Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes

Chaudhary, Saurabh; Kalkal, Meenu

doi:10.3390/life11040285

Cited by 6 publications

(3 citation statements)

References 49 publications

(83 reference statements)

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“…For example, nutrient stress caused differential AS regulation of the NRR gene in rice (Zhang Y. M. et al, 2012). Moreover, a recent study demonstrated that nitrogen starvation modulated differential AS and transcript usage of various metabolism-related genes in rice (Chaudhary and Kalkal, 2021), and AS of OsGS1;1 affects NUE, grain development, and amylose content in rice (Liu et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

OsGRF4AA compromises heat tolerance of developing pollen grains in rice

Li²,

Liu³

et al. 2023

Front. Plant Sci.

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Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of OsGRF4 (Oryza sativa growth-regulating factor 4; OsGRF4AA), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of OsGRF4 enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of OsGRF4, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in OsGRF4 affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.

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Section: Discussionmentioning

confidence: 99%

OsGRF4AA compromises heat tolerance of developing pollen grains in rice

Li²,

Liu³

et al. 2023

Front. Plant Sci.

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“…RTD is the major backbone for accurate gene quantification of RNA-seq data analysis and consists of a list of genes and possible transcript isoforms of an organism ( Brown et al, 2017 ; Zhang et al, 2017a ; Rapazote-Flores et al, 2019 ; Vitoriano et al, 2021 ). The quality of the transcriptome annotation could help with fast and accurate estimation of transcript expression and AS events using the RNA-seq data with the help of the 3DRNA-seq tool ( Chaudhary and Kalkal, 2021 ; Guo et al, 2021 ; Vitoriano et al, 2021 ; Escudero-Martinez et al, 2022 ). Despite rice being an important crop plant and several attempts being made in the past to improve its transcriptome annotation and AS diversity, IndicaRTD contains a significantly higher number of transcript isoforms ( Lu et al, 2010 ; Zhang et al, 2010 ; Zhang H. et al, 2019 ; Schaarschmidt et al, 2020 ; Wang S. et al, 2022 ; Hasan et al, 2022 ; He et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica

Srikakulam

Sridevi²,

Pandi³

2022

Front. Genet.

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The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.

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“…Chaudhary and Kalkal [1] present the results of bioinformatics analysis of publicly available transcriptome data generated from the root and shoot tissues of rice genotypes grown under optimal and nitrogen starvation conditions revealing the differentially expressed and alternatively spliced genes. This work extends our understating of nitrogen utilization efficiency mechanisms in the important crop plant.…”

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confidence: 99%