StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes.

KEY MESSAGE: We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.

Yield reduction caused by elevated temperatures and high nitrogen fertilization is mitigated by SP6A overexpression in potato (Solanum tuberosum L.).

Potatoes (Solanum tuberosum L.) are a fundamental staple for millions of people worldwide. They provide essential amino acids, vitamins, and starch - a vital component of the human diet, providing energy and serving as a source of fiber. Unfortunately, global warming is posing a severe threat to this crop, leading to significant yield losses, and thereby endangering global food security. Industrial agriculture traditionally relies on excessive nitrogen (N) fertilization to boost yields. However, it remains uncertain whether this is effective in combating heat-related yield losses of potato. Therefore, our study aimed to investigate the combinatory effects of heat stress and N fertilization on potato tuber formation. We demonstrate that N levels and heat significantly impact tuber development. The combination of high N and heat delays tuberization, while N deficiency initiates early tuberization, likely through starvation-induced signals, independent of SELF-PRUNING 6A (SP6A), a critical regulator of tuberization. We also found that high N levels in combination with heat reduce tuber yield rather than improve it. However, our study revealed that SP6A overexpression can promote tuberization under these inhibiting conditions. By utilizing the excess of N for accumulating tuber biomass, SP6A overexpressing plants exhibit a shift in biomass distribution towards the tubers. This results in an increased yield compared to wild-type plants. Our results highlight the role of SP6A overexpression as a viable strategy for ensuring stable potato yields in the face of global warming. As such, our findings provide insights into the complex factors impacting potato crop productivity.

Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses.

The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.

Plant Growth Hormones and Micro-Tuberization in Breaking the Seed Dormancy of Bunium persicum (Boiss.) Fedts.

Bunium persicum is a valuable medicinal plant with limited production but high market demand. It thrives predominantly in high-altitude regions. The main challenges hindering its widespread cultivation are seed dormancy and a lengthy seed-to-seed cycle, making its large-scale cultivation difficult. Six genotypes of Bunium persicum were collected from different altitudes to evaluate its germination behavior and seed dormancy. The study was conducted during 2020-23 and comprised three experiments (viz., seed germination under an open field, controlled conditions, and micro-tuberization). Under open field conditions, germination percent was genotype dependent, and the highest germination percentage, root length, and shoot length were recorded in Shalimar Kalazeera-1. Germination behavior assessment of the Bunium persicum revealed that treatment T9 (GA3 (25 ppm) + TDZ (9 µM/L)) is effective in breaking the dormancy of Bunium persicum as well as in obtaining a higher germination percent for early development of the tubers. Similarly, with regard to the effect of temperature and moisture conditions, stratification under moist chilling conditions showed effectiveness in breaking seed dormancy as the germination percentage in stratified seeds was at par with the most efficient growth hormone. With regard to the in vitro micro-propagation, direct regeneration showed multiple shoot primordia at the base of the tubers without intervening callus phase from the MS medium supplemented with BA (22.2 µM) and NAA (13.95 µM) 4 weeks after sub-culturing. Similarly, medium supplemented with JA (8.0 mg/L) and BA (22.2 µM) produced well-organized somatic embryos with shiny surfaces, which appeared at the swelled basal portion of apical stems. Further, the combination of JA (6.0 mg/L) and BA (22.2 M) was effective in developing the micro-tubers and also enhanced the weight and length of Bunium persicum micro-tubers.

Long-distance control of potato storage organ formation by SELF PRUNING 3D and FLOWERING LOCUS T-like 1.

