title: Protocol: a method to study the direct reprogramming of lateral root primordia to fertile shoots.
abstract: BACKGROUND
  Plants have the remarkable property to elaborate entire body plan from any tissue part. The conversion of lateral root primordium (LRP) to shoot is an ideal method for plant propagation and for plant researchers to understand the mechanism underlying trans-differentiation. Until now, however, a robust method that allows the efficient conversion of LRP to shoot is lacking. This has limited our ability to study the dynamic phases of reprogramming at cellular and molecular levels.
  
  
  RESULTS
  Here we present an efficient protocol for the direct conversion of LRP to a complete fertile shoot system. This protocol can be readily applied to the various ecotypes of Arabidopsis. We show that, the conversion process is highly responsive to developmental stages of LRP and changes in external environmental stimuli such as temperature. The entire conversion process can be adequately analyzed by histological and imaging techniques. As a demonstration, using a battery of cell fate specific markers, we show that confocal time-lapse imaging can be employed to uncover the early molecular events, intermediate developmental phases and relative abundance of stem cell regulators during the conversion of LRP to shoot.
  
  
  CONCLUSIONS
  Our method is highly efficient, independent of genotypes tested and suitable to study the reprogramming of LRP to shoot in intact plants as well as in excised roots.
authors.affiliation: School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016 India.
authors.forename: Abdul
authors.initials: A
authors.lastname: Kareem
authors.affiliation: School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016 India.
authors.forename: Dhanya
authors.initials: D
authors.lastname: Radhakrishnan
authors.affiliation: Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.|Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016 India.
authors.forename: Subhikshaa
authors.initials: S
authors.lastname: Bagavathiappan
authors.affiliation: School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016 India.
authors.forename: Zankhana B
authors.initials: ZB
authors.lastname: Trivedi
authors.affiliation: Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510 Japan.
authors.forename: Kaoru
authors.initials: K
authors.lastname: Sugimoto
authors.affiliation: Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543 Singapore.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.|Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Ari Pekka
authors.initials: AP
authors.lastname: Mähönen
authors.affiliation: School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016 India.
authors.forename: Kalika
authors.initials: K
authors.lastname: Prasad
keywords: Arabidopsis; Auxin; Cytokinin; Lateral root; Regeneration; Shoot; Trans-differentiation