Abstract
Root growth architecture is a major determinant of agricultural productivity and plant fitness in natural ecosystems. Here we describe the methods used in a Quantitative Trait Loci (QTL) study that allowed the identification of ORGANIC CATION TRANSPORTER 1 (OCT1) as a determinant of root growth response to cadaverine treatment in Arabidopsis thaliana. This protocol screens natural accessions to characterize the variation in root growth response to the naturally occurring polyamine cadaverine, then uses recombination mapping to identify loci that are responsible for the variation existing between two accessions with contrasting phenotypes.
Key words
This is a preview of subscription content, log in via an institution.
References
Li J, Mu J, Bai J et al (2013) PARAQUAT RESISTANT1, a golgi-localized putative transporter protein, is involved in intracellular transport of paraquat. Annu Rev Plant Physiol 162:470–483. doi:10.1104/pp.113.213892
Strohm AK, Vaughn LM, Masson PH (2015) Natural variation in the expression of ORGANIC CATION TRANSPORTER 1 affects root length responses to cadaverine in Arabidopsis. J Exp Bot 66:853–862. doi:10.1093/jxb/eru444
Meijón M, Satbhai SB, Tsuchimatsu T, Busch W (2013) Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis. Nature 46:77–81. doi:10.1038/ng.2824
Jancewicz AL, Gibbs NM, Masson PH (2016) Cadaverine’s functional role in plant development and environmental response. Front Plant Sci 7:1237. doi:10.1248/cpb.48.1458
Blanco CA, Peeters A, Koornneef M (1998) Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J 14:259–271. doi:10.1046/j.1365-313x.1998.00115.x
Linsmaier EM, Skoog F (1965) Organic growth factor requirements of tobacco tissue cultures. Physiol Plant 18:100–127. doi:10.1111/j.1399-3054.1965.tb06874.x
Clark KA, Krysan PJ (2007) Protocol: an improved high-throughput method for generating tissue samples in 96-well format for plant genotyping (Ice-Cap 2.0). Plant Methods 3:8. doi:10.1186/1746-4811-3-8
Roy R, Bassham DC (2014) Root growth movements: waving and skewing. Plant Sci 221-222:42–47. doi:10.1016/j.plantsci.2014.01.007
Rutherford R, Gallois P, Masson PH (1998) Mutations inArabidopsis thalianagenes involved in the tryptophan biosynthesis pathway affect root waving on tilted agar surfaces. Plant J 16:145–154. doi:10.1046/j.1365-313x.1998.00279.x
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675. doi:10.1038/nmeth.2089
Meijering E, Jacob M, Sarria JCF et al (2004) Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry 58A:167–176. doi:10.1002/cyto.a.20022
Grabov A, Ashley MK, Rigas S et al (2004) Morphometric analysis of root shape. New Phytol 165:641–652. doi:10.1111/j.1469-8137.2004.01258.x
Vaughn LM, Masson PH (2011) A QTL study for regions contributing to arabidopsis thaliana root skewing on tilted surfaces. G3 1:105–115. doi:10.1534/g3.111.000331
R Core Team (2013). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.URL
Gross J, Ligge U ((2015)) nortest:Tests for normality. R package version 1.0–4 URL https://CRAN.R-project.org/package=nortest
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890. doi:10.1093/bioinformatics/btg112
Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl. Stat Biol Health doi: 10.1007/978-0-387-92125-9
Jiang W, Zhou H, Bi H et al (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:e188–e188. doi:10.1093/nar/gkt780
Czechowski T, Stitt M, Altmann T et al (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Annu Rev Plant Physiol 139:5–17. doi:10.1104/pp.105.063743
Visscher AM, Paul A-L, Kirst M et al (2010) Growth performance and root transcriptome remodeling of arabidopsis in response to mars-like levels of magnesium sulfate. PLoS One 5:e12348–e12316. doi:10.1371/journal.pone.0012348
Clark KA, Krysan PJ (2010) Chromosomal translocations are a common phenomenon in Arabidopsis thaliana T-DNA insertion lines. Plant J 64:990–1001. doi:10.1111/j.1365-313x.2010.04386.x
Salisbury FJ, Hall A, Grierson CS, Halliday KJ (2007) Phytochrome coordinates Arabidopsis shoot and root development. Plant J 50:429–438. doi:10.1111/j.1365-313x.2007.03059.x
Zhang K-X, Xu H-H, Yuan T-T et al (2013) Blue-light-induced PIN3 polarization for root negative phototropic response in Arabidopsis. Plant J 76(2):308–321. doi:10.1111/tpj.12298
Buer CS, Wasteneys GO, Masle J (2003) Ethylene modulates root-wave responses in Arabidopsis. Annu Rev Plant Physiol 132:1085–1096. doi:10.1104/pp.102.019182
Buer CS (2006) Ethylene modulates flavonoid accumulation and gravitropic responses in roots of arabidopsis. Annu Rev Plant Physiol 140:1384–1396. doi:10.1104/pp.105.075671
Pound MP, French AP, Atkinson JA et al (2013) RootNav: navigating images of complex root architectures. Annu Rev Plant Physiol 162:1802–1814. doi:10.1104/pp.113.221531
Russino A (2013) A novel tracking tool for the analysis of plant-root tip movements. Bioinspir Biomim 8(2):025004. doi:10.1088/1748-3190/12/1/015001
Slovak R, Göschl C, Su X et al (2014) A scalable open-source pipeline for large-scale root phenotyping of arabidopsis. Plant Cell 26:2390–2403. doi:10.1105/tpc.114.124032
Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. doi:10.1111/tpj.12105
Lim J-H, Yang H-J, Jung K-H et al (2014) Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice. Mol Cells 37:149–160. doi:10.14348/molcells.2014.2336
Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report. Third Edition (Beta Distribution 3B). http://home.cc.umanitoba.ca/~psgendb/birchhomedir/doc/mapmaker/mapmaker.tutorial.pdf
Wang S, Basten CJ, Zeng Z-B (2012) Windows QTL Cartographer 2.5. Department of statistics. North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm
Ran FA, Hsu PD, Wright J et al (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8:2281–2308. doi:10.1038/nprot.2013.143
Zhao Y, Zhang C, Liu W et al (2016) An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Nature 6(23890):1–11. doi:10.1038/srep23890
User Bulletin #2 (1997) Relative quantitation of gene expression. Appl Biosyst http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_040980.pdf. Accessed 14 Mar 2017
Acknowledgments
We thank S.-H. Su, A. Jancewicz and A. Strohm for comments, advice, and/or research contribution to the material included in this manuscript. Our work was made possible by grants from the National Science Foundation (IOS-1121694), the National Aeronautics and Space Administration (NNX14AT23G), and the University of Wisconsin–Madison College of Agricultural and Life Sciences Hatch program.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Gibbs, N.M., Rouhana, L.V., Masson, P.H. (2018). Quantitative Trait Loci for Root Growth Response to Cadaverine in Arabidopsis. In: Alcázar, R., Tiburcio, A. (eds) Polyamines. Methods in Molecular Biology, vol 1694. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7398-9_22
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7398-9_22
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7397-2
Online ISBN: 978-1-4939-7398-9
eBook Packages: Springer Protocols