    Rita Costa (4)
    Daniel Castro-Fernández (1)
    Maria Isabel Fraga (1)
  • 关键词:Amplified Fragment Length Polymorphism – chloroplast microsatellites – Cistus ladanifer – Generalized Estimating Equations – heavy metals
  • 刊名:Plant and Soil
  • 出版年:2012
  • 出版时间:October 2012
  • 年:2012
  • 卷:359
  • 期:1-2
  • 页码:397-413
  • 全文大小:555.6 KB
  • 参考文献:1. Alados CL, Navarro T, Cabezudo B (1999) Tolerance assessment of Cistus ladanifer to serpentine soils by developmental stability analysis. Plant Ecol 143:51–66
    2. Alvarenga PM, Araújo MF, Silva JAL (2004) Elemental uptake and root-leaves transfer in Cistus ladanifer L. growing in a contaminated pyrite mining area (Aljustrel-Portugal). Water Air Soil Poll 152:81–96
    3. Ater M, Lefèbvre C, Gruber W, Meerts P (2000) A phytogeochemical survey of the flora of ultramafic and adjacent normal soils in North Morocco. Plant Soil 218:127–135
    4. Bastida F, Talavera S (2002) Temporal and spatial patterns of seed dispersal in two Cistus species (Cistaceae). Ann Bot 89:427–434
    5. Baumbach H, Hellwig FH (2007) Genetic differentiation of metallicolous and non-metallicolous populations of Armeria maritima (Mill.) Willd. taxa (Plumbaginaceae) in Central Europe. Plant Syst Evol 269:245–258
    6. Bonin A, Bellemain E, Eidesen PB, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273
    7. Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionist. Mol Ecol 16:3737–3758
    8. Brady KU, Kruckeberg AR, Bradshaw HD (2005) Evolutionary ecology of plant adaptation to serpentine soils. Annu Rev Ecol Evol S 36:243–266
    9. Bucci G, González-Martínez SC, Le Provost G, Plomion C, Ribeiro MM, Sebastiani F, Alía R, Vendramin GG (2007) Range-wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers. Mol Ecol 16:2137–2153
    10. Carl G, Kuhn I (2007) Analyzing spatial autocorrelation in species distribution using Gaussian and logit models. Ecol Model 207:159–170
    11. Carlier J, Leit?o J, Fonseca F (2008) Population genetic structure of Cistus ladanifer L. (Cistaceae) and genetic differentiation from co-occurring Cistus species. Plant Spec Biol 23:141–151
    12. Comes HP, Kadereit JW (1998) The effect of Quaternary climatic changes on plant distribution and evolution. Trends Plant Sci 3:432–438
    13. Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15:2833–2843
    14. Corander J, Sirén J, Arjas E (2008) Bayesian spatial modelling of genetic population structure. Comput Stat 23:111–129
    15. de la Fuente V, Rufo L, Rodríguez N, Amils R, Zuluaga J (2010) Metal accumulation screening of the Río Tinto flora (Huelva, Spain). Biol Trace Elem Res 134:318–341
    16. Demoly JP, Montserrat P (1993) Cistus L. In: Castroviejo S, Aedo C, Cirujano S, Laínz M, Montserrat P, Morales R, Mu?oz Garmendia F, Navarro C, Paiva J, Soriano C (eds) Flora Iberica, vol III. Real Jardín Botánico. CSIC, Madrid, pp 319–337
    17. Deng D, Lan C, Shu W (2007) The effects of heavy metal pollution on genetic diversity in zinc/cadmium hyperaccumulator Sedum alfredii populations. Plant Soil 297:83–92
    18. Díez-Lázaro J (2008) Fitocorrección de suelos contaminados con metales pesados: Evaluación de plantas tolerantes y optimización del proceso mediante prácticas agronómicas. Ph.D. Thesis. Universidade de Santiago de Compostela, Spain
    19. Dumolin S, Demesure B, Petit RJ (1995) Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–1256
    20. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839
    21. Epstein E, Bloom AJ (2005) Mineral nutrition of plants: principles and perspectives, 2nd edn. Sinauer Associated, Sunderland
    22. Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491
    23. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50
    24. Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
    25. Friedland AJ (1990) The movement of metals through soils and ecosystems. In: Shaw AJ (ed) Heavy metal tolerance in plants: evolutionary aspects. CRC, Boca Raton, pp 7–19
    26. Grivet D, Petit RJ (2002) Phylogeography of the common ivy (Hedera sp.) in Europe: genetic differentiation through space and time. Mol Ecol 11:1351–1362
    27. Gustafson DJ, Romano G, Latham RE, Morton JK (2003) Amplified fragment length polymorphism analysis of genetic relationships among the serpentine barrens endemic Cerastium velutinum Rafinesque var. villosissimum Pennell (Caryophyllaceae) and closely related Cerastium species. J Torrey Bot Soc 130:218–230
