Novel SNP development and analysis at a NADP+-specific IDH enzyme gene in a four species mixed oak forest

Plant Biology

Volumn 15, Issue SUPPL.1, 2013, Pages 126-137

  Vidalis, A ^a   Curtu, A L ^a,b   Finkeldey, R ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b The Faculty of Medicine   (Romania)

Author keywords

Isocitrate dehydrogenase; Quercus spp.; Single nucleotide polymorphisms

Indexed keywords

ISOCITRATE DEHYDROGENASE; ISOCITRATE DEHYDROGENASE (NADP+); VEGETABLE PROTEIN;

DECIDUOUS FOREST; DECIDUOUS TREE; ENZYME ACTIVITY; GENETIC DIFFERENTIATION; MIXED FOREST; MOLECULAR ANALYSIS; MORPHOLOGY; POLYMORPHISM; POPULATION SIZE; RECOMBINATION;

ALLELE; ARTICLE; EUROPE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; OAK; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; TREE;

ALLELES; EUROPE; ISOCITRATE DEHYDROGENASE; LINKAGE DISEQUILIBRIUM; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUERCUS; SPECIES SPECIFICITY; TREES;

QUERCUS; QUERCUS FRAINETTO; QUERCUS PETRAEA; QUERCUS PUBESCENS; QUERCUS ROBUR;

EID: 84871642427     PISSN: 14358603     EISSN: 14388677     Source Type: Journal    
DOI: 10.1111/j.1438-8677.2012.00575.x     Document Type: Article

References (80)

