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Analyses of Natural Variation: Field Experiments and Nucleotide Diversity for Your Favorite Gene

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Arabidopsis Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2200))

Abstract

Arabidopsis has become a model plant for ecological and population genomics, owing to the substantial phenotypic and genotypic variation that exists among and within natural populations. Specially, the recent availability of large worldwide collections of accessions, together with their full genome sequences, has triggered the study of Arabidopsis natural variation. In this chapter, we describe two protocols that exploit these new resources to understand the natural variation for any trait and gene: (1) the phenotypic analysis of Arabidopsis plants grown in field experiments; (2) the analysis of nucleotide diversity and environmental associations for specific genes.

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References

  1. Somerville C, Koornneef M (2002) A fortunate choice: the history of Arabidopsis as a model plant. Nat Rev Genet 3:883–889

    Article  CAS  PubMed  Google Scholar 

  2. Bergelson J, Roux F (2010) Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet 11:867–879

    Article  CAS  PubMed  Google Scholar 

  3. Weigel D, Nordborg M (2015) Population genomics for understanding adaptation in wild plant species. Annu Rev Genet 49:315–338

    Article  CAS  PubMed  Google Scholar 

  4. Kramer U (2015) Planting molecular functions in an ecological context with Arabidopsis thaliana. elife 4:e06100

    Article  PubMed Central  Google Scholar 

  5. Takou M, Wieters B, Kopriva S et al (2019) Linking genes with ecological strategies in Arabidopsis thaliana. J Exp Bot 70:1141–1151

    Article  CAS  PubMed  Google Scholar 

  6. Hoffman MH (2002) Biogeography of Arabidopsis thaliana (L.) Heynh. (Brassicaceae). J Biogeogr 29:125–134

    Article  Google Scholar 

  7. Brennan AC, Mendez-Vigo B, Haddioui A et al (2014) The genetic structure of Arabidopsis thaliana in the South-Western Mediterranean range reveals a shared history between North Africa and southern Europe. BMC Plant Biol 14:17

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Kasulin L, Rowan BA, Leon RJC et al (2017) A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina. Mol Ecol 26:3389–3404

    Article  CAS  PubMed  Google Scholar 

  9. Mandáková T, Thorbjörnsson H, Pisupati R et al (2017) Icelandic accession of Arabidopsis thaliana confirmed with cytogenetic markers and its origin inferred from whole-genome sequencing. Icel Agric Sci 30:29–38

    Article  Google Scholar 

  10. Exposito-Alonso M, Becker C, Schuenemann VJ et al (2018) The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genet 14(2):e1007155

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Alonso-Blanco C, Koornneef M, van Ooijen JW (2006) QTL analysis. In: Salinas J, Sanchez-Serrano JJ (eds) Arabidopsis protocols, 2nd edn. Humana Press, Totowa

    Google Scholar 

  12. Wijnen CL, Keurentjes JJ (2014) Genetic resources for quantitative trait analysis: novelty and efficiency in design from an Arabidopsis perspective. Curr Opin Plant Biol 18:103–109

    Article  CAS  PubMed  Google Scholar 

  13. Bazakos C, Hanemian M, Trontin C et al (2017) New strategies and tools in quantitative genetics: how to go from the phenotype to the genotype. Annu Rev Plant Biol 68:435–455

    Article  CAS  PubMed  Google Scholar 

  14. Alonso-Blanco C, Aarts MG, Bentsink L et al (2009) What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21:1877–1896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Alonso-Blanco C, Mendez-Vigo B (2014) Genetic architecture of naturally occurring quantitative traits in plants: an updated synthesis. Curr Opin Plant Biol 18:37–43

    Article  PubMed  Google Scholar 

  16. Martin A, Orgogozo V (2013) The loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution 67:1235–1250

    CAS  PubMed  Google Scholar 

  17. Barboza L, Effgen S, Alonso-Blanco C et al (2013) Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley. Proc Natl Acad Sci U S A 110:15818–15823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Durvasula A, Fulgione A, Gutaker RM et al (2017) African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 114:5213–5218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Fulgione A, Koornneef M, Roux F et al (2017) Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia. Mol Biol Evol 35:564–574

    Article  PubMed Central  CAS  Google Scholar 

  20. Zou YP, Hou XH, Wu Q et al (2017) Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol 18:239

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Hsu CW, Lo CY, Lee CR (2019) On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East. New Phytol 222:1447–1457

    Article  CAS  PubMed  Google Scholar 

  22. 1001 Genomes Consortium Group (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166:481–491

    Article  CAS  Google Scholar 

  23. Lee CR, Svardal H, Farlow A et al (2017) On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Commun 8:14458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Wilczek AM, Roe JL, Knapp MC et al (2009) Effects of genetic perturbation on seasonal life history plasticity. Science 323:930–934

    Article  CAS  PubMed  Google Scholar 

  25. Chiang GC, Barua D, Dittmar E et al (2013) Pleiotropy in the wild: the dormancy gene DOG1 exerts cascading control on life cycles. Evolution 67:883–893

