title: Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway.
abstract: The accumulation of anthocyanin in horticultural crops not only improves their stress tolerances but also their nutritional values. Many key regulatory and structural genes in anthocyanin biosynthesis have been identified in model plants, but limited information is available for non-model plant species featured with colored leaves. In this study, two Pak Choi varieties with green or purple leaves were selected to analyze the anthocyanin biosynthesis through RNA-Seq.
  
  
  
  A total of 2475 unigenes were differentially expressed between these tested varieties, including 1303 down-regulated and 1172 up-regulated genes in the purple-leafed one. The reliability of the RNA-Seq was further confirmed by using real-time quantitative PCR. Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the differentially expressed genes revealed 'flavonoid biosynthesis' was the only enriched pathway in the purple-leafed variety: In the pathway of phenylpropanoid metabolism, Bra017210, Bra039777, and Bra021637 were expressed at higher levels in the purple-leafed variety;　among the early anthocyanin biosynthetic genes, Bra037747 transcripts were only detected in the purple-leafed variety but not in the green-leafed one; among the late anthocyanin biosynthetic genes, Bra027457, Bra013652, Bra019350, Bra003021, Bra035004, and Bra038445 were all up-regulated in purple-leafed variety; and genes encoding anthocyanin-related transcription factors, such as Bra016164, and genes encoding anthocyanin transportation, such as GST F12, were also identified as up-regulated ones in the purple-leafed variety.
  
  
  
  The current result provided a valuable insight into the anthocyanin accumulation in the purple-leafed variety of Pak Choi and a bioinformatic resource for further functional identification of key allelic genes determining the difference of anthocyanin content between Pak Choi varieties.
authors.affiliation: College of Horticulture, Northeast Agricultural University, 59 Mucai street, 150030, Harbin, People's Republic of China. caszhanglu@hotmail.com.
authors.forename: Lu
authors.identifier: 0000-0001-5537-0445
authors.initials: L
authors.lastname: Zhang
authors.affiliation: College of Agro-grassland Science, Nanjing Agricultural University, 1 Weigang, 210095, Nanjing, People's Republic of China.
authors.forename: Bin
authors.initials: B
authors.lastname: Xu
authors.affiliation: College of Horticulture, Northeast Agricultural University, 59 Mucai street, 150030, Harbin, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry Sciences, 100091, Beijing, People's Republic of China.
authors.forename: Yanfang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: College of Horticulture, Northeast Agricultural University, 59 Mucai street, 150030, Harbin, People's Republic of China.
authors.forename: Lianxue
authors.initials: L
authors.lastname: Fan
authors.affiliation: College of Horticulture, Northeast Agricultural University, 59 Mucai street, 150030, Harbin, People's Republic of China.
authors.forename: Muxuan
authors.initials: M
authors.lastname: Wen
authors.affiliation: College of Horticulture, Northeast Agricultural University, 59 Mucai street, 150030, Harbin, People's Republic of China.
authors.forename: Jiaxin
authors.initials: J
authors.lastname: Sui
mesh_terms: D000872:Anthocyanins / Q000096:biosynthesis / Q000378:metabolism*; D053898:Biosynthetic Pathways / Q000235:genetics*; D001937:Brassica / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D005809:Genes, Regulator; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D019655:Quantitative Trait, Heritable; D059467:Transcriptome
chemical_list: D000872:Anthocyanins
keywords: Anthocyanin; Brassica campestris L. ssp. chinensis L. Makino; RNA-Seq; Transcriptome