Genetic control of anthocyanin pigmentation of potato tissues

Transcriptome sequencing and screening of anthocyanin related genes in purple potato tubers (Solanum tuberosum L.)

BACKGROUND

Pigmented potatoes (Solanum tuberosum L.) are rich in anthocyanin, which have antioxidantiy and play an important role in health and medical. Nevertheless, the regulation mechanism of anthocyanins in purple potato at different growth stages remain unclear.

RESULTS

In this study, through using the high-throughput sequencing and systematic bioinformatics analysis, a total of 7,176 significantly different expressed genes (DEGs) were discovered from the purple potato Huasong 66 tubers at different developmental stages. Through GO and KEGG enrichment analysis, it was found that, 43 DEGs were mainly enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism, which biological processes are closely related to anthocyanin biosynthesis. The quantitative RT-PCR were verified the reliability of transcriptome data. We demonstrated that DEGs or transcription factors (TFs) which related to flavonoid metabolism were involved in the anthocyanins biosynthesis, such as the protein-coding genes PAL, CHS, CHI, 4CL, F3H, UFGT, LAR, and the TFs MYB, bHLH, and HY5.

CONCLUSION

The key genes involved in anthocyanin synthesis in potato tubers were identificated, it provides new insights for molecular breeding new cultivars. These results are valuable for improving the anthocyanin in potato.

Contribution of the regulatory miR156-SPL9 module to the drought stress response in pigmented potato (Solanum tuberosum L.)

Potato (Solanum tuberosum L.) is nowadays an important component of diversified cropping systems due to its adaptability, yielding capacity, and nutrition contribution. Breeding programs aiming at raising potato's nutritional value have mainly focused on the accumulation in potato tubers of health-promoting phytochemicals such as anthocyanins. In different plant species, increased amounts of anthocyanins in vegetative tissues have been associated with enhanced tolerance to abiotic and biotic stresses that challenge agrifood systems in the current context of global climate change. In the present study, we aimed at gaining insight into the effect of anthocyanin accumulation on the potato plants response to drought stress using three different potato genotypes with differential canopy and tuber pigmentation: the purple fleshed commercial variety Bleuet; the red fleshed breeding clone DAR170; and the non-pigmented commercial variety Monalisa. The varieties Bleuet and DAR170 exhibiting higher anthocyanin content in vegetative tissues than the Monalisa variety showed a remarkable inhibition of stem growth development under drought stress treatment suggestive of an anthocyanin-mediated physiological shift from growth to resilience as a mechanism of stress tolerance. The results of the expression analysis of stu-miR156a and its target StSPL9 gene in the potato plants with different anthocyanin content, as well as their change in response to drought stress support the participation of the conserved miR156-SPL9 regulatory module in coordinating potato plants development and plant responses to drought stress, involving precise fine-tuning of anthocyanin biosynthesis.

Transcriptomic and Metabolic Analysis Reveals Genes and Pathways Associated with Flesh Pigmentation in Potato (Solanum tuberosum) Tubers

Anthocyanins, flavonoid pigments, are responsible for the purple and red hues in potato tubers. This study analyzed tubers from four potato cultivars-red RR, purple HJG, yellow QS9, and white JZS8-to elucidate the genetic mechanisms underlying tuber pigmentation. Our transcriptomic analysis identified over 2400 differentially expressed genes between these varieties. Notably, genes within the flavonoid biosynthesis pathway were enriched in HJG and RR compared to the non-pigmented JZS8, correlating with their higher levels of anthocyanin precursors and related substances. Hierarchical clustering revealed inverse expression patterns for the key genes involved in anthocyanin metabolism between pigmented and non-pigmented varieties. Among these, several MYB transcription factors displayed strong co-expression with anthocyanin biosynthetic genes, suggesting a regulatory role. Specifically, the expression of 16 MYB genes was validated using qRT-PCR to be markedly higher in pigmented HJG and RR versus JZS8, suggesting that these MYB genes might be involved in tuber pigmentation. This study comprehensively analyzed the transcriptome of diverse potato cultivars, highlighting specific genes and metabolic pathways involved in tuber pigmentation. These findings provide potential molecular targets for breeding programs focused on enhancing tuber color.

