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Polycystic kidney disease (PKD) is a ciliopathy characterized by fluid-filled epithelial cysts in the kidney. Although it is well established that the primary cilium is essential for hedgehog (HH) signaling and HH signaling is abnormally activated in multiple PKD models, the mechanism and function of HH activation in PKD pathogenesis remain incompletely understood. Here we used a transgenic HH reporter mouse line to identify the target tissue of HH signaling in Arl13f/f;Ksp-Cre mutant kidney, in which the cilia biogenesis gene Arl13b is specifically deleted in epithelial cells of the distal nephron. In addition, we used a co-culture system to dissect cross-talk between epithelial and mesenchymal cells in the absence of expanding cysts. Finally, we treated Arl13bf/f;Ksp-Cre mice with the GLI inhibitor GANT61 and analyzed its impact on PKD progression in this model. We found that deletion of Arl13b in epithelial cells in the mouse kidney, in vivo, led to non-cell-autonomous activation of the HH pathway in the interstitium. In vitro, when co-cultured with mesenchymal cells, Arl13b−/− epithelial cells produced more sonic hedgehog in comparison to cells expressing Arl13b. Reciprocally, HH signaling was activated in mesenchymal cells co-cultured with Arl13b−/− epithelial cells. Finally, whole body inhibition of the HH pathway by GANT61 reduced the number of proliferating cells, inhibited cyst progression and fibrosis and preserved kidney function in Arl13bf/f;Ksp-Cre mice. Our results reveal non-cell-autonomous activation of HH signaling in the interstitium of the Arl13bf/f;Ksp-Cre kidney and suggest that abnormal activation of the HH pathway contributes to disease progression.

The mechanism underlying folate degradation in foxtail millet grains remains unclear. Here, we identified

Nephronophthisis (NPHP) is a ciliopathy characterized by renal fibrosis and cyst formation, and accounts for a significant portion of end stage renal disease in children and young adults. Currently, no targeted therapy is available for this disease. INVS/NPHP2 is one of the over 25 NPHP genes identified to date. In mouse, global knockout of Invs leads to renal fibrosis and cysts. However, the precise contribution of different cell types and the relationship between epithelial cysts and interstitial fibrosis remains undefined. Here, we generated and characterized cell-type-specific knockout mouse models of Invs, investigated the impact of removing cilia genetically on phenotype severity in Invs mutants and evaluated the impact of the histone deacetylase inhibitor valproic acid (VPA) on Invs mutants. Epithelial-specific knockout of Invs in Invsflox/flox;Cdh16-Cre mutant mice resulted in renal cyst formation and severe stromal fibrosis, while Invsflox/flox;Foxd1-Cre mice, where Invs is deleted in stromal cells, displayed no observable phenotypes up to the young adult stage, highlighting a significant role of epithelial-stromal crosstalk. Further, increased cell proliferation and myofibroblast activation occurred early during disease progression and preceded detectable cyst formation in the Invsflox/flox;Cdh16-Cre kidney. Moreover, concomitant removal of cilia partially suppressed the phenotypes of the Invsflox/flox;Cdh16-Cre mutant kidney, supporting a significant interaction of cilia and Invs function in vivo. Finally, VPA reduced cyst burden, decreased cell proliferation and ameliorated kidney function decline in Invs mutant mice. Our results reveal the critical role of renal epithelial cilia in NPHP and suggest the possibility of repurposing VPA for NPHP treatment.

