Deep Transcriptome Sequencing of Wild Halophyte Rice, Porteresia coarctata, Provides Novel Insights into the Salinity and Submergence Tolerance Factors

Abstract

Porteresia coarctata is a wild relative of rice with capability of high salinity and submergence tolerance. The transcriptome analyses of Porteresia can lead to the identification of candidate genes involved in salinity and submergence tolerance. We sequenced the transcriptome of Porteresia under different conditions using Illumina platform and generated about 375 million high-quality reads. After optimized assembly, a total of 152 367 unique transcript sequences with average length of 794 bp were obtained. Many of these sequences might represent fragmented transcripts. Functional annotation revealed the presence of genes involved in diverse cellular processes and 2749 transcription factor (TF)-encoding genes in Porteresia. The differential gene expression analyses identified a total of 15 158 genes involved in salinity and/or submergence response(s). The stress-responsive members of different TF families, including MYB, bHLH, AP2-EREBP, WRKY, bZIP and NAC, were identified. We also revealed key metabolic pathways, including amino acid biosynthesis, hormone biosynthesis, secondary metabolite biosynthesis, carbohydrate metabolism and cell wall structures, involved in stress tolerance in Porteresia. The transcriptome analyses of Porteresia are expected to highlight genes/pathways involved in salinity and submergence tolerance of this halophyte species. The data can serve as a resource for unravelling the underlying mechanism and devising strategies to engineer salinity and submergence tolerance in rice.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…Because the wild relatives of rice are adapted to different biogeographic ranges (Fig. 1a) and can tolerate many biotic and abiotic stresses [1][2][3][4][5][6] , they constitute an important reservoir for crop improvement. Strategies to harness such traits for crop improvement show clear promise, as exemplified by the introgression of bacterial blight resistance (Xa21) from the wild species Oryza longistaminata 7 .…”

The Possible overlap between Salinity and Mechanical Challenges in <I>Porteresia Coarctata</I>

“…More recent next-generation transcriptome enrichment (Garg et al, 2013) indicates a close functional overlap of submergence and salinity tolerance trait in Porteresia, as is expected of mangrove habitat plants. However, Garg et al (2013) and Sengupta and Majumder (2009) made an observation that the similarity of Porteresia transcripts to rice transcripts was not very high. Candidate gene based studies showed that a large number of Porteresia genes are similar to Rice genes.…”

“…The extended families of salt-induced transcription factors reported by Garg et al, (2013) are rather significant. Most of the TFs are upregulated during salinity stress and the transcriptional activity is repressed under submergence stress (Garg et al, 2013).…”

“…The genomic and proteomic studies so far done in Porteresia have been discussed by different workers (Sengupta and Majumder, 2009;Garg et al, 2013). Porteresia has been vigorously used as a valuable bioresource for salt-tolerant gene pool in the last decade (Majee et al, 2004;Sengupta et al, 2008).…”

“…Candidate gene based studies showed that a large number of Porteresia genes are similar to Rice genes. On the other hand, a more comprehensive scenario obtained from proteomic and genomic studies highlights the fact that many of the salt-stress induced transcripts in Porteresia do not have any homologues or orthologues in rice or wild rice; and they are not even anotated (Sengupta et al, 2009;Garg et al, 2013). It has also been shown by Sengupta et al 2008 that genes like Inositol methyl Transferase, which has not been reported to be present in rice, are present in Porteresia.…”