Germplasm Resources and Genetic Breeding of Huang-Qi (Astragali Radix): A Systematic Review

Huang-Qi (Astragali radix) is one of the most widely used herbs in traditional Chinese medicine, derived from the dried roots of Astragalus membranaceus or Astragalus membranaceus var. mongholicus. To date, more than 200 compounds have been reported to be isolated and identified in Huang-Qi. However, information pertaining to Huang-Qi breeding is considerably fragmented, with fundamental gaps in knowledge, creating a bottleneck in effective breeding strategies. This review systematically introduces Huang-Qi germplasm resources, genetic diversity, and genetic breeding, including wild species and cultivars, and summarizes the breeding strategy for cultivars and the results thereof as well as recent progress in the functional characterization of the structural and regulatory genes related to horticultural traits. Perspectives about the resource protection and utilization, breeding, and industrialization of Huang-Qi in the future are also briefly discussed.

Tuber transcriptome analysis reveals a novel WRKY transcription factor StWRKY70 potentially involved in potato pigmentation

Tuber flesh pigmentation, conferred by the presence of secondary metabolite anthocyanins, is one of many key agronomic traits for potato tubers. Although several genes of potato anthocyanin biosynthesis have been reported, transcription factors (TFs) contributing to tuber flesh pigmentation are still not fully understood. In this study, transcriptomic profiling of diploid potato accessions with or without tuber flesh pigmentation was conducted and genes of the anthocyanin biosynthesis pathway were found significantly enriched within the 1435 differentially expressed genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) and connectivity analysis pinpointed a subset of 173 genes closely related to the key biosynthetic gene StDFR. Of the eight transcription factors in the subset, group III WRKY StWRKY70, was chosen for showing high connectivity to StDFR and ten other anthocyanin biosynthetic genes and homology to known WRKYs of anthocyanin pathway. The transient activation assay showed StWRKY70 predominantly stimulated the expression of StDFR and StANS as well as the accumulation of anthocyanins by enhancing the function of the MYB transcription factor StAN1. Furthermore, the interaction between StWRKY70 and StAN1 was verified by Y2H and BiFC. Our analysis discovered a new transcriptional activator StWRKY70 which potentially involved in tuber flesh pigmentation, thus may lay the foundation for deciphering how the WRKY-MYB-bHLH-WD40 (WRKY-MBW) complex regulate the accumulation of anthocyanins and provide new strategies to breed for more nutritious potato varieties with enhanced tuber flesh anthocyanins.

Enhanced UV-B Radiation in Potato Stems and Leaves Promotes the Accumulation of Anthocyanins in Tubers

Enhanced ultraviolet-B (UV-B) radiation promotes anthocyanin biosynthesis in leaves, flowers and fruits of plants. However, the effects and underlying mechanisms of enhanced UV-B radiation on the accumulation of anthocyanins in the tubers of potatoes (Solanum tuberosum L.) remain unclear. Herein, reciprocal grafting experiments were first conducted using colored and uncolored potatoes, demonstrating that the anthocyanins in potato tubers were synthesized in situ, and not transported from the leaves to the tubers. Furthermore, the enhanced UV-B radiation (2.5 kJ·m-2·d-1) on potato stems and leaves significantly increased the contents of total anthocyanin and monomeric pelargonidin and peonidin in the red-fleshed potato '21-1' tubers, compared to the untreated control. A comparative transcriptomic analysis showed that there were 2139 differentially expressed genes (DEGs) under UV-B treatment in comparison to the control, including 1724 up-regulated and 415 down-regulated genes. The anthocyanin-related enzymatic genes in the tubers such as PAL, C4H, 4CL, CHS, CHI, F3H, F3'5'H, ANS, UFGTs, and GSTs were up-regulated under UV-B treatment, except for a down-regulated F3'H. A known anthocyanin-related transcription factor StbHLH1 also showed a significantly higher expression level under UV-B treatment. Moreover, six differentially expressed MYB transcription factors were remarkably correlated to almost all anthocyanin-related enzymatic genes. Additionally, a DEGs enrichment analysis suggested that jasmonic acid might be a potential UV-B signaling molecule involved in the UV-B-induced tuber biosynthesis of anthocyanin. These results indicated that enhanced UV-B radiation in potato stems and leaves induced anthocyanin accumulation in the tubers by regulating the enzymatic genes and transcription factors involved in anthocyanin biosynthesis. This study provides novel insights into the mechanisms of enhanced UV-B radiation that regulate the anthocyanin biosynthesis in potato tubers.