Alternative splicing (AS) analysis of massive amounts of transcriptomic data is challenging due to limited functions of current software packages. To fill this gap, we present ASTK, a software package covering upstream and downstream analysis of AS. First, we provide a module to perform enrichment analysis at both the gene- and exon-level to incorporate various impacts by different spliced events on a single gene. We further cluster AS genes and spliced exons into three groups based on spliced exon sizes (micro-, mid-, and macro-), which are preferentially associated with distinct biological activities. Second, decoding the regulatory splicing codes has been a daunting task. We demonstrate that ASTK can efficiently extract sequence features and epigenetic marks related to AS events. More significantly, by utilizing machine learning algorithms, we discovered key features that affect the inclusion levels of spliced exons for most AS types. Specifically, the splice site strength is a defining factor to decide exon inclusion levels of alternative 3’/5’ splice site. Multiple sequence and epigenetic features act together to control exon inclusion/exclusion for alternative first exons and skipping exon. Our analysis proves that ASTK can facilitate the functional characterization of AS events and improve understanding of splicing regulation.

Folates content in foxtail millet (Setaria italica) are higher than that in major crops. Polyglutamylation of folates could enhance their compartmentalization, reducing their transport, increase their affinities with enzymes and increase the stability of the folates pool in Arabidopsis. The polyglutamylation reaction are catalyzed by folylpolyglutamate synthetase (FPGS). But FPGS function in foxtail millet is still elusive. In this study we identified Setaria italica FPGS2 (SiFPGS2) genes in foxtail millet by blast analysis with AtFPGS1/2/3 protein sequences. The phylogenetic tree analysis, protein function domain analysis and docking analysis results showed that SiFPGS2 belong to FPGS subfamily, possessed the tetrahydrofolypolyglutamate synthase domain, could bind tetrahydrofolate (THF) as substrate. Subcellular localization predicted that SiFPGS2 localized in the chloroplast. Cis-acting elements prediction analysis indicated that there were meristem expression motif and root specific motif in SiFPGS2 promoter. Over-expressed SiFPGS2 in Arabidopsis not only increased the folates content, but also increased the root length, and further propidium iodide staining result suggested that the increased root length was owning to the promotion of cell division in root apical meristem zone. SiFPGS2 catalyzed the polyglutamylation of THF and lead to the increase of folates content and root length by promotion of root apical meristem zone cell division. SiFPGS2 can be used as a candidate gene for biofortification of folates in Gramineae crops via genetic engineering.

Background Foxtail millet grain has higher folate content than other cereal crops. However, the folate metabolite content and the expression patterns of folate metabolite-related genes are unknown. Results Liquid chromatography-mass spectrometry was used to investigate 12 folate metabolites in a foxtail millet panicle. The content of total folate and derivatives gradually decreased during panicle development. Polyglutamate 5-formyl-tetrahydrofolate was the major form. Twenty-eight genes involved in the folate metabolic pathway were identified through bioinformatic analysis. These genes in Setaria italica, S. viridis and Zea mays showed genomic collinearity. Phylogenetic analysis revealed that the folate-related genes were closely related among the C4 plants compared to C3 plants. The gene expressions were then studied at three panicle development stages. The gene expression patterns were classified into two groups, namely SiADCL1 and SiGGH as two key enzymes, which are responsible for folate synthesis and degradation; their expression levels were highest at the early panicle development stage, up to 179.11- and 163.88-fold, respectively. Their expression levels had a similar downward trend during panicle development and were significantly positively correlated with the concentration of total folate and folate derivatives. However, SiSHMT3 expression levels were significantly negatively correlated with total folate concentration. Conclusion Besides being the major determinants of folate and folate derivatives accumulation, SiADCL1 and SiGGH expression levels are key limiting factors in the foxtail millet panicle. Therefore, SiADCL1 and SiGGH expression levels can be targeted in genetic modification studies to improve folate content in foxtail millet seeds in the future. © 2021 Society of Chemical Industry.