1. Akey J.M., Zhang G., Zhang K., Jin L., Shriver M.D. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research, 12, 1805-1814.
2. Alberto F., Niort J., Derory J., Lepais O., Vitalis R., Galop D., Kremer A. (2010) Population differentiation of sessile oak at the altitudinal front of migration in the French Pyrenees. Molecular Ecology, 19, 2626-2639.
3. Bartha D. (2006) Quercus frainetto Ten. In: Schütt P., Weisgerber H., Lang U., Roloff A., Stimm B. (Eds), Enzyklopädie der Holzsgewächse: Handbuch und Atlas der Dendrologie. Ecomed, Landsber am Lech, pp 2.
4. st tell us?Trends in Ecology and Evolution, 20, 435-440.
5. Bellarosa R., Simeone M.C., Papini A., Schirone B. (2005) Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp. Molecular Phylogenetics and Evolution, 34, 355-370.
6. Boiffin V., Hodges M., Galvez S., Balestrini R., Bonfante P., Gadal P., Martin F. (1998) Eucalypt NADP-dependent isocitrate dehydrogenase - cDNA cloning and expression in ectomycorrhizae. Plant Physiology, 117, 939-948.
7. Bradbury P.J., Zhang Z., Kroon D.E., Casstevens T.M., Ramdoss Y., Buckler E.S. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633-2635.
8. Brumfield R.T., Beerli P., Nickerson D.A., Edwards S.V. (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution, 18, 249-256.
9. Bussotti F. (2006) Quercus pubescens Willd. In: Schütt P., Weisgerber H., Lang U., Roloff A., Stimm B. (Eds), Enzyklopädie der Holzsgewächse: Handbuch und Atlas der Dendrologie. Ecomed, Landsber am Lech, pp 2-3.
10. Campbell N.R., Narum S.R. (2011) Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and Coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River. Molecular Ecology Resources, 11, 20-30.
11. Coart E., Lamote V., De Loose M., Van Bockstaele E., Lootens P., Roldan-Ruiz I. (2002) AFLP markers demonstrate local genetic differentiation between two indigenous oak species [Quercus robur L. and Quercus petraea (Matt.) Liebl] in Flemish populations. Theoretical and Applied Genetics, 105, 431-439.
12. Curtu A.L., Gailing O., Leinemann L., Finkeldey R. (2007a) Genetic variation and differentiation within a natural community of five oak species (Quercus spp.). Plant Biology, 9, 116-126.
13. Curtu A.L., Gailing O., Finkeldey R. (2007b) Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Evolutionary Biology, 7, 218.
14. Curtu A.L., Gailing O., Finkeldey R. (2009) Patterns of contemporary hybridization inferred from paternity analysis in a four-oak-species forest. BMC Evolutionary Biology, 9, 284.
15. Dang L., White D.W., Gross S., Bennett B.D., Bittinger M.A., Driggers E.M., Fantin V.R., Jang H.G., Jin S., Keenan M.C., Marks K.M., Prins R.M., Ward P.S., Yen K.E., Liau L.M., Rabinowitz J.D., Cantley L.C., Thompson C.B., Vander Heiden M.G., Su S.M. (2009) Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature, 462, 739-744.
16. Dempster A.P., Laird N.M., Rubin D.B. (1977) Maximum likelihood from incomplete data via Em algorithm. Journal of the Royal Statistical Society Series B (Methodological), 39, 1-38.
17. Derory J., Scotti-Saintagne C., Bertocchi E., Le Dantec L., Graignic N., Jauffres A., Casasoli M., Chancerel E., Bodenes C., Alberto F., Kremer A. (2010) Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks. Heredity, 104, 438-448.
18. Ellenberg H. (1988) Vegetation ecology of Central Europe. Cambridge University Press, Cambridge.
19. Eveno E., Collada C., Guevara M.A., Léger V., Soto A., Díaz L., Léger P., González- Martínez S.C., Cervera M.T., Plomion C., Garnier- Gér P.H. (2008) Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses. Molecular Biology and Evolution, 25, 417-437.
20. Excoffier L., Lischer H.E.L. (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
21. Excoffier L., Slatkin M. (1998) Incorporating genotypes of relatives into a test of linkage disequilibrium. American Journal of Human Genetics, 62, 171-180.
22. Farnir F., Coppieters W., Arranz J.J., Berzi P., Cambisano N., Grisart B., Karim L., Marcq F., Moreau L., Mni M., Nezer C., Simon P., Vanmanshoven P., Wagenaar D., Georges M. (2000) Extensive genome-wide linkage disequilibrium in cattle. Genome Research, 10, 220-227.
23. Finkeldey R. (2001) Genetic variation of oaks (Quercus spp.) in Switzerland - 2. Genetic structures in "pure" and "mixed" forests of pedunculate oak (Q. robur L.) and sessile oak (Q. petraea (Matt.) Liebl.). Silvae Genetica, 50, 22-30.
24. Finkeldey R., Mátyás G. (2003) Genetic variation of oaks (Quercus spp.) in Switzerland. 3. Lack of impact of postglacial recolonization history on nuclear gene loci. Theoretical and Applied Genetics, 106, 346-352.
25. Gailing O., Vornam B., Leinemann L., Finkeldey R. (2009) Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model. Physiologia Plantarum, 137, 509-519.
26. Gömöry D., Yakovlev I., Zhelev P., Jedinakova J., Paule L. (2001) Genetic differentiation of oak populations within the Quercus robur/Quercus petraea complex in Central and Eastern Europe. Heredity, 86, 557-563.
27. González-Martínez S.C., Wheeler N.C., Ersoz E., Nelson C.D., Neale D.B. (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics, 175, 399-409.
28. Gora V., Starke R., Ziehe M., König J., Müller-Starck G., Lunderstädt J. (1994) Influence of genetic structures and silvicultural treatments in a beech stand (Fagus sylvatica) on the population dynamics of beech scale (Cryptococcus fagisuga). Forest Genetics, 1, 157-164.
29. Goudet J. (1995) "STAT (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
30. Hall T. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
31. Helyar S.J., Hemmer-Hansen J., Bekkevold D., Taylor M.I., Ogden R., Limborg M.T., Cariani A., Maes G.E., Diopere E., Carvalho G.R., Nielsen E.E. (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11, 123-136.
32. Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S., Manolio T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of USA, 106, 9362-9367.
33. Hirschhorn J.N., Daly M.J. (2005) Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics, 6, 95-108.
34. Hodges M., Flesch V., Gálvez S., Bismuth E. (2003) Higher plant NADP+-dependent isocitrate dehydrogenases, ammonium assimilation and NADPH production. Plant Physiology and Biochemistry, 41, 577-585.
35. Huestis D.L., Oppert B., Marshall J.L. (2009) Geographic distributions of Idh-1 alleles in a cricket are linked to differential enzyme kinetic performance across thermal environments. BMC Evolutionary Biology, 9, 7-10.
36. Ingvarsson P.K. (2005) Nucleotide polymorphism and linkage disequilbrium within and among natural populations of European Aspen (Populus tremula L., Salicaceae). Genetics, 169, 945-953.
37. Ingvarsson P.K., Garcia M.V., Luquez V., Hall D., Jansson S. (2008) Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics, 178, 2217-2226.
38. Kremer A., Dupouey J.L., Deans J.D., Cottrell J., Csaikl U., Finkeldey R., Espinel S., Jensen J., Kleinschmit J., Van Dam B., Ducousso A., Forrest I., de Heredia U.L., Lowe A.J., Tutkova M., Munro R.C., Steinhoff S., Badeau V. (2002) Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands. Annals of Forest Science, 59, 777-787.
39. Le Corre V., Kremer A. (2003) Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics, 164, 1205-1219.
40. Leterrier M., Del Rio L.A., Corpas F.J. (2007) Cytosolic NADP-isocitrate dehydrogenase of pea plants: genomic clone characterization and functional analysis under abiotic stress conditions. Free Radical Research, 41, 191-199.
41. Lexer C., Widmer A. (2008) The genic view of plant speciation: recent progress and emerging questions. Philosophical Transactions of the Royal Society B: Biological Sciences, 363, 3023-3036.
42. Lexer C., Kremer A., Petit R.J. (2006) Shared alleles in sympatric oaks: recurrent gene flow is a more parsimonious explanation than ancestral polymorphism. Molecular Ecology, 15, 2007-2012.
43. Liu Y.H., Shi Y.S., Song Y.C., Wang T.Y., Li Y. (2010) Characterization of a stress-induced NADP-isocitrate dehydrogenase gene in maize confers salt tolerance in Arabidopsis. Journal of Plant Biology, 53, 107-112.
44. Marchini J., Cardon L.R., Phillips M.S., Donnelly P. (2004) The effects of human population structure on large genetic association studies. Nature Genetics, 36, 512-517.
45. Mariette S., Cottrell J., Csaikl U.M., Goikoechea P., Konig A., Lowe A.J., Van Dam B.C., Barreneche T., Bodenes C., Streiff R., Burg K., Groppe K., Munro R.C., Tabbener H., Kremer A. (2002) Comparison of levels of genetic diversity detected with AFLP and microsatellite markers within and among mixed Q. petraea (MATT.) LIEBL. and Q. robur L. stands. Silvae Genetica, 51, 72-79.
46. Montesinos A., Tonsor S.J., Alonso-Blanco C., Pico F.X. (2009) Demographic and genetic patterns of variation among populations of Arabidopsis thaliana from contrasting native environments. PLoS ONE, 4, e7213.
47. Morin P.A., Luikart G., Wayne R.K., Grp S.W. (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19, 208-216.
48. Morrell P.L., Toleno D.M., Lundy K.E., Clegg M.T. (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proceedings of the National Academy of Sciences of USA, 102, 2442-2447.
49. Muir G., Schlotterer C. (2005) Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.). Molecular Ecology, 14, 549-561.
50. Neale D.B. (2007) Genomics to tree breeding and forest health. Current Opinion in Genetics and Development, 17, 539-544.
51. Neale D.B., Savolainen O. (2004) Association genetics of complex traits in conifers. Trends in Plant Science, 9, 325-330.
52. Neophytou C., Aravanopoulos F.A., Fink S., Dounavi A. (2010) Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Q. robur L.) using small sets of microsatellite markers. Forest Ecology and Management, 259, 2026-2035.
53. Palomo J., Gallardo F., Suarez M.F., Canovas F.M. (1998) Purification and characterization of NADP(+)-linked isocitrate dehydrogenase from Scots pine - evidence for different physiological roles of the enzyme in primary development. Plant Physiology, 118, 617-626.
54. Pascual M.B., Jing Z.P., Kirby E.G., Canovas F.M., Gallardo F. (2008a) Response of transgenic poplar overexpressing cytosolic glutamine synthetase to phosphinothricin. Phytochemistry, 69, 382-389.
55. Pastinen T., Kurg A., Metspalu A., Peltonen L., Syvänen A.-C. (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Research, 7, 606-614.
