Tobacco TTG2 and ARF8 function concomitantly to control flower colouring by regulating anthocyanin synthesis genes

Identification of candidate genes associated with less-photosensitive anthocyanin phenotype using an EMS mutant (pind) in eggplant (Solanum melongena L.)

Eggplant (Solanum melongena L.) is a highly nutritious and economically important vegetable crop. However, the fruit peel of eggplant often shows poor coloration owing to low-light intensity during cultivation, especially in the winter. The less-photosensitive varieties produce anthocyanin in low light or even dark conditions, making them valuable breeding materials. Nevertheless, genes responsible for anthocyanin biosynthesis in less-photosensitive eggplant varieties are not characterized. In this study, an EMS mutant, named purple in the dark (pind), was used to identify the key genes responsible for less-photosensitive coloration. Under natural conditions, the peel color and anthocyanin content in pind fruits were similar to that of wildtype '14-345'. The bagged pind fruits were light purple, whereas those of '14-345' were white; and the anthocyanin content in the pind fruit peel was significantly higher than that in '14-345'. Genetic analysis revealed that the less-photosensitive trait was controlled by a single dominant gene. The candidate gene was mapped on chromosome 10 in the region 7.72 Mb to 11.71 Mb. Thirty-five differentially expressed genes, including 12 structural genes, such as CHS, CHI, F3H, DFR, ANS, and UFGT, and three transcription factors MYB113, GL3, and TTG2, were identified in pind using RNA-seq. Four candidate genes EGP21875 (myb domain protein 113), EGP21950 (unknown protein), EGP21953 (CAAX amino-terminal protease family protein), and EGP21961 (CAAX amino-terminal protease family protein) were identified as putative genes associated with less-photosensitive anthocyanin biosynthesis in pind. These findings may clarify the molecular mechanisms underlying less-photosensitive anthocyanin biosynthesis in eggplant.

Anthocyanin accumulation and transcriptional regulation in purple flowering stalk (Brassica campestris L. var. purpurea Bailey)

1. Purple flowering stalk (Brassica campestris L. ssp. chinensis L. var. purpurea Bailey) is a crop with the high-level anthocyanin. 2. Increased abundance of LBGs promoted the synthesis of anthocyanin. 3. TTG2 (WRKY) interacted with TTG1 (WD40), probably regulating anthocyanin accumulation by shaping a MBWW complex. Brassica crops are a class of nutrient-rich vegetables. Here, two Brassica Crops-Flowering Stalk cultivars, purple flowering stalk (Brassica campestris L. var. purpurea Bailey) and pakchoi (Brassica campestris ssp. chinensis var. communis) were investigated. HPLC-ESI-MS/MS analysis demonstrated that Cy 3-p-coumaroylsophoroside-5-malonylglucoside and Cy 3-diferuloylsophoroside-5-malonylglucoside were identified as the major anthocyanin in peel of purple flowering stalk. The transcript level of structural genes including C4H, CHS, F3H, DFR, ANS and UFGT, and regulatory genes such as TT8, TTG1, Bra004162, Bra001917 and TTG2 in peel of purple flowering stalk were significantly higher than that in peel of pakchoi. In addition, the TTG2(WRKY) interacted only with TTG1(WD40) and the interaction between TT8 (bHLH) and TTG1/Bra004162(MYB)/Bra001917(MYB) were identified. Else, the WD40-WRKY complex (TTG1-TTG2) could activate the transcript of TT12. Our study laid a foundation for the research on the anthocyanin accumulation in Brassica crops.

Downregulation of Brassica napus MYB69 (BnMYB69) increases biomass growth and disease susceptibility via remodeling phytohormone, chlorophyll, shikimate and lignin levels

MYB transcription factors are major actors regulating plant development and adaptability. Brassica napus is a staple oil crop and is hampered by lodging and diseases. Here, four B. napus MYB69 (BnMYB69s) genes were cloned and functionally characterized. They were dominantly expressed in stems during lignification. BnMYB69 RNA interference (BnMYB69i) plants showed considerable changes in morphology, anatomy, metabolism and gene expression. Stem diameter, leaves, roots and total biomass were distinctly larger, but plant height was significantly reduced. Contents of lignin, cellulose and protopectin in stems were significantly reduced, accompanied with decrease in bending resistance and Sclerotinia sclerotiorum resistance. Anatomical detection observed perturbation in vascular and fiber differentiation in stems, but promotion in parenchyma growth, accompanied with changes in cell size and cell number. In shoots, contents of IAA, shikimates and proanthocyanidin were reduced, while contents of ABA, BL and leaf chlorophyll were increased. qRT-PCR revealed changes in multiple pathways of primary and secondary metabolisms. IAA treatment could recover many phenotypes and metabolisms of BnMYB69i plants. However, roots showed trends opposite to shoots in most cases, and BnMYB69i phenotypes were light-sensitive. Conclusively, BnMYB69s might be light-regulated positive regulators of shikimates-related metabolisms, and exert profound influences on various internal and external plant traits.