Tartary buckwheat (Fagopyrum tataricum L. Gaertn., TB) is an ancient minor crop and an important food source for humans to supplement nutrients such as flavonoids and essential amino acids. Amino acid transporters (AATs) play critical roles in plant growth and development through the transport of amino acids. In this study, 104 AATs were identified in TB genome and divided into 11 subfamilies by phylogenetic relationships. Tandem and segmental duplications promoted the expansion of FtAAT gene family, and the variations of gene sequence, protein structure and expression pattern were the main reasons for the functional differentiation of FtAATs. Based on RNA-seq and qRT-PCR, the expression patterns of FtAATs in different tissues and under different abiotic stresses were analyzed, and several candidate FtAATs that might affect grain development and response to abiotic stresses were identified, such as FtAAP12 and FtCAT7. Finally, combined with the previous studies, the expression patterns and phylogenetic relationships of AATs in multiple species, the functions of multiple high-confidence FtAAT genes were predicted, and the schematic diagram of FtAATs in TB was initially drawn. Overall, this work provided a framework for further functional analysis of FtAAT genes and important clues for the improvement of TB quality and stress resistance.

The cilium is a cell surface organelle with unique composition and shape. Although it has now been well appreciated as a signaling compartment for the vertebrate cell, the regulation and function of intraciliary calcium in cilia-mediated signaling are less clear and sometimes controversial. This review focuses on publications regarding calcium in the cilium and the potential interactions between intraciliary calcium and signaling pathways mediated by cilia. Unresolved questions and future directions in the field are also discussed.

Background The grains of foxtail millet are enriched in carotenoids, which endow this plant with a yellow color and extremely high nutritional value. However, the underlying molecular regulation mechanism and gene coexpression network remain unclear. Methods The carotenoid species and content were detected by HPLC for two foxtail millet varieties at three panicle development stages. Based on a homologous sequence BLAST analysis, these genes related to carotenoid metabolism were identified from the foxtail millet genome database. The conserved protein domains, chromosome locations, gene structures and phylogenetic trees were analyzed using bioinformatics tools. RNA-seq was performed for these samples to identify differentially expressed genes (DEGs). A Pearson correlation analysis was performed between the expression of genes related to carotenoid metabolism and the content of carotenoid metabolites. Furthermore, the expression levels of the key DEGs were verified by qRT-PCR. The gene coexpression network was constructed by a weighted gene coexpression network analysis (WGCNA). Result The major carotenoid metabolites in the panicles of DHD and JG21 were lutein and β-carotene. These carotenoid metabolite contents sharply decreased during the panicle development stage. The lutein and β-carotene contents were highest at the S1 stage of DHD, with values of 11.474 μg /100 mg and 12.524 μg /100 mg, respectively. Fifty-four genes related to carotenoid metabolism were identified in the foxtail millet genome. Cis-acting element analysis showed that these gene promoters mainly contain ‘plant hormone’, ‘drought stress resistance’, ‘MYB binding site’, ‘endosperm specific’ and ‘seed specific’ cis-acting elements and especially the ‘light-responsive’ and ‘ABA-responsive’ elements. In the carotenoid metabolic pathways, SiHDS, SiHMGS3, SiPDS and SiNCED1 were more highly expressed in the panicle of foxtail millet. The expression of SiCMT, SiAACT3, SiPSY1, SiZEP1/2, and SiCCD8c/8d was significantly correlated with the lutein content. The expression of SiCMT, SiHDR, SiIDI2, SiAACT3, SiPSY1, and SiZEP1/2 was significantly correlated with the content of β-carotene. WGCNA showed that the coral module was highly correlated with lutein and β-carotene, and 13 structural genes from the carotenoid biosynthetic pathway were identified. Network visualization revealed 25 intramodular hub genes that putatively control carotenoid metabolism. Conclusion Based on the integrative analysis of the transcriptomics and carotenoid metabonomics, we found that DEGs related to carotenoid metabolism had a stronger correlation with the key carotenoid metabolite content. The correlation analysis and WGCNA identified and predicted the gene regulation network related to carotenoid metabolism. These results lay the foundation for exploring the key target genes regulating carotenoid metabolism flux in the panicle of foxtail millet. We hope that these target genes could be used to genetically modify millet to enhance the carotenoid content in the future.