Integrative analysis of metabolome and transcriptome reveals a dynamic regulatory network of potato tuber pigmentation

Potatoes consist of flavonoids that provide health benefits for human consumers. To learn more about how potato tuber flavonoid accumulation and flesh pigmentation are controlled, we analyzed the transcriptomic and metabolomic profile of potato tubers from three colored potato clones at three developmental phases using an integrated approach. From the 72 flavonoids identified in pigmented flesh, differential abundance was noted for anthocyanins, flavonols, and flavones. Weighted gene co-expression network analysis further allowed modules and candidate genes that positively or negatively regulate flavonoid biosynthesis to be identified. Furthermore, an R2R3-MYB repressor StMYB3 and an R3-MYB repressor StMYBATV involved in the modulation of anthocyanin biosynthesis during tuber development were identified. Both StMYB3 and StMYBATV could interact with the cofactor StbHLH1 and repress anthocyanin biosynthesis. Our results indicate a feedback regulatory mechanism of a coordinated MYB activator-repressor network on fine-tuning of potato tuber pigmentation during tuber development.

Anthocyanins in Plant Food: Current Status, Genetic Modification, and Future Perspectives

Anthocyanins are naturally occurring polyphenolic pigments that give food varied colors. Because of their high antioxidant activities, the consumption of anthocyanins has been associated with the benefit of preventing various chronic diseases. However, due to natural evolution or human selection, anthocyanins are found only in certain species. Additionally, the insufficient levels of anthocyanins in the most common foods also limit the optimal benefits. To solve this problem, considerable work has been done on germplasm improvement of common species using novel gene editing or transgenic techniques. This review summarized the recent advances in the molecular mechanism of anthocyanin biosynthesis and focused on the progress in using the CRISPR/Cas gene editing or multigene overexpression methods to improve plant food anthocyanins content. In response to the concerns of genome modified food, the future trends in developing anthocyanin-enriched plant food by using novel transgene or marker-free genome modified technologies are discussed. We hope to provide new insights and ideas for better using natural products like anthocyanins to promote human health.

Irrigation Effect on Yield, Skin Blemishes, Phellem Formation, and Total Phenolics of Red Potatoes

Dark Red Norland is an important potato cultivar in the fresh market due to its attractive bright, red colour, and good yield. However, skin blemishes such as silver patch, surface cracking, and russeting can negatively influence the tuber skin quality and marketability. It is well known that potato is a drought-sensitive plant. This study was conducted to determine whether irrigation would affect Dark Red Norland's yield and skin quality. A three-year field trial was conducted by Peak of the Market in Manitoba, Canada. Plants were treated under both irrigation and rainfed conditions. The results show that irrigation increased the total yield by 20.6% and reduced the severity of surface cracking by 48.5%. Microscopy imaging analysis demonstrated that tubers from the rainfed trials formed higher numbers of suberized cell layers than those of the irrigated potatoes, with a difference of 0.360 to 0.652 layers in normal skins. Surface cracking and silver patch skins had more suberized cell layers than the normal skins, with ranges of 7.805 to 8.333 and 7.740 to 8.496, respectively. A significantly higher amount of total polyphenols was found in the irrigated samples with a mean of 77.30 mg gallic acid equivalents (GAE)/100 g fresh weight (fw) than that of the rainfed samples (69.80 mg GAE/100 g fw). The outcome of this study provides a better understanding of the water regime effect causing these skin blemishes, which could potentially be used to establish strategies to improve tuber skin quality and minimize market losses.