Transcription and Metabolism Pathways of Anthocyanin in Purple Shamrock (Oxalis triangularis A.St.-Hil.)

Anthocyanins are water-soluble pigments that can impart various colors to plants. Purple shamrock (Oxalis triangularis) possesses unique ornamental value due to its purple leaves. In this study, three anthocyanins, including malvidin 3-O-(4-O-(6-O-malonyl-glucopyranoside)-rhamnopyranosyl)-5-O-(6-O-malonyl-glucopyranoside), delphinidin-3-O-rutinoside and malvidin-3,5-di-O-glucoside, were characterized with ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) in purple shamrock. To investigate the molecular mechanism of anthocyanin biosynthesis in green shamrock (Oxalis corymbosa) and purple shamrock, RNA-seq and qRT-PCR were performed, and the results showed that most of the anthocyanin biosynthetic and regulatory genes were up-regulated in purple shamrock. Then, dark treatment and low temperature treatment experiments in purple shamrock showed that both light and low temperature can induce the biosynthesis of anthocyanins.

Integrated analysis of the transcriptome, sRNAome, and degradome reveals the network regulating fruit skin coloration in sponge gourd (Luffa cylindrica)

Sponge gourd fruit skin color is an important quality-related trait because it substantially influences consumer preferences. However, little is known about the miRNAs and genes regulating sponge gourd fruit skin coloration. This study involved an integrated analysis of the transcriptome, sRNAome, and degradome of sponge gourd fruit skins with green skin (GS) and white skin (WS). A total of 4,331 genes were differentially expressed between the GS and WS, with 2,442 down-regulated and 1,889 up-regulated genes in WS. The crucial genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection were identified (e.g., HEMA, CHLM, CRD1, POR, CAO, CLH, SGR, CAB, BEL1-like, KNAT, ARF, and peroxidase genes). Additionally, 167 differentially expressed miRNAs were identified, with 70 up-regulated and 97 down-regulated miRNAs in WS. Degradome sequencing identified 125 differentially expressed miRNAs and their 521 differentially expressed target genes. The miR156, miR159, miR166, miR167, miR172, and miR393 targeted the genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection. Moreover, a flavonoid biosynthesis regulatory network was established involving miR159, miR166, miR169, miR319, miR390, miR396, and their targets CHS, 4CL, bHLH, and MYB. The qRT-PCR data for the differentially expressed genes were generally consistent with the transcriptome results. Subcellular localization analysis of selected proteins revealed their locations in different cellular compartments, including nucleus, cytoplasm and endoplasmic reticulum. The study findings revealed the important miRNAs, their target genes, and the regulatory network controlling fruit skin coloration in sponge gourd.

A Comparative Study of Flavonoids and Carotenoids Revealed Metabolite Responses for Various Flower Colorations Between Nicotiana tabacum L. and Nicotiana rustica L

Tobacco is a model plant for studying flower coloration. Flavonoids and carotenoids were reported to contribute to the flower color in many plants. We investigated the mechanism underlying flower color formation in tobacco by comparing the profiling flavonoids and carotenoids between various species Nicotiana tabacum L. and Nicotiana rustica L., as their flowers commonly presented red (pink) and yellow (orange), respectively. The metabolomes were conducted by UPLC-ESI-MS/MS system. The main findings were as follows: (1) A total of 31 flavonoids and 36 carotenoids were identified in all four cultivars involved in N. tabacum and N. rustica. (2) Flavonoids and carotenoids tended to concentrate in the red flowers (N. tabacum) and yellow flowers (N. rustica), respectively. (3) About eight flavonoids and 12 carotenoids were primarily screened out for metabolic biomarkers, such as the robust biomarker involving kaempferol-3-o-rut, quercetin-glu, rutin, lutein, and β-carotene. This is the first research of systematic metabolome involving both flavonoids and carotenoids in tobacco flower coloration. The metabolic mechanism concluded that flavonoids and carotenoids mainly contributed to red (pink) and yellow (orange) colors of the tobacco flowers, respectively. Our finding will provide essential insights into characterizing species and modifying flower color in tobacco breeding through genetic improvement or regulation of featured metabolic synthesis.

OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice

Anthocyanins play an important role in the growth of plants, and are beneficial to human health. In plants, the MYB-bHLH-WD40 (MBW) complex activates the genes for anthocyanin biosynthesis. However, in rice, the WD40 regulators remain to be conclusively identified. Here, a crucial anthocyanin biosynthesis gene was fine mapped to a 43.4-kb genomic region on chromosome 2, and a WD40 gene OsTTG1 (Oryza sativa TRANSPARENT TESTA GLABRA1) was identified as ideal candidate gene. Subsequently, a homozygous mutant (osttg1) generated by CRISPR/Cas9 showed significantly decreased anthocyanin accumulation in various rice organs. OsTTG1 was highly expressed in various rice tissues after germination, and it was affected by light and temperature. OsTTG1 protein was localized to the nucleus, and can physically interact with Kala4, OsC1, OsDFR and Rc. Furthermore, a total of 59 hub transcription factor genes might affect rice anthocyanin biosynthesis, and LOC_Os01g28680 and LOC_Os02g32430 could have functional redundancy with OsTTG1. Phylogenetic analysis indicated that directional selection has driven the evolutionary divergence of the indica and japonica OsTTG1 alleles. Our results suggest that OsTTG1 is a vital regulator of anthocyanin biosynthesis, and an important gene resource for the genetic engineering of anthocyanin biosynthesis in rice and other plants.

