title: Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies.
abstract: Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells.
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.
authors.forename: Yuvraj
authors.initials: Y
authors.lastname: Indoliya
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.
authors.forename: Poonam
authors.initials: P
authors.lastname: Tiwari
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.
authors.forename: Abhisekh Singh
authors.initials: AS
authors.lastname: Chauhan
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.
authors.forename: Ridhi
authors.initials: R
authors.lastname: Goel
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.
authors.forename: Manju
authors.initials: M
authors.lastname: Shri
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.
authors.forename: Sumit Kumar
authors.initials: SK
authors.lastname: Bag
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.
authors.forename: Debasis
authors.initials: D
authors.lastname: Chakrabarty
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000187:drug effects / Q000235:genetics*; D012275:Oryza / Q000145:classification / Q000196:embryology* / Q000235:genetics*; D010937:Plant Growth Regulators / Q000378:metabolism / Q000494:pharmacology; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D058439:Plant Somatic Embryogenesis Techniques / Q000379:methods*; D025341:Principal Component Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction; D013045:Species Specificity; D013997:Time Factors; D046509:Tissue Culture Techniques / Q000379:methods
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins