The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato.

In potato, stolon swelling is a complex and highly regulated process, and much more work is needed to fully understand the underlying mechanisms. We identified a novel tuber-specific basic helix-loop-helix (bHLH) transcription factor, StbHLH93, based on the high-resolution transcriptome of potato tuber development. StbHLH93 is predominantly expressed in the subapical and perimedullary region of the stolon and developing tubers. Knockdown of StbHLH93 significantly decreased tuber number and size, resulting from suppression of stolon swelling. Furthermore, we found that StbHLH93 directly binds to the plastid protein import system gene TIC56 promoter, activates its expression, and is involved in proplastid-to-amyloplast development during the stolon-to-tuber transition. Knockdown of the target TIC56 gene resulted in similarly problematic amyloplast biogenesis and tuberization. Taken together, StbHLH93 functions in the differentiation of proplastids to regulate stolon swelling. This study highlights the critical role of proplastid-to-amyloplast interconversion during potato tuberization.

Genome-Wide Analysis of Family-1 UDP-Glycosyltransferases in Potato (Solanum tuberosum L.): Identification, Phylogenetic Analysis and Determination of Response to Osmotic Stress.

Family-1 UDP-glycosyltransferases (UGTs) are the most common and functional glycosyltransferases in the plant world. UGT is closely related to plant growth and the response to abiotic stress. However, despite systematic research, our understanding of potato UGT genes is still unclear. In this study, we identified 174 potato UGT proteins based on their conserved plant secondary product glycosyltransferase (PSPG) motifs. Phylogenetic analyses were used to compare these proteins with Arabidopsis UGTs and other plant UGTs, and it was found that they could be clustered into 18 distinct groups. Patterns of intron gain/loss and intron phases within potato UGTs revealed highly conserved intron insertion events. The promoter cis-elements of these 174 UGT genes were systematically investigated. The promoter regions of these UGT genes are known to contain various classes of cis-acting compounds. These include elements that are light-responsive, phytohormone-responsive, and stress-responsive. Transcriptome data analysis established that 25, 10, 6, and 4 of these 174 UGT genes were specifically expressed in leaves, roots, stolons, and young tubers, respectively. The mannitol-treated transcriptomic data showed thirty-eight UGT genes were significantly upregulated. The quantitative real-time PCR results showed that the four genes were all responsive to osmotic stress under a 10% PEG6000 treatment. The results of our study provide a basis for clarifying the molecular mechanism of potato osmotic stress resistance and better understanding its function in the future.

Genome-Wide Identification and Analysis Uncovers the Potential Role of JAZ and MYC Families in Potato under Abiotic Stress.

As key regulators of the Jasmonates (JAs) signal transduction pathway, JAZ protein, and MYC transcription factors are imperative for plant response to external environmental changes, growth, and development. In this study, 18 StJAZs and 12 StMYCs were identified in potatoes. Their chromosomal position, phylogenetic development, gene structure, and promoter cis-acting parts of the StJAZ genes were analyzed. In addition, Protein-Protein Interaction (PPI) network analysis of StJAZ and StMYC gene families and yeast two-hybrid assay demonstrated that five StMYCs can interact with 16 StJAZs, which provides new insights into the operation mechanism of StJAZs and StMYCs in JA signal response. Moreover, we explored the expression profiles of StJAZs and StMYCs genes in different tissues and during abiotic stresses by RNA-seq data. Based on the PPI network and transcriptome data, the genes StJAZ11, StJAZ16, and StMYC6 were chosen for further qRT-PCR study under salt or mannitol treatment. Under mannitol-induced drought or salinity treatment, the expression patterns of StMYC6, StJAZ11, and StJAZ16 were different, indicating that the JAZ protein and MYC transcription factor may be engaged in the response of potatoes to abiotic stress, which opened up a new research direction for the genetic improvement of potatoes in response to environmental stress.

Analyses of 202 plastid genomes elucidate the phylogeny of Solanum section Petota.

Our paper analyzes full plastid DNA sequence data of 202 wild and cultivated diploid potatoes, Solanum section Petota, to explore its phylogenetic utility compared to prior analyses of the same accessions using genome-wide nuclear SNPs, and plastid DNA restriction site data. The present plastid analysis discovered the same major clades as the nuclear data but with some substantial differences in topology within the clades. The considerably larger plastid and nuclear data sets add phylogenetic resolution within the prior plastid DNA restriction site data, highlight plastid/nuclear incongruence that supports hypotheses of hybridization/introgression to help explain the taxonomic difficulty in the section.

Identification of multiple genes encoding SnRK1 subunits in potato tuber.

BACKGROUND: Many studies have proven the importance of SnRK1 in the regulation of carbohydrate metabolism and plant development. Compared to Arabidopsis, much less is known about SnRK1 complexes in crop plants, and therefore, more work needs to be done to identify SnRK1 genes and to investigate their function in crop plants. METHODS: In this study we identified five SnRK1-related genes in potato by analyzing the potato genome through BLAST, which encode one α-subunit isoform (stKIN), two ß-subunit isoforms (stKINß1 and stKINß2) and two γ-subunit isoforms (stKINγ and stKINßγ). To investigate the functions of SnRK1 in the tuber development of potato, we further made overexpression and RNAi transgenic plants of these five genes. Based on these overexpression transgenic plants, the Fast protein liquid chromatography (FPLC) were employed to purify SnRK1 complexes, which were tracked by western-blot. RESULTS: Experiments in vivo and in vitro showed that these five proteins in potato are functional SNF1/AMPK/SnRK1-related proteins. The SnRK1 activity decreased by 60% in the RNAi transgenic lines of stKIN; the starch content increased by 25% in the overexpression transgenic lines of stKIN, compared to that in the wild-type lines, whereas there is no significant difference in SnRK1 activity and starch content in the RNAi transgenic or overexpression lines of stKINß1, stKINß2, stKINγ and stKINßγ. In addition, we found that a few different SnRK1 complexes are present in potato by partially purifying SnRK1 complexes from these overexpression transgenic plants. CONCLUSIONS: Five functional SnRK1-related genes were identified in potato, including three novel genes, which encode one α-subunit isoform (stKIN), two ß-subunit isoforms (stKINß1 and stKINß2) and two γ-subunit isoforms (stKINγ and stKINßγ). We found that a few SnRK1 related genes are present in potato tuber, which form several different SnRK1 isoenzymes. We found that stKIN is the primary α subunit of SnRK1 in potato tuber and plays important roles in the development of potato tubers.

Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato.

Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota. We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota, including 146 wild and 21 cultivated diploid potato accessions with a broad geographic distribution. Genome-wide genetic variation analysis showed that the diversity of wild potatoes is higher than that of cultivated potatoes, and much higher genetic diversity in the agronomically important disease resistance genes was observed in wild potatoes. Furthermore, by exploiting information about known quantitative trait loci (QTL), we identified 609 genes under selection, including those correlated with the loss of bitterness in tubers and those involved in tuberization, two major domesticated traits of potato. Phylogenetic analyses revealed a north-south division of all species in clade 4, not just those in the S. brevicaule complex, and further supported S. candolleanum as the progenitor of cultivated potato and the monophyletic origin of cultivated potato in southern Peru. In addition, we analyzed the genome of S. candolleanum and identified 529 genes lost in cultivated potato. Collectively, the molecular markers generated in this study provide a valuable resource for the identification of agronomically important genes useful for potato breeding.

Functions of multiple genes encoding ADP-glucose pyrophosphorylase subunits in maize endosperm, embryo, and leaf.

ADP-glucose pyrophosphorylase (AGPase) provides the nucleotide sugar ADP-glucose and thus constitutes the first step in starch biosynthesis. The majority of cereal endosperm AGPase is located in the cytosol with a minor portion in amyloplasts, in contrast to its strictly plastidial location in other species and tissues. To investigate the potential functions of plastidial AGPase in maize (Zea mays) endosperm, six genes encoding AGPase large or small subunits were characterized for gene expression as well as subcellular location and biochemical activity of the encoded proteins. Seven transcripts from these genes accumulate in endosperm, including those from shrunken2 and brittle2 that encode cytosolic AGPase and five candidates that could encode subunits of the plastidial enzyme. The amino termini of these five polypeptides directed the transport of a reporter protein into chloroplasts of leaf protoplasts. All seven proteins exhibited AGPase activity when coexpressed in Escherichia coli with partner subunits. Null mutations were identified in the genes agpsemzm and agpllzm and shown to cause reduced AGPase activity in specific tissues. The functioning of these two genes was necessary for the accumulation of normal starch levels in embryo and leaf, respectively. Remnant starch was observed in both instances, indicating that additional genes encode AGPase large and small subunits in embryo and leaf. Endosperm starch was decreased by approximately 7% in agpsemzm- or agpllzm- mutants, demonstrating that plastidial AGPase activity contributes to starch production in this tissue even when the major cytosolic activity is present.