Transcriptomic and Metabolomic Analyses Providing Insights into the Coloring Mechanism of Docynia delavayi

The metabolome and transcriptome profiles of three different variations of mature Docynia delavayi fruit were synthesized to reveal their fruit color formation mechanism. A total of 787 secondary metabolites containing 149 flavonoid metabolites, most of which were flavonoids and flavonols, were identified in the three variations using ultra performance liquid chromatography- tandem mass spectrometry (UPLC-MS/MS), and we found that the secondary metabolites cyanidin-3-O-galactoside and cyanidin-3-O-glucoside were the major coloring substances in D. delavayi. This was associated with the significant upregulation of the structural genes F3H and F3′H in the anthocyanin synthesis pathway and the control genes WRKY, MYB, bZIP, bHLH, and NAC in RP. F3′H expression may play a significant role in the selection of components for anthocyanin synthesis. Our results contribute to breeding and nutritional research in D. delavayi and provide insight into metabolite studies of the anthocyanin biosynthetic pathway.

Anthocyanins accumulation analysis of correlated genes by metabolome and transcriptome in green and purple peppers (Capsicum annuum)

BACKGROUND

In order to clarify the the molecular mechanism of anthocyanin accumulation in green and purple fruits of pepper using metabolomics and transcriptomics,to identify different anthocyanin metabolites,and to analyze the differentially expressed genes involved in anthocyanin biosynthesis..

RESULTS

We analyzed the anthocyanin metabolome and transcriptome data of the fruits of 2 purple pepper and 1 green pepper. A total of 5 anthocyanin metabolites and 2224 differentially expressed genes were identified between the green and purple fruits of pepper. Among the 5 anthocyanin metabolites,delphin chloride was unique to purple pepper fruits,which is the mainly responsible for the purple fruit color of pepper. A total of 59 unigenes encoding 7 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in pepper fruit. The six enzymes (PAL,C4H,CHI,DFR,ANS,UFGT) had higher expression levels except the F3H gene in purple compared with green fruits. In addition,seven transcription factors were also found in this study. These transcription factors may contribute to anthocyanin metabolite biosynthesis in the fruits of pepper. One of differentially expressed gene novel.2098 was founded. It was not annotated in NCBI. Though blast analysis we preliminarily considered that this gene related to MYB transcription factor and was involved in anthocyanin biosynthesis in pepper fruit.

CONCLUSIONS

Overall, the results of this study provide useful information for understanding anthocyanin accumulation and the molecular mechanism of anthocyanin biosynthesis in peppers.

Identification of CaAN3 as a fruit-specific regulator of anthocyanin biosynthesis in pepper (Capsicum annuum)

