title: Genome-wide expression analysis of rice ABC transporter family across spatio-temporal samples and in response to abiotic stresses.
abstract: Although the super family of ATP-binding cassette (ABC) proteins plays key roles in the physiology and development of plants, the functions of members of this interesting family mostly remain to be clarified, especially in crop plants. Thus, systematic analysis of this family in rice (Oryza sativa), a major model crop plant, will be helpful in the design of effective strategies for functional analysis. Phylogenomic analysis that integrates anatomy and stress meta-profiling data based on a large collection of rice Affymetrix array data into the phylogenic context provides useful clues into the functions for each of the ABC transporter family members in rice. Using anatomy data, we identified 17 root-preferred and 16-shoot preferred genes at the vegetative stage, and 3 pollen, 2 embryo, 2 ovary, 2 endosperm, and 1 anther-preferred gene at the reproductive stage. The stress data revealed significant up-regulation or down-regulation of 47 genes under heavy metal treatment, 16 genes under nutrient deficient conditions, and 51 genes under abiotic stress conditions. Of these, we confirmed the differential expression patterns of 14 genes in root samples exposed to drought stress using quantitative real-time PCR. Network analysis using RiceNet suggests a functional gene network involving nine rice ABC transporters that are differentially regulated by drought stress in root, further enhancing the prediction of biological function. Our analysis provides a molecular basis for the study of diverse biological phenomena mediated by the ABC family in rice and will contribute to the enhancement of crop yield and stress tolerance.
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea. Electronic address: tuyetvan@khu.ac.kr.
authors.forename: Van Ngoc Tuyet
authors.initials: VN
authors.lastname: Nguyen
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea. Electronic address: moonsun@khu.ac.kr.
authors.forename: Sunok
authors.initials: S
authors.lastname: Moon
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea. Electronic address: khjung2010@khu.ac.kr.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics* / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D055106:Genome-Wide Association Study; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D013312:Stress, Physiological
chemical_list: D018528:ATP-Binding Cassette Transporters; D010940:Plant Proteins
keywords: ABC transporters; Abiotic stress responses; Meta-analysis of tissue specific expression profiles; Phylogenomic analysis; Rice