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Journal of Integrative Agriculture  2022, Vol. 21 Issue (4): 1015-1027    DOI: 10.1016/S2095-3119(21)63784-X
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Transcriptome analysis reveals the differential regulatory effects of red and blue light on nitrate metabolism in pakchoi (Brassica campestris L.)
FAN Xiao-xue1, BIAN Zhong-hua2, SONG Bo1, XU Hai1#br#
1 Institute of Vegetable Crops/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R.China 
2 Photobiology Research Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610200, P.R.China 
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小白菜是一种重要的叶菜。光谱尤其是红光和蓝光在调控硝酸盐代谢中起着重要作用。目前,在转录组水平上红光和蓝光对小白菜硝酸盐代谢的影响研究仍然有限,本研究通过RNA测序技术来探索其分子机制。结果表明,与白光相比,红光和蓝光处理下的差异表达基因(DEGs)分别为3939和5534个。通过 KEGG通路分析和GO分析,发现差异基因主要参与硝酸盐同化、植物与病原体的相互作用、次生代谢产物的生物合成和苯丙素的生物合成。在生理代谢水平上也证实了光谱波长对硝酸盐含量和相关酶活有不同影响。研究发现,Crys/Phys-COP1-HY5/HY5-like等不同的信号转导模块参与了红光和蓝光诱导的硝酸盐代谢,该复合物的转录水平与观察到的硝酸盐积累水平一致。通过qPCR进一步验证了15个随机选取的差异基因表达模式。综上所述,本研究结果为进一步研究光谱在转录组水平上调控小白菜硝酸盐代谢提供了帮助。

Abstract  Pakchoi (Brassica campestris L. ssp. chinensis) is an important leafy vegetable.  Various light spectra, especially red and blue light, play vital roles in the regulation of nitrate metabolism.  Information on the effects of red and blue light on nitrate metabolism at the transcriptome level in pakchoi is still limited, so this study used RNA sequencing technology to explore this molecular mechanism.  Through pairwise comparisons with white LED light, 3 939 and 5 534 differentially expressed genes (DEGs) were identified under red and blue light, respectively.  By Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, these unigenes were found to be involved in nitrate assimilation, plant–pathogen interaction, biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis.  The differential effects of light spectra on the nitrate concentration and metabolism-related enzyme activities were also confirmed at the physiological level.  Several signal transduction modules, including Crys/Phys-COP1-HY5/HY5-like, were found to be involved in red and blue light-induced nitrate metabolism, and the transcript levels for this complex were consistent with the observed degree of nitrate assimilation.  The expression patterns of 15 randomly selected DEGs were further validated using qPCR.  Taken together, the results of this study could help improve our understanding of light spectrum-regulated nitrate metabolism in pakchoi at the transcriptome level.
Keywords:  nitrate metabolism       light spectra        transcriptome        gene expression        pakchoi  
Received: 25 September 2020   Accepted: 19 July 2021
Fund: This research was financially supported by the National Key Research and Development Program of China (2017YFB0403903) and the Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (ASTIP-CAAS, 34-IUA-03). 
About author:  FAN Xiao-xue, E-mail:; Correspondence BIAN Zhong-hua, Tel: +86-28-80203196, E-mail:; XU Hai, Tel: +86-25-84390676, E-mail:

Cite this article: 

FAN Xiao-xue, BIAN Zhong-hua, SONG Bo, XU Hai. 2022. Transcriptome analysis reveals the differential regulatory effects of red and blue light on nitrate metabolism in pakchoi (Brassica campestris L.). Journal of Integrative Agriculture, 21(4): 1015-1027.

