Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain- filling under stagnant flooding

Kuanar, Sandhya Rani; Molla, Kutubuddin A.; Chattopadhyay, Krishnendu; Sarkar, Ramani Kumar; Mohapatra, Pravat K.

doi:10.1038/s41598-019-54908-2

Cited by 23 publications

(27 citation statements)

References 60 publications

(94 reference statements)

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“…Some studies showed that cytokinin is involved in regulating grain production [ 41 , 42 ]. Other plant hormones, including BR, ET, JA, and SA, also play a crucial role in seed development and grain production [ 5 , 17 , 18 , 43 , 44 , 45 ]. In this study, we observed that many differentially expressed genes were related to plant hormone biosynthesis and/or signaling pathways; these genes included PYLs (abscisic acid receptor), ABI5 (ABSCISIC ACID-INSENSITIVE 5), PP2C (probable protein phosphatase 2C), SAPKs (serine/threonine-protein kinase), SAURs (auxin-responsive protein), JAR (jasmonic acid-amido synthetase), EIN2 (ETHYLENE-INSENSITIVE 2), and TIFY ( Table S2 ).…”

Section: Discussionmentioning

confidence: 99%

“…The change in plant hormone levels could also affect the grain filling process in plants. Increasing ethylene levels in developing seeds inhibits the accumulation and activities of starch synthesis-related enzymes, and further inhibits the biosynthesis of carbohydrates in the developing spikelets and decreases the grain-filling rate [ 5 , 6 ]. Abscisic acid (ABA) also regulates the sink activity during grain filling [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.)

Wang

Song

et al. 2020

IJMS

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Grain filling is an importantly developmental process which is associated with the yield and quality of foxtail millet (Setaria italic L.). However, the molecular mechanisms of grain filling are rarely reported in foxtail millet. In our study, RNA-seq was performed to investigate the transcriptional dynamics and identify the key genes involved in grain filling in foxtail millet at five different developmental stages. A total of 11,399 differentially expressed genes (DEGs), including 902 transcription factors (TFs), were identified. Certain important genes involved in grain filling were discovered through a function annotation and temporal expression patterns analysis. These genes included genes associated with starch biosynthesis, cell-wall invertases, hormone signal transduction, and polyamine metabolism pathways. The expression levels of seven randomly selected DEGs were validated by a quantitative real-time polymerase chain reaction (qRT-PCR). This study provides the first insight into the changes in the gene expression of grain filling at different developmental stages in foxtail millet. These results could help understand the complex molecular mechanisms of the panicle formation in foxtail millet and other cereal crops.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.)

Wang

Song

et al. 2020

IJMS

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“…6c). In particular, the expression at anthesis (day 0) was higher in the former compared to the latter, when ethylene production culminates in rice spikelets resulting grain morbidity 7,13,16 irrespective of cultivar difference 44 . In comparison, the situation was just opposite for miRNAs with targets on IAA pathway (Fig.…”

Section: Genes Targeted By Differentially Expressed Mirnasmentioning

confidence: 93%

“…These miRNAs had Os11t0141000-02 and Os07t0239400-01 (PP2A regulatory subunit-like protein and ethylene-responsive small GTP-binding proteins) as targets with highest probability. Irrespective of cultivar difference, ethylene production climaxes at anthesis 44 and in all probability, these miRNA participated in the process of ethylene biosynthesis for both high and low sterile cultivars used. Further, our study identified expression of MIR396h on day 5 post anthesis, that had multiple targets, such as, Os02t0776900-01, a transcription activator involved in gibberellin induced stem elongation, Os01t0643300-02, an auxin efflux carrier protein and Os01t0643300-01, a PIN1-like auxin transport protein with maximum probability.…”

Section: Genes Targeted By Differentially Expressed Mirnasmentioning

confidence: 96%

MicroRNAs modulate ethylene induced retrograde signal for rice endosperm starch biosynthesis by default expression of transcriptome

Panigrahi

Panigrahy

Kariali

et al. 2021

Sci Rep

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Control of stage specific spike in ethylene production at anthesis has been a vauable route to potentially enhance genetic ceiling for grain filling of rice spikelet. A number of genes controlling ethylene homeostasis and starch synthesis have been identified so long, but lack of credible information on master modulation of gene expression by miRNAs and their target genes associated with hormonal dynamics obfuscate mechanisms controlling genotype difference in quantum of grain filling. The confusion accounts for consequent shrinkage of options for yield manipulation. In a two by two factorial design, miRNA regulation of spikelet specific grain development in low against high sterile recombinant inbred lines of rice Oryza sativa L. namely CR 3856-62-11-3-1-1-1-1-1-1 (SR 157) and CR 3856-63-1-1-1-1-1-1-1 (SR 159) respectively, and inferior verses superior spikelets were compared during first 10 days after anthesis. Grain filling was poorer in SR159 than SR157 and inferior spikelets in the former were most vulnerable. Between the cultivars, overall expression of unique miRNAs with targets on ethylene pathway genes was higher in SR159 than SR157 and the situation was opposite for auxin pathway genes. Precision analysis in psTarget server database identified up-regulation of MIR2877 and MIR530-5p having Os11t0141000-02 and Os07t0239400-01 (PP2A regulatory subunit-like protein and ethylene-responsive small GTP-binding proteins) and MIR396h having Os01t0643300-02 (an auxin efflux carrier protein) and Os01t0643300-01 (a PIN1-like auxin transport protein), as targets with highest probability at anthesis and 5 days after anthesis respectively, in the inferior spikelet and the fold change values of DGE matched with pattern of gene expression (relative transcript level) in the qRT-PCR studies conducted for relevant miRNAs and protein factors for ethylene and auxin signalling. In conclusion, epigenetic regulation of both auxin and ethylene homeostasis control grain filling of rice spikelet was established, but evidences were more robust for the latter.

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“…Kuanar et al . [ 186 ], investigated the response of Sub1 incorporation into high yielding rice cultivars by comparing the Sub1 incorporated and parental lines of ‘Swarna’ and ‘Savitri’ under stagnant flooding condition. They reported that the Sub 1 incorporation in to the mega cultivars increase sensitivity to stagnant flooding.…”

Section: Marker-assisted Breeding Approaches For the Development Of Flooding Tolerance In Ricementioning

confidence: 99%

Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice

Panda

Barik

Sarkar

2021

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: Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decade to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone area. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.

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Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain- filling under stagnant flooding

Cited by 23 publications

References 60 publications

Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.)

Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.)

MicroRNAs modulate ethylene induced retrograde signal for rice endosperm starch biosynthesis by default expression of transcriptome

Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice

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