Plants program their meristem-associated developmental switches for timely adaptation to a changing environment. Potato (Solanum tuberosum L.) tubers differentiate from specialized belowground branches or stolons through radial expansion of their terminal ends. During this process, the stolon apex and closest axillary buds enter a dormancy state that leads to tuber eyes, which are reactivated the following spring and generate a clonally identical plant. The potato FLOWERING LOCUS T homolog SELF-PRUNING 6A (StSP6A) was previously identified as the major tuber-inducing signal that integrates day-length cues to control the storage switch. However, whether some other long-range signals also act as tuber organogenesis stimuli remains unknown. Here, we show that the florigen SELF PRUNING 3D (StSP3D) and FLOWERING LOCUS T-like 1 (StFTL1) genes are activated by short days, analogously to StSP6A. Overexpression of StSP3D or StFTL1 promotes tuber formation under non-inductive long days, and the tuber-inducing activity of these proteins is graft transmissible. Using the non-tuber-bearing wild species Solanum etuberosum, a natural SP6A null mutant, we show that leaf-expressed SP6A is dispensable for StSP3D long-range activity. StSP3D and StFTL1 mediate secondary activation of StSP6A in stolon tips, leading to amplification of this tuberigen signal. StSP3D and StFTL1 were observed to bind the same protein partners as StSP6A, suggesting that they can also form transcriptionally active complexes. Together, our findings show that additional mobile tuber-inducing signals are regulated by the photoperiodic pathway.

Leaves and stolons transcriptomic analysis provide insight into the role of phytochrome F in potato flowering and tuberization.

Photoperiod plays a critical role in controlling the formation of sexual or vegetative reproductive organs in potato. Although StPHYF-silenced plants overcome day-length limitations to tuberize through a systemic effect on tuberigen StSP6A expression in the stolon, the comprehensive regulatory network of StPHYF remains obscure. Therefore, the present study investigated the transcriptomes of StPHYF-silenced plants and observed that, in addition to known components of the photoperiodic tuberization pathway, florigen StSP3D and other flowering-related genes were activated in StPHYF-silenced plants, exhibiting an early flowering response. Additionally, grafting experiments uncovered the long-distance effect of StPHYF silencing on gene expression in the stolon, including the circadian clock components, flowering-associated MADSs, and tuberization-related regulatory genes. Similar to the AtFT-AtAP1 regulatory module in Arabidopsis, the present study established that the AP1-like StMADS1 functions downstream of the tuberigen activation complex (TAC) and that suppressing StMADS1 inhibits tuberization in vitro and delays tuberization in vivo. Moreover, the expression of StSP6A was downregulated in StMADS1-silenced plants, implying the expression of StSP6A may be feedback-regulated by StMADS1. Overall, these results reveal that the regulatory network of StPHYF controls flowering and tuberization and targets the crucial tuberization factor StMADS1 through TAC, thereby providing a better understanding of StPHYF-mediated day-length perception during potato reproduction.

Transcriptome and Metabolome Analysis Provide New Insights into the Process of Tuberization of Sechium edule Roots.

Chayote (Sechium edule) produces edible tubers with high starch content after 1 year of growth but the mechanism of chayote tuberization remains unknown. 'Tuershao', a chayote cultivar lacking edible fruits but showing higher tuber yield than traditional chayote cultivars, was used to study tuber formation through integrative analysis of the metabolome and transcriptome profiles at three tuber-growth stages. Starch biosynthesis- and galactose metabolism-related genes and metabolites were significantly upregulated during tuber bulking, whereas genes encoding sugars will eventually be exported transporter (SWEET) and sugar transporter (SUT) were highly expressed during tuber formation. Auxin precursor (indole-3-acetamide) and ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, were upregulated, suggesting that both hormones play pivotal roles in tuber development and maturation. Our data revealed a similar tuber-formation signaling pathway in chayote as in potatoes, including complexes BEL1/KNOX and SP6A/14-3-3/FDL. Down-regulation of the BEL1/KNOX complex and upregulation of 14-3-3 protein implied that these two complexes might have distinct functions in tuber formation. Finally, gene expression and microscopic analysis indicated active cell division during the initial stages of tuber formation. Altogether, the integration of transcriptome and metabolome analyses unraveled an overall molecular network of chayote tuberization that might facilitate its utilization.

Modulation of JA signalling reveals the influence of StJAZ1-like on tuber initiation and tuber bulking in potato.

