Day length dependent restructuring of the leaf transcriptome and metabolome in potato genotypes with contrasting tuberization phenotypes

Abstract

Recent advances have defined some of the components of photoperiodic signalling that lead to tuberization in potato including orthologues of FLOWERING LOCUS T (StSP6A) and CYCLING DOF FACTOR (StCDF1). The aim of the current study is to investigate the molecular basis of permissive tuber initiation under long days in Solanum tuberosum Neo-Tuberosum by comparative analysis with an obligate short-day S. tuberosum ssp. Andigena accession. We show that the Neo-Tuberosum accession, but not the Andigena, contains alleles that encode StCDF1 proteins modified in the C-terminal region, likely to evade long day inhibition of StSP6A expression. We also identify an allele of StSP6A from the Neo-Tuberosum accession, absent in the Andigena, which is expressed under long days. Other leaf transcripts and metabolites that show different abundances in tuberizing and non-tuberizing samples were identified adding detail to tuberization-associated processes. Overall, the data presented in this study highlight the subtle interplay between components of the clock-CONSTANS-StSP6A axis which collectively may interact to fine-tune the timing of tuberization.

The Multiple Signals That Control Tuber Formation

“…Overexpression of the early-maturing/ tuberizing StCDF1.2 gene variant in the photoperioddependent potato subspecies andigena produced tubers under noninductive LD and also resulted in early tuber formation in a late-maturing line (Kloosterman et al, 2013). Consistent with these results, Morris et al (2014) reported that a Neo-Tuberosum accession adapted to tuberization in LD, but not the andigena subspecies, contained an allele that encoded for a truncated StCDF1 protein modified in the C-terminal region (similar to StCDF1.2). These genetic analyses confirm an important role of StCDF1 in controlling the timing of tuber formation.…”

The Potato Genome

“…As of March, 2017, the original publication of the DM sequence has been cited more than 500 times, providing a framework for studies of gene families (Charfeddine et al 2015;Gao et al 2016;Ma et al 2016;Schreiber et al 2014;Seo et al 2016;Tang et al 2016;Van Harsselaar et al 2017), a scaffold for alignment of transcriptomic data (Campbell et al 2014;Gong et al 2015;Goyer et al 2015;Liu et al 2015;Morris et al 2014;Tang et al 2014) or a reference genome against which to discover genomic variation (Hardigan et al 2016), to cite just a few. As sequencing platforms improve, the DM assembly will likely be supplanted by that of a more robust commercial potato line.…”

The MORPH‐R web server and software tool for predicting missing genes in biological pathways

“…We have integrated potato gene expression data from over 20 studies based on the Agilent JHI Solanum tuberosum 60 k v1 microarray (ArrayExpress ID: E‐MTAB‐1655) processed at the James Hutton Institute using standard Agilent recommended methodologies (Hancock et al ). The studies included 326 conditions derived from the following treatments: moderate heat‐stress (Hancock et al ), short‐ and long‐day growth regimes (Morris et al ), bruising (unpublished data), phosphorous growth regimes (unpublished data), acidity, Phytopthora infestans infection (Ali et al ) and β‐aminobutyric acid (BABA) (Bengtsson et al ), phosphite, abscisic acid (ABA), brassinosteroid and salicylic acid (SA) treatments (unpublished data). Different potato accessions and tissues (tuber, stem and leaf) were included.…”