Transcriptome profiling identifies ABA mediated regulatory changes towards storage filling in developing seeds of castor bean (Ricinus communis L.)

Abstract

BackgroundThe potential biodiesel plant castor bean (Ricinus communis) has been in the limelight for bioenergy research due to the availability of its genome which raises the bar for genome-wide studies claiming advances that impact the “genome-phenome challenge”. Here we report the application of phytohormone ABA as an exogenous factor for the improvement of storage reserve accumulation with a focus on the complex interaction of pathways associated with seed filling.ResultsAfter the application of exogenous ABA treatments, we measured an increased ABA levels in the developing seeds cultured in vitro using the ELISA technique and quantified the content of major biomolecules (including total lipids, sugars and protein) in treated seeds. Exogenous ABA (10 μM) enhanced the accumulation of soluble sugar content (6.3%) followed by deposition of total lipid content (4.9 %). To elucidate the possible ABA signal transduction pathways towards overall seed filling, we studied the differential gene expression analysis using Illumina RNA-Sequencing technology, resulting in 2568 (1507-up/1061-down regulated) differentially expressed genes were identified. These genes were involved in sugar metabolism (such as glucose-6-phosphate, fructose 1,6 bis-phosphate, glycerol-3-phosphate, pyruvate kinase), lipid biosynthesis (such as ACS, ACBP, GPAT2, GPAT3, FAD2, FAD3, SAD1 and DGAT1), storage proteins synthesis (such as SGP1, zinc finger protein, RING H2 protein, nodulin 55 and cytochrome P450), and ABA biosynthesis (such as NCED1, NCED3 and beta carotene). Further, we confirmed the validation of RNA-Sequencing data by Semi-quantitative RT-PCR analysis.ConclusionsTaken together, metabolite measurements supported by genes and pathway expression results indicated in this study provide new insights to understand the ABA signaling mechanism towards seed storage filling and also contribute useful information for facilitating oilseed crop functional genomics on an aim for utilizing castor bean agricultural and bioenergy use.

Heat stress during seed filling interferes with sulfur restriction on grain composition and seed germination in oilseed rape (Brassica napus L.)

“…ABA content in seeds increases during SSP deposition and then decreases during seed desiccation, and low ABA content is a precondition for seed germination (Crouch and Sussex, 1981 ; Finkelstein et al, 1985 ; Rajjou et al, 2011 ). Exogenous ABA was shown to enhance the accumulation of soluble sugars followed by the deposition of lipids (Chandrasekaran et al, 2014 ). GAs are known to be involved in cell expansion and to counterbalance the effects of ABA on germination by negatively regulating germination repressors (for review see Brian, 2008 ; Rajjou et al, 2011 ).…”

Peer Review #1 of "Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean (v0.1)"

“…Additionally, JcRbohN, JcRbohD, and JcRbohF are associated with pathogenic infection, where JcRbohN is also involved in BA response. In developing castor bean seeds cultured in vitro, transcriptome profiling also showed that RcRbohE and RcRbohH were significantly downregulated by ABA (Chandrasekaran et al, 2014). Thus far, the involvement in pathogenic infection and stress responses has been reported for various Rboh genes in other species, including AtRbohD, AtRbohF, AtRbohJ, OsRbohF1, OsRbohH1, OsRbohE1, VvRbohD1, VvrbohD2, VvRbohF, VvRbohB, VvRbohC, VvRbohH, HbRbohB, HbRbohC1, HbRbohC2, HbRbohD1, HbRbohD2, HbRbohF1, HbRbohF2, and HbRbohN (Evans et al, 2005;Sagi & Fluhr, 2006;Maruta et al, 2011;Xie et al, 2011;Chaouch et al, 2012;Cheng et al, 2013;Kaur et al, 2014;Chang et al, 2016;.…”

High-throughput sequencing in medicinal plant transcriptome studies

“…Phytohormone ABA was applied as an exogenous factor for the improvement of storage reserve accumulation with a focus on the complex interaction of pathways associated with seed filling (Chandrasekaran et al, 2014). Phytohormone ABA was applied as an exogenous factor for the improvement of storage reserve accumulation with a focus on the complex interaction of pathways associated with seed filling (Chandrasekaran et al, 2014).…”