Phytohormones and their interactions play critical roles in Solanum tuberosum (potato) tuberization. The stimulatory role of jasmonic acid (JA) in tuber development is well established because of its significant promotion of tuber initiation and tuber bulking. However, the dynamics and potential function of JA signalling in potato tuberization remain largely unknown. The present study investigated the role of the JAZ1 subtype, a suppressor of JA signalling, in potato tuberization. Using 35S:StJAZ1-like-GUS as a reporter, we showed that JA signalling was attenuated from the bud end to the stem end shortly after tuber initiation. Overexpression of StJAZ1-like suppressed tuber initiation by restricting the competence for tuber formation in stolon tips, as demonstrated by grafting an untransformed potato cultivar to the stock of StJAZ1-like-overexpressing transgenic potato plants (StJAZ1-like ox). In addition, transcriptional profiling analysis revealed that StJAZ1-like modulates the expression of genes associated with transcriptional regulators, cell cycle, cytoskeleton and phytohormones. Furthermore, we showed that StJAZ1-like is destabilised upon treatment with abcisic acid (ABA), and the attenuated tuberization phenotype in StJAZ1-like ox plants can be partially rescued by ABA treatment. Altogether, these results revealed that StJAZ1-like-mediated JA signalling plays an essential role in potato tuberization.

Toward the Design of Potato Tolerant to Abiotic Stress.

Potato is a major global crop that has an important role to play in food security, reducing poverty and improving human nutrition. Productivity in potato however is limited in many environments by its sensitivity to abiotic stresses such as elevated temperature, drought, frost, and salinity. In this chapter we focus on the effects of elevated temperature on potato yields as high temperature is the most important uncontrollable factor affecting growth and yield of potato. We describe some of the physiological impacts of elevated temperature and review recent findings about response mechanisms. We describe genetic approaches that could be used to identify allelic variants of genes that may be useful to breed for increased climate resilience, an approach that could be deployed with recent advances in potato breeding.

Expression Level of Mature miR172 in Wild Type and StSUT4-Silenced Plants of Solanum tuberosum Is Sucrose-Dependent.

In potato plants, the phloem-mobile miR172 is involved in the sugar-dependent transmission of flower and tuber inducing signal transduction pathways and a clear link between solute transport and the induction of flowering and tuberization was demonstrated. The sucrose transporter StSUT4 seems to play an important role in the photoperiod-dependent triggering of both developmental processes, flowering and tuberization, and the phenotype of StSUT4-inhibited potato plants is reminiscent to miR172 overexpressing plants. The first aim of this study was the determination of the level of miR172 in sink and source leaves of StSUT4-silenced as well as StSUT4-overexpressing plants in comparison to Solanum tuberosum ssp. Andigena wild type plants. The second aim was to investigate the effect of sugars on the level of miRNA172 in whole cut leaves, as well as in whole in vitro plantlets that were supplemented with exogenous sugars. Experiments clearly show a sucrose-dependent induction of the level of mature miR172 in short time as well as long time experiments. A sucrose-dependent accumulation of miR172 was also measured in mature leaves of StSUT4-silenced plants where sucrose export is delayed and sucrose accumulates at the end of the light period.

Validation of molecular response of tuberization in response to elevated temperature by using a transient Virus Induced Gene Silencing (VIGS) in potato.

Temperature plays an important role in potato tuberization. The ideal night temperature for tuber formation is ~17 °C while temperature beyond 22 °C drastically reduces the tuber yield. Moreover, high temperature has several undesirable effects on the plant and tubers. Investigation of the genes involved in tuberization under heat stress can be helpful in the generation of heat-tolerant potato varieties. Five genes, including StSSH2 (succinic semialdehyde reductase isoform 2), StWTF (WRKY transcription factor), StUGT (UDP-glucosyltransferase), StBHP (Bel1 homeotic protein), and StFLTP (FLOWERING LOCUS T protein), involved in tuberization and heat stress in potato were investigated. The results of our microarray analysis suggested that these genes regulate and function as transcriptional factors, hormonal signaling, cellular homeostasis, and mobile tuberization signals under elevated temperature in contrasting KS (Kufri Surya) and KCM (Kufri Chandramukhi) potato cultivars. However, no detailed report is available which establishes functions of these genes in tuberization under heat stress. Thus, the present study was designed to validate the functions of these genes in tuber signaling and heat tolerance using virus-induced gene silencing (VIGS). Results indicated that VIGS transformed plants had a consequential reduction in StSSH2, StWTF, StUGT, StBHP, and StFLTP transcripts compared to the control plants. Phenotypic observations suggest an increase in plant senescence, reductions to both number and size of tubers, and a decrease in plant dry matter compared to the control plants. We also establish the potency of VIGS as a high-throughput technique for functional validation of genes.

