Gene Expression Dynamics in Rice Peduncles at the Heading Stage

Effects of Water Isotope Composition on Stable Isotope Distribution and Fractionation of Rice and Plant Tissues

Rice origin authenticity is important for food safety and consumer confidence. The stable isotope composition of rice is believed to be closely related to its water source, which affects its origin characteristics. However, the influence of water availability on the distribution of rice stable isotopes (δ2H and δ18O) is not clear. In this study, three irrigation waters with different isotopic values were used to investigate isotopic water use effects of Indica and Japonica rice, using pot experiments. Under three different water isotope treatments, the δ2H values of Indica polished rice showed significant differences (-65.0 ± 2.3, -60.5 ± 0.8 and -55.8 ± 1.7‰, respectively, p < 0.05) compared to δ13C and δ15N, as did Japonica polished rice. The values of δ2H and δ18O of rice became more positive when applying more enriched (in 2H and 18O) water, and the enrichment effect was higher in rice than in the corresponding plant tissue. In addition, the δ2H and δ18O values of Indica rice leaves decreased at the heading stage, increased at the filling stage, and then decreased at the harvest stage. Japonica rice showed a similar trend. δ2H changes from stem to leaf were more negative, but δ18O changes were more positive, and δ2H and δ18O values from leaf to rice were more positive for both brown and polished rice. The results from this study will clarify different water isotopic composition effects on rice and provide useful information to improve rice origin authenticity using stable isotope-based methods.

Expression profiling of yield related genes in rice cultivars under terminal drought stress

BACKGROUND

Rice crop may experience a significant reduction in yield-up to 50%-due to two occurrences during drought stress: unsuccessful peduncle elongation in panicle exertion and ineffective grain filling. The comprehension of mechanisms that promote drought tolerance during these growth phases is crucial for the production of rice that can withstand drought conditions, thus averting a decrease in crop yield.

METHODS AND RESULTS

The expression of two xyloglucan endo transhydrolase/glucosylase genes (OsXTH 5 and 19) in peduncle tissue and a sucrose transporter gene (OsSUT1) in flag leaf sheath were assessed. An experiment was carried out in a factorial arrangement based on completely randomized design in which, factor A was two rice cultivars (Vandana as tolerant and Tarom mahalli as local susceptible to drought) and factor B was five drought stress treatments (full irrigation, drought stress duration in 72 and 96 h, re-watering after 120 and 192 h). Results showed that expression of OsXTH19 and OsXTH5 genes were upregulated in both Vandana and Tarom mahalli cultivars due to stress treatments. OsXTH19 expression was found to decrease while OsXTH5 expression increased during re-watering treatments. It is likely that the persistence of peduncle growth in the drought-tolerant Vandana cultivar can be attributed to the presence of OsXTH19 under drought conditions and OsXTH5 after re-watering. The expression of OsSUT1 in flag leaf sheath of Vandana in re-watering treatments was reached 8-60-fold re-watering.

CONCLUSIONS

Peduncle elongation was attributed to two XTH genes under drought stress condition. Panicle exertion may be promoted by sustaining peduncle growth despite drought stress. Consequently, this may led to reduce in non fertile florets and decrease in grain yield by 50%. As grain filling depend to expression of OsSUT1 in flag leaf sheath under drought stress, to improve rice cultivars under aerobic production system and drought stress, it is advised to apply these findings in rice breeding programs.

Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice

Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5'-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F2 mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01412-1.

Gene Expression in the Developing Seed of Wild and Domesticated Rice

The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value.

The dynamics of carbohydrate and associated gene expression in the stems and roots of upland cotton (Gossypiumhirsutum L.) during carbon remobilization

Carbohydrates remobilization in non-leaf organs has a potential association with the formation of cotton yield. However, our understanding of the physiological and molecular mechanisms regulating carbon remobilization during flowering is still limited. The objectives of the study were to: i) evaluate the potential of carbohydrate remobilization in stems and roots to yield formation; ii) unravel the carbon metabolism and transport associated gene expression patterns regulating carbon remobilization. Two cotton lines 4003-6 and 4003-10 were employed to examine leaf photosynthesis, reproductive biomass accumulation, and carbon dynamics in stems and roots during reproductive growth. The results showed that decreasing leaf photosynthetic capacity combined with rapidly increasing reproductive biomass and leaf area index is accompanied by the initiation of carbohydrate remobilization during first flowering to peak flowering. The proportion of sucrose to total nonstructural carbohydrate was also decreased at that period. The upper and lower of stem recorded higher soluble sugars and starch concentrations, respectively compared to the two others. The gross contribution rate of carbon remobilization to seed cotton yield ranged from 2.83% to 7.12%. Key genes and sugar transporters related to starch and sucrose metabolism in the lower stem exhibited significant up- or down-regulated expressions indicating their important roles in carbon reserves remobilization. Three pivotal sugar transporters SWEET1, TMT2, and ERLD5 presented higher transcript levels at peak flowering suggesting more active sugar movement occurring at that stage. The present study provides potential target genes for engineering carbohydrate metabolism and transport to improve the remobilization efficiency of nonstructural carbohydrates.

Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage

Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01059-2.