Appenroth K J, Meço R, Jourdan V, Lillo C. 2000. Phytochrome and post-translational regulation of nitrate reductase in higher plants. Plant Science, 159, 51–56.
Ashworth A, Mitchell K, Blackwell J R, Vanhatalo A, Jones A M. 2015. High-nitrate vegetable diet increases plasma nitrate and nitrite concentrations and reduces blood pressure in healthy women. Public Health Nutrition, 18, 2669–2678.
Barneix A J. 2007. Physiology and biochemistry of source-regulated protein accumulation in the wheat grain. Journal of Plant Physiology, 164, 581–590.
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple hypothesis testing. Journal of The Royal Statistical Society (Series B: Statistical Methodology), 57, 289–300.
Bian Z H, Cheng R F, Yang Q C, Wang J, Lu C G. 2016. Continuous light from red, blue, and green light-emitting diodes reduces nitrate content and enhances phytochemical concentrations and antioxidant capacity in lettuce. Journal of the American Society for Horticultural Science, 141, 186–195.
Bian Z H, Wang Y, Zhang X Y, Li T, Grundy S, Yang Q C, Cheng R F. 2020. A review of environment effects on nitrate accumulation in leafy vegetables grown in controlled environments. Foods, 9, 732.
Bian Z H, Yang Q C, Li T, Cheng R F, Barnett Y, Lu C G. 2018. Study of the beneficial effects of green light on lettuce grown under short-term continuous red and blue light-emitting diodes. Physiologia Plantarum, 164, 226–240.
Bian Z H, Yang Q C, Liu W K. 2015. Effects of light quality on the accumulation of phytochemicals in vegetables produced in controlled environments: A review. Journal of the Science of Food and Agriculture, 95, 869–877.
Bondonno C P, Croft K D, Hodgson J M. 2016. Dietary nitrate, nitric oxide, and cardiovascular health. Critical Reviews in Food Science and Nutrition, 56, 2036–2052.
Castillon A, Shen H, Huq E. 2009. Blue light induces degradation of the negative regulator phytochrome interacting factor 1 to promote photomorphogenic development of Arabidopsis seedlings. Genetics, 182, 161–171.
Chen B M, Wan, Z H, Li S X, Wang G X, Song H X, Wang X N. 2004. Effects of nitrate supply on plant growth, nitrate accumulation, metabolic nitrate concentration and nitrate reductase activity in three leafy vegetables. Plant Science, 167, 635–643.
Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X. 2011. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biology, 11, 1–6.
Contreras R A, Pizarro M, Köhler H, Zamora P, Zúñiga G E. 2019. UV-B shock induces photoprotective flavonoids but not antioxidant activity in Antarctic Colobanthus quitensis (Kunth) Bartl. Environmental and Experimental Botany, 159, 179–190.
Elmlinger M, Bolle C, Batschauer A, Oelmüller R, Mohr H. 1994. Coaction of blue light and light absorbed by phytochrome in control of glutamine synthetase gene expression in Scots pine (Pinus sylvestris L.) seedlings. Planta, 192, 189–194.
Fan X X, Xue F, Song B, Chen L H, Xu G, Xu H. 2019. Effects of blue and red light on growth and nitrate metabolism in pakchoi. Open Chemistry, 17, 456–464.
Forde B G, Lea P J. 2007. Glutamate in plants: metabolism, regulation, and signalling. Journal of Experimental Botany, 58, 2339–2358.
Gangappa S N, Botto J F. 2016. The multifaceted roles of HY5 in plant growth and development. Molecular Plant, 9, 1353–1365.
Ghaffari H R, Nasseri S, Yunesian M, Nabizadeh R, Pourfarzi F, Poustchi H, Sadjadi A, Fattahi M R, Safarpour A R. 2019. Monitoring and exposure assessment of nitrate intake via fruits and vegetables in high and low risk areas for gastric cancer. Journal of Environmental Health Science and Engineering, 17, 445–456.
Hageman R, Reed A. 1980. Nitrate reductase from higher plants. Methods in Enzymology, 69, 270–280. 
Han X Z, Tohge T, Lalor P, Dockery P, Devaney N, Esteves-Ferreira A A, Fernie A R, Sulpice R. 2017. Phytochrome A and B regulate primary metabolism in Arabidopsis leaves in response to light. Frontiers in Plant Science, 8, 1394.
Jiao D, Huang X, Li X, Chi W, Kuang T, Zhang Q, Ku M S, Cho D. 2002. Photosynthetic characteristics and tolerance to photo-oxidation of transgenic rice expressing C4 photosynthesis enzymes. Photosynthesis Research, 72, 85–93.
Jonassen E M, Sandsmark B A, Lillo C. 2009. Unique status of NIA2 in nitrate assimilation: NIA2 expression is promoted by HY5/HYH and inhibited by PIF4. Plant Signaling & Behavior, 4, 1084–1086.
Kaur G, Wadhwa A, Abdin M, Sarwat M, Ahmad A. 2013. Molecular network of nitrogen and sulphur signaling in plants. In: Sarwat M, Ahmad A, Abdin M Z, Ibrahim M M, eds., Stress Signaling in Plants: Genomics and Proteomics Perspective, Volume 1. Springer. pp. 191–223. 
Kim D, Langmead B, Salzberg S L. 2015. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.
Kim Y J, Kim Y B, Li X, Choi S R, Park S, Park J S, Lim Y P, Park S U. 2015. Accumulation of phenylpropanoids by white, blue, and red light irradiation and their organ-specific distribution in Chinese cabbage (Brassica rapa ssp. pekinensis). Journal of Agricultural and Food Chemistry, 63, 6772–6778. 
Lei B, Bian Z H, Yang Q C, Wang J, Cheng R F, Li K, Liu W K, Zhang Y, Fang H, Tong Y X. 2018. The positive function of selenium supplementation on reducing nitrate accumulation in hydroponic lettuce (Lactuca sativa L.). Journal of Integrative Agriculture, 17, 837–846.
Li C X, Xu Z G, Dong R Q, Chang S X, Wang L Z, Khalil-Ur-Rehman M, Tao J M. 2017. An RNA-seq analysis of grape plantlets grown in vitro reveals different responses to blue, green, red LED light, and white fluorescent light. Frontiers in Plant Science, 8, 78.
Lillo C, Appenroth K J. 2001. Light regulation of nitrate reductase in higher plants: Which photoreceptors are involved? Plant Biology, 3, 455–465.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.
Machha A, Schechter A N. 2011. Dietary nitrite and nitrate: a review of potential mechanisms of cardiovascular benefits. European Journal of Nutrition, 50, 293–303.
Maier A, Schrader A, Kokkelink L, Falke C, Welter B, Iniesto E, Rubio V, Uhrig J F, Hülskamp M, Hoecker U. 2013. Light and the E3 ubiquitin ligase COP1/SPA control the protein stability of the MYB transcription factors PAP1 and PAP2 involved in anthocyanin accumulation in Arabidopsis. The Plant Journal, 74, 638–651.
Matt P, Krapp A, Haake V, Mock H P, Stitt M. 2002. Decreased Rubisco activity leads to dramatic changes of nitrate metabolism, amino acid metabolism and the levels of phenylpropanoids and nicotine in tobacco antisense RBCS transformants. The Plant Journal, 30, 663–677.
Monostori I, Heilmann M, Kocsy G, Rakszegi M, Ahres M, Altenbach S B, Szalai G, Pál M, Toldi D, Simon-Sarkadi L. 2018. LED lighting - modification of growth, metabolism, yield and flour composition in wheat by spectral quality and intensity. Frontiers in Plant Science, 9, 605.
Osterlund M T, Wei N, Deng X W. 2000. The roles of photoreceptor systems and the COP1-targeted destabilization of HY5 in light control of Arabidopsis seedling development. Plant Physiology, 124, 1520–1524.
Qi J, Yu S, Zhang F, Shen X, Zhao X, Yu Y, Zhang D. 2010. Reference gene selection for real-time quantitative polymerase chain reaction of mRNA transcript levels in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Plant Molecular Biology Reporter, 28, 597–604.
Qi L D, Liu S Q, Xu L, Yu W Y, Lang Q L, Hao S Q. 2007. Effects of light qualities on accumulation of oxalate, tannin and nitrate in spinach. Transactions of the Chinese Society of Agricultural Engineering, 4, 201–205.
Qu C, Hao B, Xu X, Wang Y, Yang C, Xu Z, Liu G. 2019. Functional research on three presumed asparagine synthetase family members in poplar. Genes, 10, 326.
Razal R A, Ellis S, Singh S, Lewis N G, Towers G N. 1996. Nitrogen recycling in phenylpropanoid metabolism. Phytochemistry, 41, 31–35.
Sakuraba Y, Yanagisawa S. 2018. Year: Light signalling-induced regulation of nutrient acquisition and utilisation in plants. Seminars in Cell & Developmental Biology, 83, 123–132.
Shapiro B, Stadtman E. 1970. The regulation of glutamine synthesis in microorganisms. Annual Reviews in Microbiology, 24, 501–524.
Sivasankar S, Oaks A. 1996. Nitrate assimilation in higher plants: The effect of metabolites and light. Plant Physiology and Biochemistry, 34, 609–620.
Tao R, Bai S, Ni J, Yang Q, Zhao Y, Teng Y. 2018. The blue light signal transduction pathway is involved in anthocyanin accumulation in ‘Red Zaosu’ pear. Planta, 248, 37–48.
Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: A matter of depth. Genome Research, 21, 2213–2223.
Tegeder M, Masclaux-Daubresse C. 2018. Source and sink mechanisms of nitrogen transport and use. New Phytologist, 217, 35–53.
Tevini M, Teramura A H. 1989. UV-B effects on terrestrial plants. Photochemistry and Photobiology, 50, 479–487.
Trapnell C, Pachter L, Salzberg S L. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105–1111.
Unamba C I, Nag A, Sharma R K. 2015. Next generation sequencing technologies: The doorway to the unexplored genomics of non-model plants. Frontiers in Plant Science, 6, 1074.
Vega-Mas I, Rossi M, Gupta K J, González-Murua C, Ratcliffe R, Estavillo J, González-Moro M. 2019. Tomato roots exhibit in vivo glutamate dehydrogenase aminating capacity in response to excess ammonium supply. Journal of Plant Physiology, 239, 83–91.
Zhang F X, Miao Y, Ruan J G, Meng S P, Dong J, Yin H, Huang Y, Chen F R, Wang Z C, Lai Y F. 2019. Association between nitrite and nitrate intake and risk of gastric cancer: A systematic review and meta-analysis. Medical Science Monitor, 25, 1788.
Zhang X B, Liu C J. 2015. Multifaceted regulations of gateway enzyme phenylalanine ammonia-lyase in the biosynthesis of phenylpropanoids. Molecular Plant, 8, 17–27.

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