Potato CYCLING DOF FACTOR 1 and its lncRNA counterpart StFLORE link tuber development and drought response.

Plants regulate their reproductive cycles under the influence of environmental cues, such as day length, temperature and water availability. In Solanum tuberosum (potato), vegetative reproduction via tuberization is known to be regulated by photoperiod, in a very similar way to flowering. The central clock output transcription factor CYCLING DOF FACTOR 1 (StCDF1) was shown to regulate tuberization. We now show that StCDF1, together with a long non-coding RNA (lncRNA) counterpart, named StFLORE, also regulates water loss through affecting stomatal growth and diurnal opening. Both natural and CRISPR-Cas9 mutations in the StFLORE transcript produce plants with increased sensitivity to water-limiting conditions. Conversely, elevated expression of StFLORE, both by the overexpression of StFLORE or by the downregulation of StCDF1, results in an increased tolerance to drought through reducing water loss. Although StFLORE appears to act as a natural antisense transcript, it is in turn regulated by the StCDF1 transcription factor. We further show that StCDF1 is a non-redundant regulator of tuberization that affects the expression of two other members of the potato StCDF gene family, as well as StCO genes, through binding to a canonical sequence motif. Taken together, we demonstrate that the StCDF1-StFLORE locus is important for vegetative reproduction and water homeostasis, both of which are important traits for potato plant breeding.

The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato.

Polycomb repressive complex (PRC) group proteins regulate various developmental processes in plants by repressing target genes via H3K27 trimethylation, and they function antagonistically with H3K4 trimethylation mediated by Trithorax group proteins. Tuberization in potato has been widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1, a PRC2 member, alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2, a potential H3K27 methyltransferase in potato. Here, we demonstrate that a short-day photoperiod influences StE(z)2 expression in the leaves and stolons. StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhances yield. ChIP-sequencing using stolons induced by short-days indicated that several genes related to tuberization and phytohormones, such as StBEL5/11/29, StSWEET11B, StGA2OX1, and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we observed that another important tuberization gene, StSP6A, is targeted by StE(z)2 in leaves and that it has increased deposition of H3K27me3 under long-day (non-induced) conditions compared to short days. Overall, our results show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks might regulate the expression of key tuberization genes in potato.

BEL1-like protein (StBEL5) regulates CYCLING DOF FACTOR1 (StCDF1) through tandem TGAC core motifs in potato.

Tuberization in potato is governed by many intrinsic and extrinsic factors. Various molecular signals, such as red light photoreceptor (StPHYB), BEL1-like transcription factor (StBEL5), CYCLING DOF FACTOR1 (StCDF1), StCO1/2 (CONSTANS1/2) and StSP6A (Flowering Locus T orthologue), function as crucial regulators during the photoperiod-dependent tuberization pathway. StCDF1 induces tuberization by increasing StSP6A levels via StCO1/2 suppression. Although the circadian clock proteins, GIGANTEA (StGI) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (StFKF1), are reported as StCDF1 interactors, how the StCDF1 gene is regulated in potato is unknown. The BEL-KNOX heterodimer regulates key tuberization genes through tandem TGAC core motifs in their promoters. A recent study reported the presence of six tandem TGAC core motifs in the StCDF1 promoter, suggesting possible regulation of StCDF1 by StBEL5. In our study, we observed a positive correlation between StBEL5 and StCDF1 expression, whereas StCDF1 and its known repressor, StFKF1, showed a negative correlation for the tested tissue types. To investigate the StBEL5-StCDF1 interaction, we generated transgenic potato promoter lines containing a wild-type or mutated (deletion of six tandem TGAC sites) StCDF1 promoter fused to GUS. Wild-type promoter transgenic lines exhibited widespread GUS activity, whereas this activity was absent in the mutated promoter transgenic lines. Moreover, StBEL5 and StCDF1 transcript levels were significantly higher in the stolon-to-tuber stages under short-day conditions compared to long-day conditions. Using wild-type and mutated prStCDF1 as baits in Y1H assays, we further demonstrated that StBEL5 interacts with the StCDF1 promoter through tandem TGAC motifs, indicating direct regulation of StCDF1 by StBEL5 in potato.

