Rice metabolic regulatory network spanning the entire life cycle.

As one of the most important crops in the world, rice (Oryza sativa) is a model plant for metabolome research. Although many studies have focused on the analysis of specific tissues, the changes in metabolite abundance across the entire life cycle have not yet been determined. In this study, combining both targeted and nontargeted metabolite profiling methods, a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle. The contents of metabolites in different tissues of rice were significantly different, with various metabolites accumulating in the plumule and radicle during seed germination. Combining these data with transcriptome data obtained from the same time period, we constructed the Rice Metabolic Regulation Network. The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across development. Using this dataset, we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity. This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agronomic traits.

Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.).

BACKGROUND: Black pepper (Piper nigrum L.), an important and long-cultivated spice crop, is native to South India and grown in the tropics. Piperine is the main pungent and bioactive alkaloid in the berries of black pepper, but the molecular mechanism for piperine biosynthesis has not been determined. MicroRNAs (miRNAs), which are classical endogenous noncoding small RNAs, play important roles in regulating secondary metabolism in many species, but less is known regarding black pepper or piperine biosynthesis. RESULTS: To dissect the functions of miRNAs in secondary metabolism especially in piperine biosynthesis, 110 known miRNAs, 18 novel miRNAs and 1007 individual targets were identified from different tissues of black pepper by small RNA sequencing. qRT-PCR and 5'-RLM-RACE experiments were conducted to validate the reliability of the sequencing data and predicted targets. We found 3 miRNAs along with their targets including miR166-4CL, miR396-PER and miR397-CCR modules that are involved in piperine biosynthesis. CONCLUSION: MiRNA regulation of secondary metabolism is a common phenomenon in plants. Our study revealed new miRNAs that regulate piperine biosynthesis, which are special alkaloids in the piper genus, and they might be useful for future piperine genetic improvement of black pepper.

Cloning and expression analysis of betalain biosynthesis genes in Amaranthus tricolor.

OBJECTIVES: To clone genes involved in the betalain biosynthesis pathway and to assess the effects of phytohormones on betalain biosynthesis in Amaranthus tricolor. RESULTS: Five betalain biosynthesis genes were cloned by reverse transcription PCR and rapid amplification of cDNA ends. Betacyanin analyses revealed that pigments accumulated differently in various tissues and under different phytohormone treatments. Quantitative RT-PCR analysis indicated that gene expression levels did not correlate with pigment accumulation. Notably, gene expression and pigment accumulation were negatively regulated by 2,4-dichlorophenoxyacetic acid. The expression of AmaDOPA5-GT, AmaDODA, and AmaB5-GT was induced by pigmentation-promoting 6-benzyl aminopurine (6-BA). and pigmentation-inhibiting gibberellin A3 while AmaTyDC expression was suppressed. AmaTyDC expression was also suppressed by pigmentation-promoting kinetin. Additionally, the expression of AmaB6-GT was suppressed by 6-BA. CONCLUSIONS: The changes in betacyanin levels among various tissues and following phytohormone treatments were related to the differences in betalain biosynthesis gene expression levels.