    Article  CAS  PubMed  Google Scholar 

  26. Kerdaffrec E, Filiault DL, Korte A et al (2016) Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis. elife 5:e22502

    Article  PubMed  PubMed Central  Google Scholar 

  27. Kerwin RE, Feusier J, Muok A et al (2017) Epistasis x environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field. New Phytol 215:1249–1263

    Article  CAS  PubMed  Google Scholar 

  28. Malmberg RL, Held S, Waits A et al (2005) Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and in the greenhouse. Genetics 171:2013–2027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Brachi B, Faure N, Horton M et al (2010) Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 6:e1000940

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Oakley CG, Agren J, Atchison RA et al (2014) QTL mapping of freezing tolerance: links to fitness and adaptive trade-offs. Mol Ecol 23:4304–4315

    Article  PubMed  Google Scholar 

  31. Postma FM, Agren J (2016) Early life stages contribute strongly to local adaptation in Arabidopsis thaliana. Proc Natl Acad Sci U S A 113:7590–7595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Price N, Moyers BT, Lopez L et al (2018) Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana. Proc Natl Acad Sci U S A 115:5028–5033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hepworth J, Antoniou-Kourounioti RL, Bloomer RH et al (2018) Absence of warmth permits epigenetic memory of winter in Arabidopsis. Nat Commun 9:639

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Fournier-Level A, Korte A, Cooper MD et al (2011) A map of local adaptation in Arabidopsis thaliana. Science 334:86–89

    Article  CAS  PubMed  Google Scholar 

  35. Mendez-Vigo B, Gomaa NH, Alonso-Blanco C et al (2013) Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions. New Phytol 197:1332–1343

    Article  CAS  PubMed  Google Scholar 

  36. Wilczek AM, Cooper MD, Korves TM et al (2014) Lagging adaptation to warming climate in Arabidopsis thaliana. Proc Natl Acad Sci U S A 111:7906–7913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hu J, Lei L, de Meaux J (2017) Temporal fitness fluctuations in experimental Arabidopsis thaliana populations. PLoS One 12:e0178990

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Taylor MA, Cooper MD, Sellamuthu R et al (2017) Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field. New Phytol 216:291–302

    Article  CAS  PubMed  Google Scholar 

  39. Exposito-Alonso M, Brennan AC, Alonso-Blanco C et al (2018) Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana. Evolution 72:157–1586

    Article  Google Scholar 

  40. Frachon L, Libourel C, Villoutreix R et al (2017) Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nat Ecol Evol 1:1551–1561

    Article  PubMed  Google Scholar 

  41. Gomez R, Mendez-Vigo B, Marcer A et al (2018) Quantifying temporal change in plant population attributes: insights from a resurrection approach. AoB Plants 10:ply063

    Article  PubMed  PubMed Central  Google Scholar 

  42. Kawakatsu T, Huang SC, Jupe F et al (2016) Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166:492–505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Togninalli M, Seren U, Meng D et al (2017) The AraGWAS catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. Nucleic Acids Res 46:D1150–D1156

    Article  PubMed Central  CAS  Google Scholar 

  44. Seren U, Vilhjalmsson BJ, Horton MW et al (2012) GWAPP: a web application for genome-wide association mapping in Arabidopsis. Plant Cell 24:4793–4805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Grimm DG, Roqueiro D, Salome PA et al (2017) easyGWAS: a cloud-based platform for comparing the results of genome-wide association studies. Plant Cell 29:5–19

    Article  CAS  PubMed  Google Scholar 

  46. Seren U, Grimm D, Fitz J, Weigel D, Nordborg M, Borgwardt K, Korte A (2017) AraPheno: a public database for Arabidopsis thaliana phenotypes. Nucleic Acids Res 45:D1054–D1059

    Article  CAS  PubMed  Google Scholar 

  47. Bradbury PJ, Zhang Z, Kroon DE et al (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  48. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC et al (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34:3299–3302

    Article  CAS  PubMed  Google Scholar 

  49. Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Leigh J, Bryant D (2015) PopART: full-feature software for haplotype network construction. Methods Ecol Evol 6:1110–1116

    Article  Google Scholar 

  51. Goodstein DM, Shu S, Howson R et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186

    Article  CAS  PubMed  Google Scholar 

  52. Madeira F, Park YM, Lee J et al (2019) The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 47:W636–W641. https://doi.org/10.1093/nar/gkz268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Nicholas KB, Nicholas HBJ, Deerfield DW (1997) GeneDoc: analysis and visualization of genetic variation. EMBNETWNEWS 4:1–4

    Google Scholar 

  54. Wang Y, Lu J, Yu J et al (2013) An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res 23:833–842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Ferrero-Serrano A, Assmann SM (2019) Phenotypic and genome-wide association with the local environment of Arabidopsis. Nat Ecol Evol 3:274–285