Comparative transcription analysis of photosensitive and non-photosensitive eggplants to identify genes involved in dark regulated anthocyanin synthesis

BACKGROUND

Light is a key environmental factor in regulation of anthocyanin biosynthesis. Through a large number of bagging screenings, we obtained non-photosensitive eggplants that still have decent amount of anthocyanin synthesized after bagging. In the present study, transcriptome was made to explore the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant.

RESULTS

The transcriptome of the pericarp at 0 h, 0.5 h, 4 h, and 8 h after bag removal were sequenced and analyzed. Comparison of the sequencing data with those of photosensitive eggplant for the same time period showed that anthocyanin synthesis genes had different expression trends. Based on the expression trends of the structural genes, it was discovered that 22 transcription factors and 4 light signal transduction elements may be involved in the anthocyanin synthesis in two types of eggplants. Through transcription factor target gene prediction and yeast one-hybrid assay, SmBIM1, SmAP2, SmHD, SmMYB94, SmMYB19, SmTT8, SmYABBY, SmTTG2, and SmMYC2 were identified to be directly or indirectly bound to the promoter of the structural gene SmCHS. These results indicate that the identified 9 genes participated in the anthocyanin synthesis in eggplant peel and formed a network of interactions among themselves.

CONCLUSIONS

Based on the comparative transcription, the identified 22 transcription factors and 4 light signal transduction elements may act as the key factors in dark regulated anthocyanin synthesis in non-photosensitive eggplant. The results provided a step stone for further analysis of the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant.

Integrated analysis of high-throughput sequencing data shows abscisic acid-responsive genes and miRNAs in strawberry receptacle fruit ripening

The perception and signal transduction of the plant hormone abscisic acid (ABA) are crucial for strawberry fruit ripening, but the underlying mechanism of how ABA regulates ripening-related genes has not been well understood. By employing high-throughput sequencing technology, we comprehensively analyzed transcriptomic and miRNA expression profiles simultaneously in ABA- and nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker)-treated strawberry fruits with temporal resolution. The results revealed that ABA regulated many genes in different pathways, including hormone signal transduction and the biosynthesis of secondary metabolites. Transcription factor genes belonging to WRKY and heat shock factor (HSF) families might play key roles in regulating the expression of ABA inducible genes, whereas the KNOTTED1-like homeobox protein and Squamosa Promoter-Binding-like protein 18 might be responsible for ABA-downregulated genes. Additionally, 20 known and six novel differentially expressed miRNAs might be important regulators that assist ABA in regulating target genes that are involved in versatile physiological processes, such as hormone balance regulation, pigments formation and cell wall degradation. Furthermore, degradome analysis showed that one novel miRNA, Fa_novel6, could degrade its target gene HERCULES1, which likely contributed to fruit size determination during strawberry ripening. These results expanded our understanding of how ABA drives the strawberry fruit ripening process as well as the role of miRNAs in this process.

Integrated analysis of high-throughput sequencing data shows abscisic acid-responsive genes and miRNAs in strawberry receptacle fruit ripening

The perception and signal transduction of the plant hormone abscisic acid (ABA) are crucial for strawberry fruit ripening, but the underlying mechanism of how ABA regulates ripening-related genes has not been well understood. By employing high-throughput sequencing technology, we comprehensively analyzed transcriptomic and miRNA expression profiles simultaneously in ABA- and nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker)-treated strawberry fruits with temporal resolution. The results revealed that ABA regulated many genes in different pathways, including hormone signal transduction and the biosynthesis of secondary metabolites. Transcription factor genes belonging to WRKY and heat shock factor (HSF) families might play key roles in regulating the expression of ABA inducible genes, whereas the KNOTTED1-like homeobox protein and Squamosa Promoter-Binding-like protein 18 might be responsible for ABA-downregulated genes. Additionally, 20 known and six novel differentially expressed miRNAs might be important regulators that assist ABA in regulating target genes that are involved in versatile physiological processes, such as hormone balance regulation, pigments formation and cell wall degradation. Furthermore, degradome analysis showed that one novel miRNA, Fa_novel6, could degrade its target gene HERCULES1, which likely contributed to fruit size determination during strawberry ripening. These results expanded our understanding of how ABA drives the strawberry fruit ripening process as well as the role of miRNAs in this process.