    28. Guzmán B, Vargas P (2009) Long-distance colonization of the Western Mediterranean by Cistus ladanifer (Cistaceae) despite the absence of special dispersal mechanisms. J Biogeogr 36:954–968
    29. Holderegger R, Herrmann D, Poncet B, Gugerli F, Thuiller W, Taberlet P, Gielly L, Rioux D, Brodbeck S, Aubert S, Manel S (2008) Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol Divers 1:273–283
    30. Jiménez-Ambriz G, Petit C, Bourrié I, Dubois S, Olivieri I, Ronce O (2007) Life history variation in the heavy metal tolerant plant Thlaspi caerulescens growing in a network of contaminated and noncontaminated sites in southern France: role of gene flow, selection and phenotypic plasticity. New Phytol 173:199–215
    31. Kremer A, Kleinschmit J, Cottrell J, Cundall EP, Deans JD, Ducousso A, K?nig AO, Lowe AJ, Munro RC, Petit RJ, Stephan BR (2002) Is there a correlation between chloroplastic and nuclear divergence, or what are the roles of history and selection on genetic diversity in European oaks? Forest Ecol Manag 156:75–87
    32. Lefèbvre C, Vernet P (1990) Microevolutionary processes on contaminated deposits. In: Shaw AJ (ed) Heavy metal tolerance in plants: evolutionary aspects. CRC, Boca Raton, pp 285–299
    33. Legendre P, Legendre L (1998) Numerical ecology, 2nd English ed. Elsevier, Amsterdam
    34. Linhart YB, Grant MC (1996) Evolutionary significance of local genetic differentiation in plants. Annu Rev Ecol Syst 27:237–277
    35. Loveless MD, Hamrick JL (1984) Ecological determinants of genetic structure of plant populations. Annu Rev Ecol Syst 15:65–95
    36. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99
    37. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220
    38. Martín Bola?os M, Guinea López E (1949) Jarales y Jaras (Cistografia Hispanica). Ministerio de Agricultura, Madrid
    39. Médail F, Diadema K (2009) Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J Biogeogr 36:1333–1345
    40. Mengoni A, Gonnelli C, Galardi F, Gabbrielli R, Bazzicalupo M (2000) Genetic diversity and heavy metal tolerance in populations of Silene paradoxa L. (Caryophyllaceae): a RAPD analysis. Mol Ecol 9:1319–1324
    41. Mengoni A, Barabesi C, Gonelli C, Galardi F, Gabbrielli R, Bazzicalupo M (2001) Genetic diversity of heavy metal-tolerant populations in Silene paradoxa L. (Caryophyllaceae): a chloroplast microsatellite analysis. Mol Ecol 10:1909–1916
    42. Mengoni A, Selvi F, Cusimano N, Galardi F, Gonnelli C (2006) Genetic diversity inferred from AFLP fingerprinting in populations of Onosma echioides (Boraginaceae) from serpentine and calcareous soils. Plant Biosyst 140:211–219
    43. Metcalfe DB, Kunin WE (2006) The effects of plant density upon pollination success, reproductive effort and fruit parasitism in Cistus ladanifer L. (Cistaceae). Plant Ecol 185:41–47
    44. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117
    45. Meyer CL, Vitalis R, Saumitou-Laprade P, Castric V (2009) Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal. Mol Ecol 18:2050–2062
    46. Nú?ez-Olivera E, Martínez-Abaiga J, Escudero JC (1996) Adaptability of leaves of Cistus ladanifer to widely varying environmental conditions. Funct Ecol 10:636–646
    47. Nyberg Berglund AB, Dahlgren S, Westerbergh A (2004) Evidence for parallel evolution and site-specific selection of serpentine tolerance in Cerastium alpinum during the colonization of Scandinavia. New Phytol 161:199–209
    48. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155
    49. Olalde M, Herrán A, Espinel S, Goicoechea PG (2002) White oak phylogeography in the Iberian Peninsula. Forest Ecol Manag 156:89–102
    50. Pan W (2001) Model selection in estimating equations. Biometrics 57:529–534
    51. Papazoglou EG, Karantounias GA, Vemmos SN, Bouranis DL (2005) Photosynthesis and growth responses of giant reed (Arundo donax L.) to the heavy metals Cd and Ni. Environ Int 31:243–249
    52. Pauwels M, Willems G, Roosens N, Frérot H, Saumitou-Laprade P (2008) Merging methods in molecular and ecological genetics to study the adaptation of plants to anthropogenic metal-polluted sites: implications for phytoremediation. Mol Ecol 17:108–119
    53. Pérez-García F (1997) Germination of Cistus ladanifer seeds in relation to parent material. Plant Ecol 133:57–62
    54. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701
    55. Pollard AJ, Powell KD, Harper FA, Smith JAC (2002) The genetic basis of metal hyperaccumulation in plants. Cr Rev Plant Sci 21:539–566