The novel gene CaAN3 encodes an R2R3 MYB transcription factor that regulates fruit-specific anthocyanin accumulation. The key regulatory gene CaAN2 encodes an R2R3 MYB transcription factor that regulates anthocyanin biosynthesis in various tissues in pepper (Capsicum annuum). However, CaAN2 is not expressed in certain pepper accessions showing fruit-specific anthocyanin accumulation. In this study, we identified the novel locus CaAN3 as a regulator of fruit-specific anthocyanin biosynthesis, using an F₂ population derived from a hybrid cultivar with purple immature fruits and segregating for CaAN3. We extracted total RNA, assembled two RNA pools according to fruit color, and carried out bulked segregant RNA sequencing. We aligned the raw reads to the pepper reference genome Dempsey and identified 6,672 significant single nucleotide polymorphisms (SNPs) by calculating the Δ(SNP-index) between the two pools. We then conducted molecular mapping to delimit the target region of CaAN3 to the interval 184.6-186.4 Mbp on chromosome 10. We focused on Dem.v1.00043895, encoding an R2R3 MYB transcription factor, as the strongest candidate gene. Sequence analysis revealed four insertion/deletion polymorphisms in the promoter region of the green CaAN3 allele. We employed virus-induced gene silencing and transient overexpression assays to characterize the function of the candidate gene. When Dem.v1.00043895 was silenced in pepper, anthocyanin accumulation decreased in the pericarp, while the transient overexpression of Dem.v1.00043895 in Nicotiana benthamiana leaves resulted in the accumulation of anthocyanins around the infiltration sites. These results showed that Dem.v1.00043895 is CaAN3, an activator of anthocyanin biosynthesis in pepper fruits.

Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression

BACKGROUND

Anthocyanins, which account for color variation and remove reactive oxygen species, are widely synthesized in plant tissues and organs. Using targeted metabolomics and nanopore full-length transcriptomics, including differential gene expression analysis, we aimed to reveal potato leaf anthocyanin biosynthetic pathways in different colored potato varieties.

RESULTS

Metabolomics analysis revealed 17 anthocyanins. Their levels varied significantly between the different colored varieties, explaining the leaf color differences. The leaves of the Purple Rose2 (PurpleR2) variety contained more petunidin 3-O-glucoside and malvidin 3-O-glucoside than the leaves of other varieties, whereas leaves of Red Rose3 (RedR3) contained more pelargonidin 3-O-glucoside than the leaves of other varieties. In total, 114 genes with significantly different expression were identified in the leaves of the three potato varieties. These included structural anthocyanin synthesis-regulating genes such as F3H, CHS, CHI, DFR, and anthocyanidin synthase and transcription factors belonging to multiple families such as C3H, MYB, ERF, NAC, bHLH, and WRKY. We selected an MYB family transcription factor to construct overexpression tobacco plants; overexpression of this factor promoted anthocyanin accumulation, turning the leaves purple and increasing their malvidin 3-o-glucoside and petunidin 3-o-glucoside content.

CONCLUSIONS

This study elucidates the effects of anthocyanin-related metabolites on potato leaves and identifies anthocyanin metabolic network candidate genes.

The combination of R2R3-MYB gene AmRosea1 and hairy root culture is a useful tool for rapidly induction and production of anthocyanins in Antirrhinum majus L

Anthocyanins are the largest group of water-soluble pigments and beneficial for human health. Although most plants roots have the potential to express natural biosynthesis pathways required to produce specialized metabolites such as anthocyanins, the anthocyanin synthesis is specifically silenced in roots. To explore the molecular mechanism of absence and production ability of anthocyanin in the roots, investigated the effect of a bHLH gene AmDelila, and an R2R3-MYB gene AmRosea1, which are the master regulators of anthocyanin biosynthesis in Antirrhinum majus flowers, by expressing these genes in transformed hairy roots of A. majus. Co-ectopic expression of both AmDelila and AmRosea1 significantly upregulated the expression of the key target structural genes in the anthocyanin biosynthesis pathway. Furthermore, this resulted in strongly enhanced anthocyanin accumulation in transformed hairy roots. Ectopic expression of AmDelila alone did not gives rise to any significant anthocyanin accumulation, however, ectopic expression of AmRosea1 alone clearly upregulated expression of the main structural genes as well as greatly promoted anthocyanin accumulation in transformed hairy roots, where the contents reached 0.773–2.064 mg/g fresh weight. These results suggest that AmRosea1 plays a key role in the regulatory network in controlling the initiation of anthocyanin biosynthesis in roots, and the combination of AmRosea1 and hairy root culture is a powerful tool to study and production of anthocyanins in the roots of A. majus.

