RNA-Seq Analysis of Diverse Rice Genotypes to Identify the Genes Controlling Coleoptile Growth during Submerged Germination

Abstract

The rate of coleoptile elongation varies between different rice varieties that are grown under water during the germination stage. Compared to sensitive varieties, submergence-tolerant rice exhibits substantial coleoptile elongation in order to uptake oxygen (O2) from the surface and thus have a better chance to survive water stress. We conducted RNA-seq analysis in order to investigate 7-day-old shoot transcriptome dynamics in six rice genotypes that exhibit different coleoptile elongation rates under water. This enabled us to identify the genes involved in photosynthesis, lipid metabolism, glycolysis, anaerobic fermentation, hormone synthesis, cell wall growth and elongation, and to demonstrate that these genes are differentially regulated within, and between, genotypes. Further, in addition to determining how allelic variation affects anaerobic germination, we compared the expression patterns and genomic sequences of six genotypes; this enabled us to discover that some genes carry small-to-large deletions in the coding region of sensitive varieties. These structural variations may explain the absence of transcripts in the dataset, as well as the failure of sensitive variety to respond to submergence. On the basis of these results, we hypothesize that transcriptional regulation enhances coleoptile elongation. Although this is an area for future research, the outcome of this study is expected to facilitate rice breeding for direct-seeding.

Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination

“…Transcriptomic studies have shown that low oxygen induces a myriad of gene responsiveness in terms of transcript abundance (Lasanthi-Kudahettige et al, 2007; Narsai et al, 2009; Narsai et al, 2011; Sadiq et al, 2011; Narsai et al, 2015; Hsu and Tung, 2017). Accordingly, transcriptional regulation in oxygen sensing pathways has been extensively studied in plants.…”

“…With the development of large profiling techniques, considerable efforts have been made to study the global transcripts changes, protein abundance and metabolic variation during rice hypoxic germination (Lasanthi-Kudahettige et al, 2007; Narsai et al, 2009; Narsai et al, 2011; Sadiq et al, 2011; Narsai et al, 2015; Hsu and Tung, 2017). Although comparative analysis indicates that part of the hypoxic responsive pathways are conserved among several species (Narsai et al, 2011), the mechanism of adult flooding tolerance may be largely different from that of seed flooding tolerance (Lu et al, 2007; Lee et al, 2009).…”

Transcriptome Analysis for Abiotic Stresses in Rice (Oryza sativa L.)

“…Two different types of molecular mechanisms are adapted by rice ecotypes to survive under stress, SUB1A-mediated "quiescence strategy" [37,38] and "escape strategy" induced by SNORKEL1/2 [13]. The submergence response in rice consists of the differential expression of genes related to gibberellin biosynthesis, trehalose biosynthesis, anaerobic fermentation, cell wall modification, and transcription factors that include ethylene-responsive factor genes [39]. Though the regulatory mechanism in rice during submergence response has been comprehensively studied, the genome-wide gene expression as well as allelic variation among the cultivars for specific quantitative traits remained elusive.…”

“…Though the regulatory mechanism in rice during submergence response has been comprehensively studied, the genome-wide gene expression as well as allelic variation among the cultivars for specific quantitative traits remained elusive. One of the studies was conducted in six rice genotypes to estimate the coleoptile elongation rates during submergence [39]. The result postulated that the coleoptile elongation was augmented by transcriptional regulation.…”

“…The result postulated that the coleoptile elongation was augmented by transcriptional regulation. Further, the reason for the variation in anaerobic germination was due to the allelic variation caused by the small-to-large deletions in the coding region of susceptible varieties [39].…”