    56. Poncet B, Herrmann D, Gugerli F, Taberlet P, Holderegger R, Gielly L, Rioux D, Thuiller W, Aubert S, Manel S (2010) Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 19:2896–2907
    57. Poschenrieder C, Bech J, Llugany M, Pace A, Fenés E, Barceló J (2001) Copper in plant species in a copper gradient in Catalonia (North East Spain) and their potential for phytoremediation. Plant Soil 230:247–256
    58. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
    59. Quintela-Sabarís C (2011) Evolutionary origin and ecophysiology of metallicolous populations of Cistus ladanifer L. Ph.D. Thesis. Universidade de Santiago de Compostela, Spain
    60. Quintela-Sabarís C, Vendramin GG, Castro-Fernández D, Fraga MI (2010) Chloroplast microsatellites reveal that metallicolous populations of the Mediterranean shrub Cistus ladanifer have multiple origins. Plant Soil 334:161–174
    61. R Development Core Team (2007) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org
    62. Ribeiro MM, Mariette S, Vendramin GG, Szmidt AE, Plomion C, Kremer A (2002) Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data. Mol Ecol 11:869–877
    63. Rohlf FJ (2002) NTSYSpc: numerical taxonomy system, ver. 2.11L. Exeter Publishing, Ltd, Setauket
    64. Ruttens A, Mench M, Colpaert JV, Boisson J, Carleer R, Vangronsveld J (2006) Phytostabilization of a metal contaminated sandy soil. I: influence of compost and/or inorganic metal immobilizing soil amendments on phytotoxicity and plant availability of metals. Environ Pollut 144:524–532
    65. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    66. Shaw BP, Sahu SK, Mishra RK (2004) Heavy metal induced oxidative damage in terrestrial plants. In: Prasad MNV, Hagemeyer J (eds) Heavy metal stress in plants: from molecules to ecosystems, 2nd edn. Springer, Berlin, pp 84–126
    67. Sim?es MP, Madeira M, Gazarini L (2009) Ability of Cistus L. shrubs to promote soil rehabilitation in extensive oak woodlands of Mediterranean areas. Plant Soil 323:249–265
    68. Staton JL, Schizas NV, Chandler GT, Coull BC, Quattro JM (2001) Ecotoxicology and population genetics: the emergence of “Phylogeographic and Evolutionary Ecotoxicology”. Ecotoxicology 10:217–222
    69. Storey JD (2002) A direct approach to false discovery rates. J Roy Stat Soc B 64:479–498
    70. Talavera S, Gibbs PE, Herrera J (1993) Reproductive biology of Cistus ladanifer (Cistaceae). Plant Syst Evol 186:123–134
    71. Tordoff GM, Baker AJM, Willis AJ (2000) Current approaches to the revegetation and reclamation of metalliferous mine wastes. Chemosphere 41:219–228
    72. Vekemans X (2002) AFLP-SURV version 1.0. Distributed by the author. Laboratoire de Génétique et Ecologie Végétale, Université Libre de Bruxelles, Belgium
    73. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151
    74. Vendramin GG, Anzidei M, Madaghiele A, Bucci G (1998) Distribution of genetic diversity in Pinus pinaster Ait. as revealed by chloroplast microsatellites. Theor Appl Genet 97:456–463
    75. Vos P, Hagers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
    76. Wenzel WW, Lombi E, Adriano D (2004) Root and rhizosphere processes in metal hyperaccumulation and phytoremediation technology. In: Prasad MNV, Hagemeyer J (eds) Heavy metal stress in plants: from molecules to ecosystems, 2nd edn. Springer, Berlin, pp 313–344
    77. White TL, Adams WT, Neale DB (2007) Forest genetic. CAB International, Oxfordshire
    78. Yan J, Fine JP (2004) Estimating equations for association structures. Stat Med 23:859–880
    79. Ye ZH, Baker AJM, Wong MH, Willis AJ (1997) Zinc, lead and cadmium tolerance, uptake and accumulation by Typha latifolia. New Phytol 136:469–480
    80. Zhivotovsky LA (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Mol Ecol 8:907–913
  • 作者单位:1. Departamento de Botánica, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, 15782 Spain2. Departamento de Recursos Naturais e Desenvolvimento Sustentável, Escola Superior Agrária, 6001-909 Castelo Branco, Portugal3. Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France4. INRB L-INIA Molecular Biology Laboratory, Ava da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
  • ISSN:1573-5036
文摘
Aims To assess the genetic patterns of colonisation of metalliferous areas by the pseudometallophyte Cistus ladanifer with AFLP genome scan, to compare those estimates with previous cpSSR results, and to identify loci potentially linked to tolerance to metalliferous soils.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700