E183K Mutation in Chalcone Synthase C2 Causes Protein Aggregation and Maize Colorless

Flavonoids give plants their rich colors and play roles in a number of physiological processes. In this study, we identified a novel colorless maize mutant showing reduced pigmentation throughout the whole life cycle by EMS mutagenesis. E183K mutation in maize chalcone synthase C2 (ZmC2) was mapped using MutMap strategy as the causal for colorless, which was further validated by transformation in Arabidopsis. We evaluated transcriptomic and metabolic changes in maize first sheaths caused by the mutation. The downstream biosynthesis was blocked while very few genes changed their expression pattern. ZmC2-E183 site is highly conserved in chalcone synthase among Plantae kingdom and within species' different varieties. Through prokaryotic expression, transient expression in maize leaf protoplasts and stable expression in Arabidopsis, we observed that E183K and other mutations on E183 could cause almost complete protein aggregation of chalcone synthase. Our findings will benefit the characterization of flavonoid biosynthesis and contribute to the body of knowledge on protein aggregation in plants.

Pathway-based analysis of anthocyanin diversity in diploid potato

Anthocyanin biosynthesis is one of the most studied pathways in plants due to the important ecological role played by these compounds and the potential health benefits of anthocyanin consumption. Given the interest in identifying new genetic factors underlying anthocyanin content we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses. By using an expanded SNP dataset, we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein. Importantly, a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS. Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters. We identified multiple anthocyanin homologs in this genomic region, including four transcription factors and five enzymes that could be governing anthocyanin variation. For instance, a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured. Finally, we combined a pathway analysis and GWAS of other agronomic traits to identify pathways related to anthocyanin biosynthesis in potatoes. We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis. The results contribute to the understanding of anthocyanins regulation in potatoes and can be used in future breeding programs focused on nutraceutical food.

Antioxidants in Potatoes: A Functional View on One of the Major Food Crops Worldwide

With a growing world population, accelerating climate changes, and limited arable land, it is critical to focus on plant-based resources for sustainable food production. In addition, plants are a cornucopia for secondary metabolites, of which many have robust antioxidative capacities and are beneficial for human health. Potato is one of the major food crops worldwide, and is recognized by the United Nations as an excellent food source for an increasing world population. Potato tubers are rich in a plethora of antioxidants with an array of health-promoting effects. This review article provides a detailed overview about the biosynthesis, chemical and health-promoting properties of the most abundant antioxidants in potato tubers, including several vitamins, carotenoids and phenylpropanoids. The dietary contribution of diverse commercial and primitive cultivars are detailed and document that potato contributes much more than just complex carbohydrates to the diet. Finally, the review provides insights into the current and future potential of potato-based systems as tools and resources for healthy and sustainable food production.

Characterization of the F Locus Responsible for Floral Anthocyanin Production in Potato

Anthocyanins are pigmented secondary metabolites produced via the flavonoid biosynthetic pathway and play important roles in plant stress responses, pollinator attraction, and consumer preference. Using RNA-sequencing analysis of a cross between diploid potato (Solanum tuberosum L.) lines segregating for flower color, we identified a homolog of the ANTHOCYANIN 2 (AN2) gene family that encodes a MYB transcription factor, herein termed StFlAN2, as the regulator of anthocyanin production in potato corollas. Transgenic introduction of StFlAN2 in white-flowered homozygous doubled-monoploid plants resulted in a recovery of purple flowers. RNA-sequencing revealed the specific anthocyanin biosynthetic genes activated by StFlAN2 as well as expression differences in genes within pathways involved in fruit ripening, senescence, and primary metabolism. Closer examination of the locus using genomic sequence analysis revealed a duplication in the StFlAN2 locus closely associated with gene expression that is likely attributable to nearby genetic elements. Taken together, this research provides insight into the regulation of anthocyanin biosynthesis in potato while also highlighting how the dynamic nature of the StFlAN2 locus may affect expression.