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_6hours vs OTR_6hours and between OCR_24hours vs OTR_24hours, respectively (P < 0.001, q < 0.05). Among these DEGs, 262 genes showed constant differential expression at both 6 hours and 24 hours, 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 F_2:3 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. 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.

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The
objective
of this study was to detect QTLs for rice seedling traits under normal water (control) and low water conditions (drought stress). Ninety-eight recombinant inbred lines (RILs) from a cross between closely-related japonica cultivars, M-203 and M-206 were grown under both low water and normal water conditions. QTLs for morphological traits were investigated at seedling stage using 5,164 single nucleotide polymorphisms via genotyping-by-sequencing. Twenty-three QTLs were associated with four seedling traits: shoot length (SL), root length (RL), shoot dry weight (SW) and root dry weight (RW), were detected and most QTLs were clustered on chromosome 1, 6, 7 and 11. Under normal water conditions, nine QTLs for seedling traits were detected and M-203 alleles increased all the values. The locations of most QTLs were consistent with genes that regulate or respond to auxin and gibberellin. For drought tolerance, fourteen QTLs were detected including seven for drought stress conditions and seven for relative performance (values from drought stress conditions/normal water conditions). Seven QTLs from drought stress conditions coincided with the loci of previously identified drought tolerance genes. Based on the shoot and root length under drought stress conditions, five lines exhibiting the highest values in common were selected as a drought tolerance group. Those lines exhibited better growth than the parents under drought stress conditions and had QTLs alleles for drought tolerance detected in this study. QTL information and selected lines may be used for improving seedling vigor and drought tolerance of rice in breeding programs.

Citations

Citations to this article as recorded by  

• Morpho-physiological and biochemical response of rice (Oryza sativa L.) to drought stress: A review
  Utsav Bhandari, Aakriti Gajurel, Bharat Khadka, Ishwor Thapa, Isha Chand, Dibya Bhatta, Anju Poudel, Meena Pandey, Suraj Shrestha, Jiban Shrestha
  Heliyon.2023; 9(3): e13744.     CrossRef
• Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions
  Bahman Khahani, Elahe Tavakol, Vahid Shariati, Laura Rossini
  Scientific Reports.2021;[Epub]     CrossRef