Abstract
Genome-wide association studies (GWAS) are an effective method for investigating the genetics of natural phenotypic variation in many different model organisms.
Here we present GWA-Portal, an interactive web application that enables researchers to upload their phenotypes and easily carry out GWAS directly in the browser. We will present all the steps needed—from uploading the phenotype to interpreting the results—using a published root phenotype.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, TT H, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis Thaliana inbred lines. Nature 465(7298):627–631. https://doi.org/10.1038/nature08800
Brachi B, Morris GP, Borevitz JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12(10):232. https://doi.org/10.1186/gb-2011-12-10-232
Todesco M, Balasubramanian S, TT H, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RA, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D (2010) Natural allelic variation underlying a major fitness trade-off in Arabidopsis Thaliana. Nature 465(7298):632–636. https://doi.org/10.1038/nature09083
Genomes Consortium. Electronic address mngoaa, Genomes C (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis Thaliana. Cell 166(2):481–491. https://doi.org/10.1016/j.cell.2016.05.063
Seren U, Vilhjalmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M (2012) GWAPP: a web application for genome-wide association mapping in Arabidopsis. Plant Cell 24(12):4793–4805. https://doi.org/10.1105/tpc.112.108068
Meijon M, Satbhai SB, Tsuchimatsu T, Busch W (2014) Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis. Nat Genet 46(1):77–81. https://doi.org/10.1038/ng.2824
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjalmsson BJ, Nordborg M, Borevitz JO, Bergelson J (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis Thaliana accessions from the RegMap panel. Nat Genet 44(2):212–216. https://doi.org/10.1038/ng.1042
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjalmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandakova T, Lysak MA, Seren U, Hellmann I, Nordborg M (2013) Massive genomic variation and strong selection in Arabidopsis Thaliana lines from Sweden. Nat Genet 45(8):884–890. https://doi.org/10.1038/ng.2678
Box GEP, Cox DR (1964) An analysis of transformations. J R Stat Soc Series 26(2):211–252
Wilcoxon F (1946) Individual comparisons of grouped data by ranking methods. J Econ Entomol 39:269
Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42(4):348–354. https://doi.org/10.1038/ng.548
Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42(4):355–360. https://doi.org/10.1038/ng.546
Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178(3):1709–1723. https://doi.org/10.1534/genetics.107.080101
Cwiek-Kupczynska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone SA, Scholz U, van Schriek M, Seren U, Usadel B, Weise S, Kersey P, Krajewski P (2016) Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods 12:44. https://doi.org/10.1186/s13007-016-0144-4
Korte A, Farlow A (2013) The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9:29. https://doi.org/10.1186/1746-4811-9-29
Vilhjalmsson BJ, Nordborg M (2013) The nature of confounding in genome-wide association studies. Nat Rev Genet 14(1):1–2. https://doi.org/10.1038/nrg3382
Platt A, Vilhjalmsson BJ, Nordborg M (2010) Conditions under which genome-wide association studies will be positively misleading. Genetics 186(3):1045–1052. https://doi.org/10.1534/genetics.110.121665
Acknowledgment
GWA-Portal was developed in the course of the transPLANT project, which was funded by the European Commission within its 7th Framework Programme, under the thematic area “Infrastructures,” contract number 283496.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
1 Electronic Supplementary Material
(MP4 220755 kb)
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Seren, Ü. (2018). GWA-Portal: Genome-Wide Association Studies Made Easy. In: Ristova, D., Barbez, E. (eds) Root Development. Methods in Molecular Biology, vol 1761. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7747-5_22
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7747-5_22
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7746-8
Online ISBN: 978-1-4939-7747-5
eBook Packages: Springer Protocols