BackgroundNephronophthisis (NPHP) is a ciliopathy characterized by renal fibrosis and cyst formation, and accounts for a significant portion of end stage renal disease in children and young adults. Currently no targeted therapy is available for this disease. NPHP2 is one of the 25 NPHP genes identified to date. In mouse, global knockout of Nphp2 leads to renal fibrosis and cysts. However, the precise contribution of different cell types and the relationship between epithelial cysts and interstitial fibrosis remains undefined.MethodsHere, we generated cell-type specific knockout mouse models of Nphp2 and characterized kidney morphology and phenotype. We additionally investigated the impact of removing cilia via deletion of the cilia biogenesis gene Ift88 on phenotype severity in Nphp2 mutants.ResultsEpithelial specific knockout of Nphp2 in Nphp2flox/flox; Ksp-Cre mutant mice resulted in renal cyst formation and severe fibrosis, while Nphp2flox/flox; Foxd1-Cre mice, where Nphp2 is deleted in stromal cells, displayed no observable phenotypes. Further, myofibroblast activation occurred early during disease progression and preceded detectable cyst formation in the Nphp2flox/flox; Ksp-Cre kidney. Moreover, concomitant removal of cilia partially suppressed the phenotypes of the Nphp2flox/flox; Ksp-Cre mutant kidney, supporting a significant role of cilia in Nphp2 function in vivo.ConclusionsOur results highlight the critical role of renal epithelial cilia and epithelial-stromal communication in NPHP.Significance statementNephronophthisis (NPHP) is a ciliopathy characterized by interstitial fibrosis and epithelial cysts in the kidney. A significant portion of end stage renal disease occurring before age 30 results from NPHP. However, the molecular etiology of NPHP remains to be elucidated. By generating and analyzing tissue specific knockout mouse models of Nphp2/Inversin, authors pinpoint defective epithelial cells as the driver for both epithelial cysts and interstitial fibrosis. Moreover, the profibrotic response is triggered before cyst formation in the epithelial-specific Nphp2 knockout model. Mechanistically, authors provide evidence that Nphp2 may function to inhibit a cilia-dependent pro-fibrotic and pro-cystic pathway.

Introduction and objectives Long non-coding RNAs (lncRNAs) have great potential as therapeutic targets in hepatocellular carcinoma (HCC). In this study, we aimed to uncover the function and molecular mechanism of long intergenic non-protein coding RNA 1006 (LINC01006) in HCC. Materials and methods Mice were injected with HCC cells in order to establish the HCC model. Quantitative reverse transcription polymerase chain reaction was used to determine the expression levels of LINC01006, cell adhesion molecule 1 (CADM1), and microRNA (miR)-194-5p in HCC tissues and cells. The cell proliferation, invasion, and migration abilities were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide, transwell, and wound healing assays. The interrelation between LINC01006, miR-194-5p, and CADM1 was confirmed by a dual-luciferase reporter assay. Western blotting was employed to assess the relative protein expression level of CADM1. Results LINC01006 and CADM1 displayed upregulation, but miR-194-5p exhibited downregulation in HCC cells and tissues. Short hairpin (sh)-LINC01006 and miR-194-5p mimics repressed the proliferative, migratory, and invasive capacities of HCC cells, and injection of sh-LINC01006 restrained the growth of HCC tumours in mice. LINC01006 served as a competing endogenous RNA of miR-194-5p and was inversely correlated with miR-194-5p. CADM1 was targeted by miR-194-5p, inversely correlated with miR-194-5p, and positively associated with LINC01006. Furthermore, transfection of pcDNA-CADM1 or the miR-194-5p inhibitor reversed the suppressive effects of sh-LINC01006 on the proliferation, invasion, and migration abilities of HCC cells. Conclusions Downregulation of LINC01006 repressed the development of HCC by sponging miR-194-5p to modulate the expression of CADM1, implying its potential as a therapeutic target for HCC.

Epidemiological studies revealed that prenatal caffeine exposure (PCE) is associated with adverse gestational outcomes and susceptibility to chronic diseases in offspring, yet the effects of PCE on glomerulosclerosis susceptibility in adult female offspring and its intergenerational transmission remain to be further investigated. Here, we found that PCE caused fetal kidney dysplasia and glomerulosclerosis of the female offspring. Besides, the kidney of F1 offspring in PCE group exhibited the "low expressional programming of AT2R" and "GC-IGF1 programming" alteration. Intergenerational genetic studies revealed that the renal defect and GC-IGF1 programming alteration was inherited to F2 adult female offspring derived from the female germ line, but Low expression of AT2R did not extend to the F2 female offspring. Taken together, PCE caused renal dysplasia and adult glomerulosclerosis in the F1 female offspring, which might be mediated by renal AT2R low expressional programming and GC-IGF1 axis alteration. Furthermore, PCE induced transgenerational toxicity on kidney, and GC-IGF1 programming alteration might be the potential molecular mechanism. This study provided experimental evidence for the mechanism study of the intergenerational inheritance of kidney developmental toxicity caused by PCE.

Particulate matter (PM) in air has seriously endangered human health. Especially, PM0.3 can easily enter the lungs and blood through breathing. Herein, an air filter with a three-dimensional (3D) network consisting of core-shell structured fibers was designed by in situ growth of zeolitic imidazolate framework-8 on tunicate nanocellulose/glass fiber composite filter media (ZIF-8@TNC/GF). The filtration performance of the obtained ZIF-8@TNC/GF membranes against sodium chloride particles with the MPPS (most penetrating particle size) was investigated. The air filter media at the optimal ratio of ZIF-8 exhibited an ultrahigh efficiency of 99.998% and a quality factor of 0.0308 Pa-1 for PM0.3. Further characterizations showed that the ZIF-8@TNC/GF air filter had a hierarchical and rich pore structure, showing a large specific surface area (50.3 m2 g-1). More significantly, compared with the TNC/GF prepared by the dipping method, TNCs changed from the original two-dimensional (2D) nonuniform network to a uniform 3D network after the ZIF-8 was introduced. Moreover, the ZIF-8@TNC fibers with a core-shell structure inhibited the aggregation of nanocellulose. This study will shed light on the fabrication of high-efficiency TNC composite air filter media with fluffy 3D networks.

Algal blooms in urban water system is an international concern, which especially in China, have become a major obstacle to the urban water environment improvement since the preliminary achievements were made in the treatment of black and odorous water bodies. The complex blooming mechanisms require a joint regulation plan. This study established a framework that consisted of three steps, i.e., simulation, optimization, and verification, to build an optimal joint regulation plan. By taking the urban river network in Suzhou Pingjiang Xincheng as a case study, the cost-benefits of six alternative regulation measures were assessed using an algal bloom mechanism model and the discounted cash flow model based on 70 regulation scenarios. The joint regulation plan was optimized using the marginal-cost-based greedy strategy on the basis of the cost-benefits of different measures. The optimized joint plans, which were verified to be global optima, were more cost-effective than the designed regulation scenarios, and reduced the average chlorophyll-a concentrations by 55.3%-60.1% compared with the status quo. Applying the optimized cost allocation ratios of each measure to adjust the existing regulation scheme of another similar case verified that the optimization results had great generalizability.

The characteristics of flavonoid metabolism in different Tartary buckwheat (TB) tissues and the related gene regulation network are still unclear at present. One hundred forty-seven flavonoids were identified from six TB tissues using the ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method. The roadmap of the rutin synthesis pathway was revealed. Through transcriptomic analysis it was revealed that the differentially expressed genes (DEGs) are mainly enriched in the "Phenylpropanoid biosynthesis" pathway. Fifty-two DEGs involved in the "flavonol synthesis" pathway were identified. The weighted gene correlation network analysis revealed four co-expression network modules correlated with six flavonol metabolites. Eventually, 74 genes revealed from MEblue and MElightsteelblue modules were potentially related to flavonol synthesis. Of them, 7 MYB transcript factors had been verified to regulate flavonoid synthesis. Furthermore, overexpressed FtMYB31 enhanced the rutin content in vivo. The present findings provide a dynamic flavonoid metabolism profile and co-expression network related to rutin synthesis and are thus valuable in understanding the molecular mechanisms of rutin synthesis in TB.

Background Tartary buckwheat is an important minor crop species with high nutritional and medicinal value and is widely planted worldwide. Cultivated Tartary buckwheat plants are tall and have hollow stems that lodge easily, which severely affects their yield and hinders the development of the Tartary buckwheat industry. Methods Heifeng No. 1 seeds were treated with ethylmethanesulfonate (EMS) to generate a mutant library. The dwarf mutant ftdm was selected from the mutagenized population, and the agronomic characteristics giving rise to the dwarf phenotype were evaluated. Ultra-fast liquid chromatography-electrospray ionization tandem mass spectrometry (UFLC-ESI–MS/MS) was performed to determine the factors underlying the different phenotypes between the wild-type (WT) and ftdm plants. In addition, RNA sequencing (RNA-seq) was performed via the HiSeq 2000 platform, and the resulting transcriptomic data were analysed to identify differentially expressed genes (DEGs). Single-nucleotide polymorphism (SNP) variant analysis revealed possible sites associated with dwarfism. The expression levels of the potential DEGs between the WT and ftdm mutant were then measured via qRT-PCR and fragments per kilobase of transcript per million mapped reads (FPKM). Result The plant height (PH) of the ftdm mutant decreased to 42% of that of the WT, and compared with the WT, the mutant and had a higher breaking force (BF) and lower lodging index (LI). Lower GA4 and GA7 contents and higher contents of jasmonic acid (JA), salicylic acid (SA) and brassinolactone (BR) were detected in the stems of the ftdm mutant compared with the WT. Exogenous application of GAs could not revert the dwarfism of the ftdm mutant. On the basis of the transcriptomic analysis, 146 homozygous SNP loci were identified. In total, 12 DEGs with nonsynonymous mutations were ultimately identified, which were considered potential candidate genes related to the dwarf trait. When the sequences of eight genes whose expression was downregulated and four genes whose expression was upregulated were compared, SKIP14, an F-box protein whose sequence is 85% homologous to that of SLY1 in Arabidopsis, presented an amino acid change (from Ser to Asn) and was expressed at a lower level in the stems of the ftdm mutant compared with the WT. Hence, we speculated that this amino acid change in SKIP14 resulted in a disruption in GA signal transduction, indirectly decreasing the GA content and downregulating the expression of genes involved in GA biosynthesis or the GA response. Further studies are needed to determine the molecular basis underlying the dwarf phenotype of the ftdm mutant. Conclusion We report a Tartary buckwheat EMS dwarf mutant, ftdm, suitable for high-density planting and commercial farming. A significant decrease in GA4 and GA7 levels was detected in the ftdm mutant, and 12 DEGs expressed in the stems of the ftdm mutant were selected as candidates of the dwarfing gene. One nonsynonymous mutation was detected in the SKIP14 gene in the ftdm mutant, and this gene had a lower transcript level compared with that in the WT.

