Project description:Potato (Solanum tuberosum L) is a natural host of Potato spindle tuber viroid (PSTVd) which can cause characteristic symptoms on developing plants including stunting phenotype and distortion of leaves and tubers. PSTVd is the type species of the family Pospiviroidae, it can replicate in the nucleus and the viroid RNA moves systemically in infected plants. Its KF440-2 strain can cause severe symptoms in potato. It is not well understood how the viroid can affect host genes for successful invasion and which genes show altered expression levels upon infection. In this study, we used a high-scale method to identify differentially expressed genes in potato. We have identified defence, stress and sugar metabolism related genes having altered expression levels upon infection. Additionally, hormone pathways connected genes showed up- or down-regulation. Our primary focus is on the identification of genes which can affect tuber formation as the viroid infection can strongly influence tuber development, especially tuber shape is affected. DWARF1/DIMINUTO, Gibberellin 7-oxidase and BEL5 protein were identified and validated which showed differential expression in viroid infected tissues suggesting that gibberellin and brassinosteroid pathways have a possible role in tuber development upon PSTVd infection.
Project description:Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economical importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still a lot to learn about this complex phenotype. Here, we used genotype by sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis for tuber bruising. In addition, we collected transcriptomics data to enrich the GWAS results, by performing a differential expression analysis between samples with high- and low-bruising susceptibility.
Project description:For many potato cultivars, tuber yield is optimal at average day time temperatures in the range of 14-22 ⁰C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. In our previous work we observed that the steady-state expression level of the core circadian clock gene, TIMING OF CAB EXPRESSION 1 (TOC1), in potato tubers increased at moderately elevated temperature, whereas expression of the tuberisation signal gene StSP6A decreased along with tuber yield. In this study we investigated the potential roles of StTOC1 in linking environmental signalling and potato tuberisation. We show that transgenic lines with decreased expression of StTOC1 exhibit enhanced StSP6A transcript levels in tuberising stolons, and show changes in gene expression consistent with elevated tuber sink strength.
Project description:Effects of different parameters on the transcriptome in potato tuber: effect of infection with potato virus Y (PVY) on potato tubers, effects of two different storage times of potato tubers compared to no storage, effect of different storage temperature on potato tubers, effect of tuber necrosis development, effects of interactions between the above parameters. Lists of interaction factors and the differentially-expressed genes associated with each factor are provided as a series of Additional Files to this submission (see http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1071).
