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.

Highlights

  • Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application

  • Considerable variations in regeneration efficiency among a multiplicity of rice cultivars, especially between these sub-species exist based on research with model varieties such as Nipponbare, PB-1 and IR64 [indica]13,14

  • The 2,4-D induced embryogenic calli were examined at different time points for shoot initiation frequency in MS+ TDZ and MS-1 containing regeneration medium as described in materials and methods

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Summary

Introduction

Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Somatic embryogenesis is the process of developing bipolar structures that derived from haploid or diploid somatic cells and formed through an embryological stage without fusion of gametes that are not connected to the primary vascular tissues of the mother calli It is a unique process in plants and has considerable interest for biotechnological application such as clonal propagation, production of synthetic seeds and genetic transformation[4,5]. Somatic embryogenesis in integration with classical breeding programs and molecular biology techniques provides a valuable tool to enhance the genetic improvement of crop species[4] Likewise it is useful in studying embryo development processes and several plant physiological aspects[6,7,8]. As a model species with completely sequenced genomes of two subspecies, indica and japonica, rice holds a unique position to study questions regarding genomic network regulating developmental events of somatic embryogenesis and regeneration. Our approach is based on the use of comparative trascriptome profiling of Nipponbare (japonica) and PB-1 (indica) at six different developmental stages of somatic embryogenesis and regeneration (Stage 1–6) using the Illumina Hiseq 2000 transcriptome sequencing platform

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