Identification of TIMING OF CAB EXPRESSION 1 as a temperature-sensitive negative regulator of tuberization in potato.

For many potato cultivars, tuber yield is optimal at average daytime temperatures in the range 14-22 °C. Above this range, tuber yield is reduced for most cultivars. We previously reported that moderately elevated temperature increases steady-state expression of the core circadian clock gene TIMING OF CAB EXPRESSION 1 (StTOC1) in developing tubers, whereas expression of the StSP6A tuberization signal is reduced, along with tuber yield. In this study we provide evidence that StTOC1 links environmental signalling with potato tuberization by suppressing StSP6A autoactivation in the stolons. We show that transgenic lines silenced in StTOC1 expression exhibit enhanced StSP6A transcript levels and changes in gene expression in developing tubers that are indicative of an elevated sink strength. Nodal cuttings of StTOC1 antisense lines displayed increased tuber yields at moderately elevated temperatures, whereas tuber yield and StSP6A expression were reduced in StTOC1 overexpressor lines. Here we identify a number of StTOC1 binding partners and demonstrate that suppression of StSP6A expression is independent of StTOC1 complex formation with the potato homolog StPIF3. Down-regulation of StTOC1 thus provides a strategy to mitigate the effects of elevated temperature on tuber yield.

Post-transcriptional Regulation of FLOWERING LOCUS T Modulates Heat-Dependent Source-Sink Development in Potato.

Understanding tuberization in the major crop plant potato (Solanum tuberosum L.) is of importance to secure yield even under changing environmental conditions. Tuber formation is controlled by a homolog of the floral inductor FLOWERING LOCUS T, referred to as SP6A. To gain deeper insights into its function, we created transgenic potato plants overexpressing a codon-optimized version of SP6A, SP6Acop, to avoid silencing effects. These plants exhibited extremely early tuberization at the juvenile stage, hindering green biomass development and indicating a tremendous shift in the source sink balance. The meristem identity was altered in dormant buds of transgenic tubers. This strong phenotype, not being reported so far for plants overexpressing an unmodified SP6A, could be due to post-transcriptional regulation. In fact, a putative SP6A-specific small regulatory RNA was identified in potato. It was effectively repressing SP6A mRNA accumulation in transient assays as well as in leaves of young potato plants prior to tuber formation. SP6A expression is downregulated under heat, preventing tuberization. The molecular mechanism has not been elucidated yet. We showed that this small RNA is strongly upregulated under heat. The importance of the small RNA was demonstrated by overexpression of a target mimicry construct, which led to an increased SP6A expression, enabling tuberization even under continuous heat conditions, which abolished tuber formation in the wild-type. Thus, our study describes an additional regulatory mechanism for SP6A besides the well-known pathway that integrates both developmental and environmental signals to control tuberization and is therefore a promising target for breeding of heat-tolerant potato.

Auxins in potato: molecular aspects and emerging roles in tuber formation and stress resistance.

The study of the effects of auxins on potato tuberization corresponds to one of the oldest experimental systems in plant biology, which has remained relevant for over 70 years. However, only recently, in the postgenomic era, the role of auxin in tuber formation and other vital processes in potatoes has begun to emerge. This review describes the main results obtained over the entire period of auxin-potato research, including the effects of exogenous auxin; the content and dynamics of endogenous auxins; the effects of manipulating endogenous auxin content; the molecular mechanisms of auxin signaling, transport and inactivation; the role and position of auxin among other tuberigenic factors; the effects of auxin on tuber dormancy; the prospects for auxin use in potato biotechnology. Special attention is paid to recent insights into auxin function in potato tuberization and stress resistance. Taken together, the data discussed here leave no doubt on the important role of auxin in potato tuberization, particularly in the processes of tuber initiation, growth and sprouting. A new integrative model for the stage-dependent auxin action on tuberization is presented. In addition, auxin is shown to differentially affects the potato resistance to biotrophic and necrotrophic biopathogens. Thus, the modern auxin biology opens up new perspectives for further biotechnological improvement of potato crops.

Phytochrome F plays critical roles in potato photoperiodic tuberization.

The transition to tuberization contributes greatly to the adaptability of potato to a wide range of environments. Phytochromes are important light receptors for the growth and development of plants, but the detailed functions of phytochromes remain unclear in potato. In this study, we first confirmed that phytochrome F (StPHYF) played essential roles in photoperiodic tuberization in potato. By suppressing the StPHYF gene, the strict short-day potato genotype exhibited normal tuber formation under long-day (LD) conditions, together with the degradation of the CONSTANTS protein StCOL1 and modulation of two FLOWERING LOCUS T (FT) paralogs, as demonstrated by the repression of StSP5G and by the activation of StSP6A during the light period. The function of StPHYF was further confirmed through grafting the scion of StPHYF-silenced lines, which induced the tuberization of untransformed stock under LDs, suggesting that StPHYF was involved in the production of mobile signals for tuberization in potato. We also identified that StPHYF exhibited substantial interaction with StPHYB both in vitro and in vivo. Therefore, our results indicate that StPHYF plays a role in potato photoperiodic tuberization, possibly by forming a heterodimer with StPHYB.

Genome-wide survey of potato MADS-box genes reveals that StMADS1 and StMADS13 are putative downstream targets of tuberigen StSP6A.

BACKGROUND: MADS-box genes encode transcription factors that are known to be involved in several aspects of plant growth and development, especially in floral organ specification. To date, the comprehensive analysis of potato MADS-box gene family is still lacking after the completion of potato genome sequencing. A genome-wide characterization, classification, and expression analysis of MADS-box transcription factor gene family was performed in this study. RESULTS: A total of 153 MADS-box genes were identified and categorized into MIKC subfamily (MIKCC and MIKC*) and M-type subfamily (Mα, Mß, and Mγ) based on their phylogenetic relationships to the Arabidopsis and rice MADS-box genes. The potato M-type subfamily had 114 members, which is almost three times of the MIKC members (39), indicating that M-type MADS-box genes have a higher duplication rate and/or a lower loss rate during potato genome evolution. Potato MADS-box genes were present on all 12 potato chromosomes with substantial clustering that mainly contributed by the M-type members. Chromosomal localization of potato MADS-box genes revealed that MADS-box genes, mostly MIKC, were located on the duplicated segments of the potato genome whereas tandem duplications mainly contributed to the M-type gene expansion. The potato MIKC subfamily could be further classified into 11 subgroups and the TT16-like, AGL17-like, and FLC-like subgroups found in Arabidopsis were absent in potato. Moreover, the expressions of potato MADS-box genes in various tissues were analyzed by using RNA-seq data and verified by quantitative real-time PCR, revealing that the MIKCC genes were mainly expressed in flower organs and several of them were highly expressed in stolon and tubers. StMADS1 and StMADS13 were up-regulated in the StSP6A-overexpression plants and down-regulated in the StSP6A-RNAi plant, and their expression in leaves and/or young tubers were associated with high level expression of StSP6A. CONCLUSION: Our study identifies the family members of potato MADS-box genes and investigate the evolution history and functional divergence of MADS-box gene family. Moreover, we analyze the MIKCC expression patterns and screen for genes involved in tuberization. Finally, the StMADS1 and StMADS13 are most likely to be downstream target of StSP6A and involved in tuber development.

Core features of the hormonal status in in vitro grown potato plants.

Some time ago, potato transformants expressing Agrobacterium-derived auxin synthesis gene tms1 were generated. These tms1-transgenic plants, showing enhanced productivity, were studied for their hormonal status, turnover and responses in comparison with control plants. For this purpose, contents of phytohormones belonging to six different classes (auxins, cytokinins, gibberellins, abscisic, jasmonic and salicylic acids) were determined by a sensitive UPLC-MS/MS method in tubers and shoots of in vitro grown plants. To date, this study represents the most comprehensive analysis of the potato hormonal system. On the basis of obtained results, several new generalizations concerning potato hormonal status were drawn. Overall, these data can serve as a framework for forthcoming integrative studies of the hormonal system in potato plants.