title: Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation.
abstract: To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify key regulatory genes, we performed an integrated analysis of the transcriptome and metabolome in sprouts germinated from three colored potato cultivars: light-red Hongyoung, dark-purple Jayoung, and white Atlantic. We investigated transcriptional and metabolic changes using statistical analyses and gene-metabolite correlation networks. Transcript and metabolite profiles were generated through high-throughput RNA-sequencing data analysis and ultraperformance liquid chromatography quadrupole time-of-flight tandem mass spectrometry, respectively. The identification and quantification of changes in anthocyanin were performed using molecular formula-based mass accuracy and specific features of their MS(2) spectra. Correlation tests of anthocyanin contents and transcriptional changes showed 823 strong correlations (correlation coefficient, R (2)>0.9) between 22 compounds and 119 transcripts categorized into flavonoid metabolism, hormones, transcriptional regulation, and signaling. The connection network of anthocyanins and genes showed a regulatory system involved in the pigmentation of light-red Hongyoung and dark-purple Jayoung potatoes, suggesting that this systemic approach is powerful for investigations into novel genes that are potential targets for the breeding of new valuable potato cultivars.
authors.affiliation: Environmental Risk and Welfare Research Team, Korea Basic Science Institute (KBSI), Seoul 02855, Republic of Korea.
authors.forename: Kyoungwon
authors.initials: K
authors.lastname: Cho
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Republic of Korea nammh@kbsi.re.kr kscholove@korea.kr.
authors.forename: Kwang-Soo
authors.initials: KS
authors.lastname: Cho
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Republic of Korea.
authors.forename: Hwang-Bae
authors.initials: HB
authors.lastname: Sohn
authors.affiliation: Omics System Research Team, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.
authors.forename: In Jin
authors.initials: IJ
authors.lastname: Ha
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Republic of Korea.
authors.forename: Su-Young
authors.initials: SY
authors.lastname: Hong
authors.affiliation: Environmental Risk and Welfare Research Team, Korea Basic Science Institute (KBSI), Seoul 02855, Republic of Korea.
authors.forename: Hyerim
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration (RDA), Jeongju 54874, Republic of Korea.
authors.forename: Young-Mi
authors.initials: YM
authors.lastname: Kim
authors.affiliation: Environmental Risk and Welfare Research Team, Korea Basic Science Institute (KBSI), Seoul 02855, Republic of Korea nammh@kbsi.re.kr kscholove@korea.kr.
authors.forename: Myung Hee
authors.initials: MH
authors.lastname: Nam
mesh_terms: D000872:Anthocyanins / Q000378:metabolism; D053898:Biosynthetic Pathways; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D055442:Metabolome / Q000235:genetics*; D010858:Pigmentation / Q000235:genetics*; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D011198:Solanum tuberosum / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D000872:Anthocyanins; D012333:RNA, Messenger
keywords: Anthocayanin; RNA-seq; colored potato; metabolomics; ultrapressure liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS).