Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis

Abstract

BackgroundEven though the process of potato tuber starch biosynthesis is well understood, mechanisms regulating biosynthesis are still unclear. Transcriptome analysis provides valuable information as to how genes are regulated. Therefore, this work aimed at investigating transcriptional regulation of starch biosynthetic genes in leaves and tubers of potato plants under various conditions. More specifically we looked at gene expression diurnally in leaves and tubers, during tuber induction and in tubers growing at different velocities. To determine velocity of potato tuber growth a new method based on X-ray Computed Tomography (X-ray CT) was established.ResultsComparative transcriptome analysis between leaves and tubers revealed striking similarities with the same genes being differentially expressed in both tissues. In tubers, oscillation of granule bound starch synthase (GBSS) expression) was observed which could be linked to sucrose supply from source leaves. X-ray CT was used to determine time-dependent changes in tuber volume and the growth velocity was calculated. Although there is not a linear correlation between growth velocity and expression of starch biosynthetic genes, there are significant differences between growing and non-growing tubers. Co-expression analysis was used to identify transcription factors positively correlating with starch biosynthetic genes possibly regulating starch biosynthesis.ConclusionMost starch biosynthetic enzymes are encoded by gene families. Co-expression analysis revealed that the same members of these gene families are co-regulated in leaves and tubers. This suggests that regulation of transitory and storage starch biosynthesis in leaves and tubers, respectively, is surprisingly similar. X-ray CT can be used to monitor growth and development of belowground organs and allows to link tuber growth to changes in gene expression. Comparative transcriptome analysis provides a useful tool to identify transcription factors possibly involved in the regulation of starch biosynthesis.

AtHsp70‐15‐deficient Arabidopsis plants are characterized by reduced growth, a constitutive cytosolic protein response and enhanced resistance to TuMV

“…Microarray analysis of purified RNA was performed as described previously (Ferreira et al, 2010) on a Agilent Technologies platform using Agilent Arabidopsis V4 (Design number 21169) microarray chips (http://www.agilent.com). For RNA extraction, amiRNAAtHsp70-14/15 line 4, hsp70-14 knockout, hsp70-15 knockout and wild-type Col-0 plants were grown without BASTA selection in a randomized arrangement under normal conditions, and fully expanded leaves of 6-week-old plants were harvested at midday in pools of 10 individuals per line (four replicates each).…”

Regulation of potato tuber sprouting

“…The bulk of tuber tissue is subsequently formed by cell expansion, randomly oriented cell division (Jackson 1999) and massive deposition of C-and N-assimilates such as starch and storage proteins (Visser et al 1994;Appeldoorn et al 1999), making the tuber a strong storage sink (Fernie and Willmitzer 2001). Tuber development is regulated by an interplay between endogenous and environmental signals and is orchestrated by coordinated transcriptional and metabolic changes (Kloosterman et al 2005(Kloosterman et al , 2008Ferreira et al 2010). The process was shown to be controlled by phytohormones including gibberellins (GAs), auxin and strigolactones (SLs) (Carrera et al 2000;Kloosterman et al 2007;Roumeliotis et al 2012;Pasare et al 2013).…”

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

“…Here, images are primarily acquired in vivo allowing to scan the same nest or colony several times during its developmental cycle (Eyer, Neumann, & Dietemann, 2016; Greco, Bell, Spooner‐Hart, & Holford, 2006; Greco, Spooner‐Hart, Beattie, Barchia, & Holford, 2011; Greco, Spooner‐Hart, & Holford, 2005; Rademacher, Fahlberg, Raddatz, Schneider, & Voigt, 2013). X‐ray CT has also proven to be a valuable tool for assessing processes in samples that do not allow direct visual evaluation without disturbing the organisms, such as parasitic relationships (Diez, Orensanz, Márquez, & Cremonte, 2013; Schwabe, Holtheuer, & Schories, 2014), seed‐feeding insects (Tarver et al., 2006), and growth strategies of animals (Cantin, Cohen, Karnauskas, Tarrant, & McCorkle, 2010; Fujiwara, Oji, Tanaka, & Kondo, 2005; Schönberg, 2001; Silbiger, Guadayol, Thomas, & Donahue, 2016), fungi (Van den Bulcke, Boone, Van Acker, & Van Hoorebeke, 2009), and plants (Dhondt et al., 2010; Ferreira et al., 2010; Gregory et al., 2003; Mairhofer et al., 2012; Mooney, Morris, & Berry, 2006; Perret, Al‐Belushi, & Deadman, 2007). …”