56. Petit R.J., Csaikl U.M., Bordacs S., Burg K., Coart E., Cottrell J., van Dam B., Deans J.D., Dumolin-Lapegue S., Fineschi S., Finkeldey R., Gillies A., Glaz I., Goicoechea P.G., Jensen J.S., Konig A.O., Lowe A.J., Madsen S.F., Matyas G., Munro R.C., Olalde M., Pemonge M.H., Popescu F., Slade D., Tabbener H., Taurchini D., de Vries S.G.M., Ziegenhagen B., Kremer A. (2002a) Chloroplast DNA variation in European white oaks - phylogeography and patterns of diversity based on data from over 2600 populations. Forest Ecology and Management, 156, 5-26.
57. Petit R.J., Brewer S., Bordacs S., Burg K., Cheddadi R., Coart E., Cottrell J., Csaikl U.M., van Dam B., Deans J.D., Espinel S., Fineschi S., Finkeldey R., Glaz I., Goicoechea P.G., Jensen J.S., Konig A.O., Lowe A.J., Madsen S.F., Matyas G., Munro R.C., Popescu F., Slade D., Tabbener H., de Vries S.G.M., Ziegenhagen B., de Beaulieu J.L., Kremer A. (2002b) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. Forest Ecology and Management, 156, 49-74.
58. Petit R.J., Bodenes C., Ducousso A., Roussel G., Kremer A. (2004) Hybridization as a mechanism of invasion in oaks. New Phytologist, 161, 151-164.
59. Porth I., Scotti-Saintagne C., Barreneche T., Kremer A., Burg K. (2005) Linkage mapping of osmotic stress induced genes of oak. Tree Genetics & Genomes, 1, 31-40.
60. Pritchard J.K., Stephens M., Donnelly P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
61. Quang N.D., Ikeda S., Harada K. (2008) Nucleotide variation in Quercus crispula Blume. Heredity, 101, 166-174.
62. Quang N.D., Ikeda S., Harada K. (2009) Patterns of nucleotide diversity at the methionine synthase locus in fragmented and continuous populations of a wind-pollinated tree, Quercus mongolica var. crispula. Journal of Heredity, 100, 762-770.
63. Quintana-Murci L., Barreiro L.B. (2010) The role played by natural selection on Mendelian traits in humans. The Year in Human and Medical Genetics: New Trends in Mendelian Genetics, 1214, 1-17.
64. Quintana-Murci L., Barreiro L.B., Laval G., Quach H., Patin E. (2008) Natural selection has driven population differentiation in modern humans. Nature Genetics, 40, 340-345.
65. Rosenberg N.A., Li L.M., Ward R., Pritchard J.K. (2003) Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetics, 73, 1402-1422.
66. Rozen S., Skaletsky H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, 132, 365-386.
67. Salvini D., Bruschi P., Fineschi S., Grossoni P., Kjaer E.D., Vendramin G.G. (2009) Natural hybridisation between Quercus petraea (Matt.) Liebl. and Quercus pubescens Willd. within an Italian stand as revealed by microsatellite fingerprinting. Plant Biology, 11, 758-765.
68. Schlötterer C. (2004) The evolution of molecular markers - just a matter of fashion?Nature Reviews. Genetics, 5, 63-69.
69. Schwarz O. (1993) Quercus. In: Tutin T.G., Burges N.A., Chater A.O., Edmondson J.R., Heywood V.H., Moore D.M., Valentine D.H., Walters S.M., Webb D.A. (Eds), Flora Europaea. Cambridge University Press, Cambridge, UK, pp 1.
70. Scotti-Saintagne C., Mariette S., Porth I., Goicoechea P.G., Barreneche T., Bodenes K., Burg K., Kremer A. (2004) Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics, 168, 1615-1626.
71. Seeb J.E., Carvalho G., Hauser L., Naish K., Roberts S., Seeb L.W. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11, 1-8.
72. Slate J., Gratten J., Beraldi D., Stapley J., Hale M., Pemberton J.M. (2009) Gene mapping in the wild with SNPs: guidelines and future directions. Genetica, 136, 97-107.
73. Slatkin M., Excoffier L. (1996) Testing for linkage disequilibrium in genotypic data using the expectation-maximization algorithm. Heredity, 76, 377-383.
74. Sork V.L., Davis F.W., Westfall R., Flint A., Ikegami M., Wang H.F., Grivet D. (2010) Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Nee) in the face of climate change. Molecular Ecology, 19, 3806-3823.
75. Thompson J.D., Higgins D.G., Gibson T.J. (1994) Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
76. Via S. (2009) Natural selection in action during speciation. Proceedings of the National Academy of Sciences of USA, 106, 9939-9946.
77. Vornam B., Gailing O., Finkeldey R., Collada C., Guevara M.A., Soto A., de María N., González-Martínez, S., Díaz L., Alia R., Aranda I., Climent J., Cervera M.T., Goicoechea P., Léger V., Eveno E., Derory J., Garnier-Gére P., Kremer A., Plomion C. (2007) Naturally occurring nucleotide diversity in candidate genes for forest tree adaptation: magnitude, distribution and association with quantitative trait variation. The German Plant Genome Research Program Progress Report 2004-2007. GABI, Potsdam-Golm, Germany, pp 116-120.
78. Yamasaki M., Tenaillon M.I., Bi I.V., Schroeder S.G., Sanchez-Villeda H., Doebley J.F., Gaut B.S., McMullen M.D. (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. The Plant Cell, 17, 2859-2872.
79. Zhang D.-q., Zhang Z.-y. (2005) Single nucleotide polymorphisms (SNPs) discovery and linkage disequilibrium (LD) in forest trees. Forestry Studies in China, 7, 1-14.
80. Zhu Q.H., Zheng X.M., Luo J.C., Gaut B.S., Ge S. (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Molecular Biology and Evolution, 24, 875-888.