Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana

PLoS Genetics

Volumn 6, Issue 3, 2010, Pages

  Bomblies, Kirsten ^a,b   Yant, Levi ^a   Laitinen, Roosa A ^a   Kim, Sang Tae ^a   Hollister, Jesse D ^b   Warthmann, Norman ^a   Fitz, Joffrey ^a   Weigel, Detlef ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; GERMINATION; HETEROZYGOSITY; HOMOZYGOSITY; NONHUMAN; PLANT GENETICS; POPULATION MIGRATION; POPULATION RESEARCH; POPULATION SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; GENETICS; HYBRIDIZATION;

ARABIDOPSIS THALIANA;

ARABIDOPSIS; GENETIC VARIATION; GENOTYPE; HYBRIDIZATION, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 77950380766     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000890     Document Type: Article

References (74)

1. Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456: 720-723.
2. Mitchell-Olds T, Schmitt J (2006) Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441: 947-952. (Pubitemid 43980343)
3. Abbott RJ, Gomes MF (1989) Population genetic structure and outcrossing rate of Arabidopsis thaliana (L.) Heynh. Heredity 62: 411-418.
4. Bergelson J, Stahl E, Dudek S, Kreitman M (1998) Genetic variation within and among populations of Arabidopsis thaliana. Genetics 148: 1311-1323. (Pubitemid 28169038)
5. Bakker EG, Stahl EA, Toomajian C, Nordborg M, Kreitman M, et al. (2006) Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Mol Ecol 15: 1405-1418.
6. Picó FX, Mendez-Vigo B, Martinez-Zapater JM, Alonso-Blanco C (2008) Natural genetic variation of Arabidopsis thaliana is geographically structured in the Iberian peninsula. Genetics 180: 1009-1021.
7. Brown AHD, Marshall DR, Albrecht L (1974) The maintenance of alcohol dehydrogenase polymorphism in Bromus mollis L. Austr J Biol Sci 27: 545-549.
8. Brown AHD, Zohary D, Nevo E (1978) Outcrossing rates and heterozygosity in natural populations of Hordeum spontaneum Koch in Israel. Heredity 41: 49-62.
9. Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B Biol Sci 351: 1291-1298. (Pubitemid 27206196)
10. Allard RW (1975) The mating system and microevolution. Genetics 79 Suppl: 115-126.
11. Allard RW, Zhang Q, Maroof MA, Muona OM (1992) Evolution of multilocus genetic structure in an experimental barley population. Genetics 131: 957-969.
12. Harding J, Allard RW, Smeltzer DG (1966) Population studies in predominantly self-pollinated species, IX. Frequency-dependent selection in Phaseolus lunatus. Proc Natl Acad Sci USA 56: 99-104.
13. Imam AG, Allard RW (1965) Population studies in predominantly self-pollinated species. VI. Genetic variability between and within natural populations of wild oats from differing habitats in California. Genetics 51: 49-62.
14. Jain SK, Allard RW (1960) Population studies in predominantly self-pollinated species. I. Evidence for heterozygote advantage in a closed population of barley. Proc Natl Acad Sci USA 46: 1371-1377.
15. Marshall DR, Allard RW (1970) Maintenance of isozyme polymorphisms in natural populations of Avena barbata. Genetics 66: 393-399.
16. Schoen DJ, Brown AH (1991) Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants. Proc Natl Acad Sci USA 88: 4494-4497.
17. Jones ME (1971) The population genetics of Arabidopsis thaliana. I. The breeding system. Heredity 27: 39-50.
18. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3: e196. doi:10.1371/journal.pbio.0030196.
19. Le Corre V (2005) Variation at two flowering time genes within and among populations of Arabidopsis thaliana: comparison with markers and traits. Mol Ecol 14: 4181-4192.
20. Kuittinen H, Mattila A, Savolainen O (1997) Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana. Heredity 79(Pt 2): 144-152. (Pubitemid 27340954)
21. Jorgensen S, Mauricio R (2004) Neutral genetic variation among wild North American populations of the weedy plant Arabidopsis thaliana is not geographically structured. Mol Ecol 13: 3403-3413. (Pubitemid 39428762)
22. Berge G, Nordal I, Hestmark G (1998) The effect of breeding systems and pollination vectors on the genetic variation of small plant populations within an agricultural landscape. OIKOS 81: 17-29. (Pubitemid 28091322)
23. Jorgensen TH, Emerson BC (2008) Functional variation in a disease resistance gene in populations of Arabidopsis thaliana. Mol Ecol 17: 4912-4923.
24. Husband B, Barrett S (1996) A metapopulation perspective in plant population biology. J Ecol 84: 461-469. (Pubitemid 27003705)
25. Stenøien HK, Fenster CB, Tonteri A, Savolainen O (2005) Genetic variability in natural populations of Arabidopsis thaliana in northern Europe. Mol Ecol 14: 137-148. (Pubitemid 40141482)
26. Beck JB, Schmuths H, Schaal BA (2008) Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics. Mol Ecol 17: 902-915.
27. Sharbel TF, Haubold B, Mitchell-Olds T (2000) Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Mol Ecol 9: 2109-2118. (Pubitemid 32053344)
28. François O, Blum MG, Jakobsson M, Rosenberg NA (2008) Demographic history of european populations of Arabidopsis thaliana. PLoS Genet 4: e1000075. doi:10.1371/journal.pgen.1000075.
29. Schmid KJ, Ottó T, Meyer R, Schmuths H, Hoffmann MH, et al. (2006) Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers. Theor Appl Genet 112: 1104-1114.
30. Platt A, Horton M, Huang YS, Li Y, Anastasio AE, et al. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genet 6: e1000843. doi:10.1371/journal.pgen.1000843.
31. Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, et al. (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39: 1151-1555. (Pubitemid 47340659)
32. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, et al. (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30: 190-193.
33. Morrell PL, Toleno DM, Lundy KE, Clegg MT (2002) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102: 2442-2447.
34. Weigel D, Mott R (2009) The 1001 Genomes Project for Arabidopsis thaliana. Genome Biol 10: 107.
35. Warthmann N, Fitz J, Weigel D (2007) MSQT for choosing SNP assays from multiple DNA alignments. Bioinformatics 23: 2784-2787. (Pubitemid 350048345)
36. Wagner DB, Allard RW (1991) Pollen migration in predominantly self-fertilizing plants - barley. J Hered 82: 302-304.
37. Leberg P (2002) Estimating allelic richness: Effects of sample size and bottlenecks. Mol Ecol 11: 2445-2449.
38. Wahlund S (1928) Composition of populations and correlation appearances viewed in relation to the studies of inheritance. Hereditas 11: 65-106.
39. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
40. Smouse PE, Peakall R (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82: 561-573.
41. Degen B (2000) SGS: Spatial Genetic Software. Computer program and user's manual.
42. Sokal RR, Oden NL (1978) Spatial autocorrelation in biology. 1. Methodology. Biol J Linn Soc 10: 199-228.
43. Sokal RR, Wartenberg DE (1983) A test of spatial autocorrelation analysis using an isolation-by-distance model. Genetics 105: 219-237.
44. Gregorius HR (1978) The concept of genetic diversity and its formal relationship to heterozygosity and genetic distance. Mathemat Biosci 41: 253-271.
45. Vekemans X, Hardy OJ (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol 13: 921-935. (Pubitemid 38390597)
46. Tibshirani R, Walther G, Hastie T (2001) Estimating the number of clusters in a data set via the gap statistic. J R Statist Soc B 63: 411-423. (Pubitemid 33267694)
47. Gao X, Starmer J (2008) AWclust: point-and-click software for non-parametric population structure analysis. BMC Bioinformatics 9: 77.
48. He F, Kang D, Ren Y, Qu LJ, Zhen Y, et al. (2007) Genetic diversity of the natural populations of Arabidopsis thaliana in China. Heredity 99: 423-431. (Pubitemid 47482641)
49. Innan H, Stephan W (2000) The coalescent in an exponentially growing metapopulation and its application to Arabidopsis thaliana. Genetics 155: 2015-2019. (Pubitemid 30626416)
50. Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM, et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
51. Turner ME, Stephens JC, Anderson WW (1982) Homozygosity and patch structure in plant populations as a result of nearest-neighbor pollination. Proc Natl Acad Sci USA 79: 203-207.
52. Ritland K (1984) The effective proportion of self-fertilization with consanguineous matings in inbred populations Genetics 106: 139-152.
53. Ritland K, Jain S (1981) A model for the estimation of outcrossing rate and gene frequencies using n independent loci. Heredity 47: 35-52.
54. Doligez A, Baril C, Joly HI (1998) Fine-scale spatial genetic structure with nonuniform distribution of Individuals. Genetics 148: 905-919. (Pubitemid 28087638)
55. Lloyd DG (1992) Self- and cross-fertilization in plants. II. The selection of selffertilization. Int J Plant Sci 153: 370.
56. Mable BK, Adam A (2007) Patterns of genetic diversity in outcrossing and selfing populations of Arabidopsis lyrata. Mol Ecol 16: 3565-3580. (Pubitemid 47383108)
57. Mable BK, Robertson AV, Dart S, Di Berardo C, Witham L (2005) Breakdown of self-incompatibility in the perennial Arabidopsis lyrata (Brassicaceae) and its genetic consequences. Evolution 59: 1437-1448. (Pubitemid 41102229)
58. Ingvarsson PK (2002) A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants. Evolution 56: 2368-2373.
59. Hoffmann MH, Bremer M, Schneider K, Burger F, Stolle E, et al. (2003) Flower visitors in a natural population of Arabidopsis thaliana. Plant Biol 5: 491-494. (Pubitemid 37491873)
60. Chen F, Tholl D, D'Auria JC, Farooq A, Pichersky E, et al. (2003) Biosynthesis and emission of terpenoid volatiles from Arabidopsis flowers. Plant Cell 15: 481-494. (Pubitemid 36229999)
61. Allard RW, Bradshaw AD (1964) Implications of genotype-environmental interactions in applied plant breeding. Crop Sci 4: 503-508.
62. Abdel-Ghani AH, Parzies HK, Omary A, Geiger HH (2004) Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan. Theor Appl Genet 109: 588-595. (Pubitemid 39138789)
63. Akinola M, Thompson K, Buckland S (1998) Soil seed bank of an upland calcerous grassland after 6 years of climate and management manipulations. J Appl Ecol 35: 544-552. (Pubitemid 29010043)
64. Roberts H (1968) The changing population of viable weed seeds in an arable soil. Weed Res 8: 253-256.
65. Baskin J, Baskin C (1983) Seasonal changes in the germination responses of buried seeds of Arabidopsis thaliana and ecological interpretation. Bot Gaz 144: 540-543.
66. Montesinos A, Tonsor S, Alonso-Blanco C, Picó X (2009) Demographic and genetic patterns of variation among populations of Arabidopsis thaliana from contrasting native environments. PLoS ONE 4: e7213. doi:10.1371/journal. pone.0007213.
67. Malo J, LJiménez B, Suárez F (1995) Seed bank build-up in small disturbances in a Mediterranean pasture: the contribution of endozoochorous dispersal by rabbits. Ecogeography 18: 73-82.
68. Koornneef M, Alonso-Blanco C, Vreugdenhil D (2004) Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Physiol Plant Mol Biol 55: 141-172. (Pubitemid 38940929)
69. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317: 338-342.
70. Rousset F (2007) Genepop'007: a complete reimplementation of software for Windows and Linux. Mol Ecol Notes 8: 103-106.
71. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
72. Weir B (1996) Genetic data analysis II: Methods for discrete population genetic data. Sunderland, MA, USA: Sinauer Assoc.
73. Degen B, Petit R, Kremer A (2001) SGS - Spatial Genetic Software: A computer program for analysis of spatial genetic and phenotypic structures of individuals and populations. J Hered 92: 447-448. (Pubitemid 34038426)
74. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599. (Pubitemid 47236692)