Characterization of genes associated with salt tolerance using transcriptome analysis and quantitative trait loci mapping in rice

Authors: KIM, DONG-MIN - Chungnam National University; KANG, J - Chungnam National University; SHIM, KYU-CHAN - Chungnam National University; KIM, HYUNJUNG - Lg Chem; Tai, Thomas; AHN, SANG-NAG - Chungnam National University

Submitted to: Plant Breeding and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2021
Publication Date: 12/1/2021
Citation: Kim, D., Kang, J., Shim, K., Kim, H., Tai, T., Ahn, S. 2021. Characterization of genes associated with salt tolerance using transcriptome analysis and quantitative trait loci mapping in rice. Plant Breeding and Biotechnology. 9(4):318-330. https://doi.org/10.9787/PBB.2021.9.4.318.
DOI: https://doi.org/10.9787/PBB.2021.9.4.318

Interpretive Summary: Rice is a very salt sensitive crop and the salinity levels in reclaimed paddy fields causes reduced rice production in Asia and Africa. Using two approaches, transcriptome analysis (i.e., RNA-seq) and quantitative trait loci mapping, salt tolerance-associated genes and loci were identified from African cultivated rice (Oryza glaberrima). Introgression lines, derived from crossing the Korean rice cultivar Milyang23 and an accession of O. glaberrima, exhibiting improved seedling stage salt tolerance compared to the salt-sensitive parent Milyang23 were identified. The introgressed segments derived from O. glaberrima were defined with simple sequence repeat markers. Concurrently, RNA-seq was used to identify genes from the roots of O. glaberrima seedlings exposed to salt stress (100 mM NaCl) and non-stress conditions at two time points (6 and 24 hours after exposure). Several hundred differentially expressed genes (stress versus non-stress) at the two time points were identified and 7 of these genes were found to reside in one O. glaberrima segment on chromosome 2 of some of the salt-tolerant introgression lines. This study establishes the foundation for further investigations to establish the role these genes may play in enhancing salt tolerance in rice seedlings. Moreover, the differentially expressed transcripts identified may find utility as markers for selection strategies.

Technical Abstract: We conducted transcriptome profiling analysis of O. glaberrima root using RNA-Seq at the control (OCR) and 100 mM NaCl treatment (OTR) at two time points (6 and 24 hours after treatment) to detect genes induced by salt stress. RNA-Seq analysis generated 102,690,698 sequence reads representing 30,388 predicted transcripts including 6,189 unannotated in Rice Annotation Project database. A total of 539 and 424 of differentially expressed genes (DEGs) were detected between OCR_6h vs OTR_6h and between OCR_24h vs OTR_24h, respectively (p < 0.001, q < 0.05). Among these DEGs, 262 genes showed constant differential expression at both 6h and 24h, and these included a bHLH containing protein, WRKY transcription factor, serine/threonine kinase, R2R3 MYB protein, and amino acid transporters. Interestingly, an enhanced seedling salt tolerant introgression line IL55 from a cross between a salt sensitive indica cultivar “Milyang23” and O. glaberrima harbors one DEG, Os02g0787300 encoding a mitogen activated protein kinase kinase (MAPKK) on chromosome 2. Analysis of the salt tolerance of the F2:3 lines from a cross between IL55 and Milyang23 indicated that the O. glaberrima segment on chromosome 2 containing the MAPKK gene was responsible for better shoot growth under salt stress at the seedling stage (p < 0.05). The salt inducible genes will be evaluated in introgression lines (ILs) to understand whether the expression of these genes is associated with salt tolerance in ILs having the Milyang23 genetic background. Transcriptome sequence information in this study may be useful for developing DNA markers linked to salinity tolerance for MAS breeding.