    Article  PubMed  Google Scholar 

  57. Frichot E, Schoville SD, Bouchard G et al (2013) Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol 30:1687–1699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Gunther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195:205–220

    Article  PubMed  PubMed Central  Google Scholar 

  59. Rangel TF, Diniz-Filho JAF, Bini LM (2010) SAM: a comprehensive application for spatial analysis in macroecology. Ecography 33:46–50

    Article  Google Scholar 

  60. Nordborg M, Hu TT, Ishino Y et al (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:e196

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  61. Clewer AG, Scarisbrick DH (2008) Practical statistics and experimental design for plant and crop science. John Wiley & Sons Ltd, West Sussex

    Google Scholar 

  62. Picó FX (2012) Demographic fate of Arabidopsis thaliana cohorts of autumn- and spring-germinated plants along an altitudinal gradient. J Ecol 100:1009–1018

    Article  Google Scholar 

  63. Duncan S, Holm S, Questa J et al (2015) Seasonal shift in timing of vernalization as an adaptation to extreme winter. elife 4:e06620

    Article  PubMed Central  Google Scholar 

  64. Donohue K (2009) Completing the cycle: maternal effects as the missing link in plant life histories. Philos Trans R Soc B 364:1059–1074

    Article  CAS  Google Scholar 

  65. Alonso-Blanco C, Blankestijn-de Vries H, Hanhart CJ et al (1999) Natural allelic variation at seed size loci in relation to other life history traits of Arabidopsis thaliana. Proc Natl Acad Sci U S A 96:4710–4717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Busoms S, Paajanen P, Marburger S et al (2018) Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana. Proc Natl Acad Sci U S A 115:E12443–E12452

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Exposito-Alonso M, Vasseur F, Ding W et al (2018) Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Nat Ecol Evol 2:352–358

    Article  PubMed  Google Scholar 

  68. Postma FM, Agren J (2018) Among-year variation in selection during early life stages and the genetic basis of fitness in Arabidopsis thaliana. Mol Ecol 27:2498–2511

    Article  CAS  PubMed  Google Scholar 

  69. Gomaa NH, Montesinos-Navarro A, Alonso-Blanco C et al (2011) Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations. Mol Ecol 20:3540–3554

    PubMed  Google Scholar 

  70. Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290

    Article  CAS  PubMed  Google Scholar 

  71. Kuittinen H, Salguero D, Aguade M (2002) Parallel patterns of sequence variation within and between populations at three loci of Arabidopsis thaliana. Mol Biol Evol 19:2030–2034

    Article  CAS  PubMed  Google Scholar 

  72. Manzano-Piedras E, Marcer A, Alonso-Blanco C et al (2014) Deciphering the adjustment between environment and life history in annuals: lessons from a geographically-explicit approach in Arabidopsis thaliana. PLoS One 9(2):e87836

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Sokal RR, Oden NL (1978) Spatial autocorrelation in biology 1. Methodology. Biol J Linn Soc 10:199–228

    Article  Google Scholar 

  74. Manel S, Joost S, Epperson BK et al (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol Ecol 19:3760–3772

    Article  CAS  PubMed  Google Scholar 

  75. Tabas-Madrid D, Mendez-Vigo B, Arteaga N et al (2018) Genome-wide signatures of flowering adaptation to climate temperature: regional analyses in a highly diverse native range of Arabidopsis thaliana. Plant Cell Environ 41:1806–1820

    Article  CAS  PubMed  Google Scholar 

  76. François O, Martins H, Caye K et al (2016) Controlling false discoveries in genome scans for selection. Mol Ecol 25:454–469

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

C.A.-B. and F.X.P. laboratories have been funded by grants BIO2016-75754-P and CGL2016-77720-P (AEI/FEDER, UE), respectively.

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Authors and Affiliations

  1. Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain

    Carlos Alonso-Blanco & Belén Méndez-Vigo

  2. Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain

    F. Xavier Picó

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  1. Carlos Alonso-Blanco
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  2. Belén Méndez-Vigo
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  3. F. Xavier Picó
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Correspondence to Carlos Alonso-Blanco .

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Editors and Affiliations

  1. Centro Nacional de Biotecnología, CSIC Centro Nacional de Biotecnología, Madrid, Spain

    Jose J. Sanchez-Serrano

  2. Centro de Investigaciones Biologicas, CSIC Madrid Centro de Investigaciones Biologicas, Madrid, Spain

    Julio Salinas

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Alonso-Blanco, C., Méndez-Vigo, B., Xavier Picó, F. (2021). Analyses of Natural Variation: Field Experiments and Nucleotide Diversity for Your Favorite Gene. In: Sanchez-Serrano, J.J., Salinas, J. (eds) Arabidopsis Protocols . Methods in Molecular Biology, vol 2200. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0880-7_3

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  • DOI: https://doi.org/10.1007/978-1-0716-0880-7_3

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  • Online ISBN: 978-1-0716-0880-7

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