Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

Abstract

BackgroundStarch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in starch metabolism and their genome organization in potato plants is still missing. Moreover, mechanisms regulating the expression of starch genes in leaves and tubers remain elusive with regard to differences between transitory and storage starch metabolism, respectively. This study aimed at identifying and mapping the complete set of potato starch genes, and to study their expression pattern in leaves and tubers using different sets of transcriptome data. Moreover, we wanted to uncover transcription factors co-regulated with starch accumulation in tubers in order to get insight into the regulation of starch metabolism.ResultsWe identified 77 genomic loci encoding enzymes involved in starch metabolism. Novel isoforms of many enzymes were found. Their analysis will help to elucidate mechanisms of starch biosynthesis and degradation. Expression analysis of starch genes led to the identification of tissue-specific isoenzymes suggesting differences in the transcriptional regulation of starch metabolism between potato leaf and tuber tissues. Selection of genes predominantly expressed in developing potato tubers and exhibiting an expression pattern indicative for a role in starch biosynthesis enabled the identification of possible transcriptional regulators of tuber starch biosynthesis by co-expression analysis.ConclusionsThis study provides the annotation of the complete set of starch metabolic genes in potato plants and their genomic localizations. Novel, so far undescribed, enzyme isoforms were revealed. Comparative transcriptome analysis enabled the identification of tuber- and leaf-specific isoforms of starch genes. This finding suggests distinct regulatory mechanisms in transitory and storage starch metabolism. Putative regulatory proteins of starch biosynthesis in potato tubers have been identified by co-expression and their expression was verified by quantitative RT-PCR.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3381-z) contains supplementary material, which is available to authorized users.

Deciphering source and sink responses of potato plants (Solanum tuberosum L.) to elevated temperatures

“…Previously, SuSy was identified as a major determinant of tuber sink strength and starch accumulation (Baroja‐Fernández et al, ; Zrenner et al, ). Our microarray data indicated a lower expression (but not more than twofold) of StSuSy4, the main isoform in tubers (Fu & Park, ; Van Harsselaar et al, ), under all stress conditions. Quantitative PCR with StSuSy4‐ specific primers confirmed that StSuSy4 expression clearly decreased in tubers grown under elevated temperatures (heat and heat plate) while cooling the root space attenuated the effect (Figure b).…”

“…Because the accumulation of transitory starch was clearly decreased in leaves grown under heat conditions (Figure c), expression profiles of starch genes as described by Van Harsselaar, Lorenz, Senning, Sonnewald, and Sonnewald () were analysed (Table S7). Expression of important starch biosynthetic genes, such as ADP‐glucose pyrophosphorylase large subunits 1 and 3 ( StAPL1 , StAPL3 ), granule‐bound starch synthase 1 ( StGBSS1 ), or starch branching enzyme 3 ( StSBE3 ), was clearly reduced under heat and cold plate conditions suggesting that starch biosynthesis was hampered by elevated temperatures (Figure d).…”

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 Solanum Tuberosum Knowledge Base: The Section on Molecular-Genetic Regulation of Metabolic Pathways

“…Ветвление амилопектина осуществляет ветвящий фермент SBE (starch-branching enzyme, EC 2.4.1.18), который отщепляет от неразветвлен-ной цепочки фрагмент и переносит его к шестому атому углерода глюкозы (Zhang et al, 2017). Путь биосинтеза крахмала описан во многих источниках, в то время как регуляция этого процесса до сих пор остается малоизу-ченной (Van Harsselaar et al, 2017).…”

“…Так, например, на сети по-казана активация аденозиндифосфат-глюкоза-пирофос-форилазы белком NADP-зависимой тиоредоксинредукта-зой C (NTR3), которая приводит к накоплению крахмала (Jenner et al, 2001;Michalska et al, 2009;Geigenberger, 2011). Известно, что экспрессия генов LOB, TIFY5a и WRKY4 положительно коррелирует с экспрессией генов SuSy4 и GPT2.1 (Van Harsselaar et al, 2017). На рис.…”