The investigation of filtration and loading performance of fibrous filters with different structures is of high importance for designing filters with long lifetime used in applications with high soot concentrations. Penetration of the soot agglomerates and NaCl particles (with the mobility diameters of 50, 80, 100, 200 and 300 nm) through two types of composite filter media (with the nanostructured layer of electrospun nanofibers and PTFE membrane, respectively) was analyzed. Meanwhile, evolution of the experimental and modeled pressure drop during the particles loading process at the velocities of 6.7 and 11.1 cm/s was also studied. The cake thickness was measured by a new and non-contact method utilizing a 3D optical profiler which would not alter the cake structure. The results showed that the soot penetration was lower than that of NaCl particles under the same condition, because the soot agglomerates had larger effective interception length than the NaCl particles with the same mobility diameter. The pressure drop of the filters loaded with soot agglomerates increased faster than that with NaCl particles. Furthermore, the pressure drop increased faster at the velocity of 11.1 cm/s because of formation of more compact cake. In addition, the pressure drop of the filter with a lower solidity nanostructured layer increased slower because more particles could penetrate into its inner part. The model data agreed with the experimental data well in the case of soot loading. Our results indicate that the filters which have relatively low filtration efficiency against the standard compact aerosol particles yet sufficient efficiency against the soot agglomerates and an open structure can be used in the applications with high soot concentrations to gain a long lifetime.

The R2R3-MYB transcription factors play an important role in regulating secondary metabolism biosynthesis and abiotic stress in plants. In this article, we report the identification of the transcription factor gene, FtMYB31, from the popular Eurasian crop tartary buckwheat (Fagopyrum tataricum) that enhances accumulation of the nutritionally beneficial compound rutin in transgenic tobacco leaves. The FtMYB31 complete cDNA coding sequence was isolated from the leaves of tartary buckwheat, and multiple protein sequence alignments and conserved domain analysis showed it contained a typical R2R3 MYB domain. Subcellular location experiments showed the FtMYB31 protein is localized in nucleus. The phylogenetic tree clustered FtMYB31 with VvMYBPA1 from Vitis vinifera, and AtMYB123 from Arabidopsis thaliana, belonging to the Subgroup 5 cluster. Comparison by qRT-PCR of FtMYB31 transcripts and those from rutin synthesis-related genes showed a relationship between FtMYB31, Ft4CL, and FtUFGT transcripts and rutin content in different tissues of F. tataricum, with correlation coefficients of − 0.68, 0.69, and 0.47, respectively. Transgenic experiments indicated that FtMYB31 upregulated CHS, F3H, and FLS genes in transgenic tobacco and enhanced the accumulation of rutin and total flavonols. These results suggest that FtMYB31 encodes an R2R3-MYB transcription factor that positively regulates flavonol biosynthesis in tartary buckwheat and tobacco and is a possible target for genetically modifying tartary buckwheat to enhance the content of beneficial compounds such as rutin.

Foxtail millet [Setaria italica (L.) Beauv], an important minor crop in semi-arid regions of Northern China, is valued for its flavor, color and nutrition. In order to understand the relationship between carotenoid accumulation and expression of related genes in foxtail millet, two contrasting varieties were studied. 'Jingu21', which produces yellow millet and 'Zhisheng', white millet, were analyzed for the accumulation and composition of millet carotenoids and for the expression profiles of genes involved in their metabolism.The total yellow pigment content in Jingu21 was 19.23 mg kg−1 due to the high levels of lutein (13.58 mg kg−1) and zeaxathin (3.77 mg kg−1), whereas Zhisheng contained only 2.01 mg kg−1 with 0.81 mg kg−1 lutein and 0.22 mg kg−1 zeaxathin. The expression patterns of 14 carotenoid-related genes at different grain maturing stages indicated that the marked differences in the accumulation of carotenoids in foxtail millet might be explained by the continued up-regulation of SiPSY1 accompanied by the significant down-regulation of SiCCD1 in Jingu21.

Additional file 6.

Additional file 2: Fig. S2. Heat map showing inter-sample correlations between the WT and ftdm mutant. All the samples involved three biological replication.

Additional file 1: Fig. S1. Peak area (A) and standard curve (B) of rutin, as determined via HPLC.

Additional file 3.

Additional file 5.

Additional file 4.