Black rice cultivar from Java Island of Indonesia revealed  genomic, proteomic, and anthocyanin nutritional value

Dewi Ratih Tirto  Sari; Atchara  Paemanee; Sittiruk  Roytrakul; James Robert Ketudat  Cairns; Anna Safitri; Fatchiyah Fatchiyah

doi:10.18388/abp.2020_5386

Dewi Ratih Tirto Sari 1Research Center of Smart Molecule of Natural Genetics Resources, Brawijaya University, Indonesia; 2Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia https://orcid.org/0000-0002-3937-841X
Atchara Paemanee 3Proteomic Laboratory, National Center for Biotechnology and Genetic Engineering, National Science and Development Agency, Pathumthani, Thailand https://orcid.org/0000-0001-9206-3153
Sittiruk Roytrakul Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand https://orcid.org/0000-0003-3696-8390
James Robert Ketudat Cairns School of Chemistry, Institute of Science, and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand https://orcid.org/0000-0003-3042-1626
Anna Safitri 1Research Center of Smart Molecule of Natural Genetics Resources, Brawijaya University, Indonesia; 2Department of Chemistry, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia https://orcid.org/0000-0003-4262-8640
Fatchiyah Fatchiyah 1Research Center of Smart Molecule of Natural Genetics Resources, Brawijaya University, Indonesia; 2Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia; https://orcid.org/0000-0001-6241-9665

DOI: https://doi.org/10.18388/abp.2020_5386

Abstract

Black rice is considered to be functional food containing anthocyanins as bioactive compounds. This study examined the genomic and proteomic patterns in local black rice from Java Island, Indonesia, with attention to the mechanism of anthocyanin synthesis. Three kinds of black rice from Java Island, including black rice from East Java (BREJ), black rice from Central Java (BRCJ), and black rice from West Java (BRWJ), were studied in comparison to white rice (WREJ) and red rice (RREJ). Genomic profiling was done by simple sequence repeat (SSR) analysis, and sequencing of red coleoptile (Rc) and glycosyltransferase (GT) genes, followed by in silico analysis. Total anthocyanin was investigated by ultra-high performance liquid chromatography- diode array detector (UHPLC-DAD). The proteomic profiles were determined by liquid-chromatography and mass spectrometry of tryptic peptides. The SSR profiles showed a specific band in each black rice variant. The Rc gene exon-2 sequences were similar in the three black rice cultivars. The GT gene sequence was identified as a new variant that correlates with the purple stem, leaf, bran, and whole grain morphology seen exclusively in the BRWJ cultivar. The anthocyanin composition in Java black rice is diverse. The highest cyanidin level was seen in BRWJ and the highest level of peonidin-3-O-glucoside in BREJ. Proteomic profiling of the black rice cultivars demonstrated that the expression of proteins that might be related to the levels of anthocyanin synthesis varied. These studies conclude that the genomic, proteomic and anthocyanins composition of Java black rice cultivars may be used the improvement of their functional nutrition values.