Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice

Peng, Ting; Sun, Hong; Qiao, Mengmeng; Zhao, Yongju; Du, Yanxiu; Zhang, Jing; Li, Junzhou; Tang, Guiliang; Zhao, Quanzhi

doi:10.1186/s12870-014-0196-4

Cited by 73 publications

(74 citation statements)

References 62 publications

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“…The typical IS are physically located on the proximal secondary branches in a rice panicle where the grains receive less photosynthesis during the grain-filling processes in comparison to SS (Peng et al, 2014). Consistently, our quantitative proteomics data revealed that most of the differentially expressed photosynthesis-related proteins showed reduced abundance during the grain-filling in IS compared to SS.…”

Section: Resultsmentioning

confidence: 99%

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

Zhu

Chen

et al. 2016

Front. Plant Sci.

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Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.

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Section: Resultsmentioning

confidence: 99%

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

Zhu

Chen

et al. 2016

Front. Plant Sci.

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“…2a), many of which belonged to known miRNA families including miR156, miRNA160, miR166, miR169, miR1846, miR1861 and miR319 (Additional file 3: Table S2). Members of the miRNA families were reported to be involved not only in growth, development, grain size and hormone signaling, but also in response to biotic and abiotic stress [21][22][23][24][25][26][27][28][29][30][31]. These BPH6 responsive DEMs might be involved in response to BPH.…”

Section: Identification Of Mirnas Related To Bph Resistancementioning

confidence: 99%

“…miRNAs specifically regulate target gene expression through binding complementary sequences to degrade mRNA or inhibit translation [19]. Plant miRNAs are involved in many development processes, including hormone signal transduction, and leaf, floral, shoot, root and vascular development [20][21][22], and play significant roles in abiotic and biotic stress responses [23][24][25][26][27][28]. miR160 is associated with local defense and systemic acquired resistance to potato late blight [24].…”

Section: Introductionmentioning

confidence: 99%

A combined microRNA and transcriptome analyses illuminates the resistance response of rice against brown planthopper

Tan

Guo

et al. 2020

BMC Genomics

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Background: The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6, was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood.Results: Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6-transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6-mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis. Conclusions:For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPHinduced miRNA and mRNA expression profiles and enable to comprehend plant-insect interactions and find a way for efficient insect control.

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“…Within a panicle, the superior spikelets can inhibit the inferiors, and this apical spikelets superiority of superior spikelets over inferior spikelets can partly be demonstrated by application of the exogenous auxin (IAA) (Wang et al, 2001, 2003). Furthermore, different expressions and functions of miRNAs exist between the superior and inferior spikelets (Peng et al, 2011, 2014). The interaction among the factors inside spikelets, including the hormones, mRNA transcriptions, protein expressions, and activities of key enzymes involved in sucrose-to-starch conversion, regulate the grain-filling process of superior and inferior spikelets (Yang et al, 2006; Zhang et al, 2009; Yang and Zhang, 2010).…”

Section: Introductionmentioning

confidence: 99%

Heat Stress Is More Damaging to Superior Spikelets than Inferiors of Rice (Oryza sativa L.) due to Their Different Organ Temperatures

Feng

Zhang

et al. 2016

Front. Plant Sci.

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In general, the fertility and kernel weight of inferior spikelets of rice (Oryza Sativa L.) are obviously lower than those of superior spikelets, especially under abiotic stress. However, different responses to heat stress are seemed to show between the superior and inferior spikelet, and this response is scarcely documented that the intrinsic factors remain elusive. In order to reveal the mechanism underlying, two rice plants with different heat tolerance were subjected to heat stress of 40°C at anthesis. The results indicated that a greater decrease in fertility and kernel weight was observed in superior spikelets compared to inferior spikelets. This decrease was primarily ascribed to their different organ temperatures, in which the temperature of the superior spikelets was significantly higher than that of inferior spikelets. We inferred the differences in canopy temperature, light intensity and panicle types, were the primary reasons for the temperature difference between superior and inferior spikelets. Under heat stress, the fertility and kernel weight of superior and inferior spikelets decreased as the panicle numbers per plant were reduced, which was accompanied by significantly increasing the canopy temperatures. Thus, it was suggested that the rice plant with characteristic features of an upright growth habit and loose panicles might be more susceptible to heat stress resulting from their higher canopy and spikelets temperatures.

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Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice

Cited by 73 publications

References 62 publications

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

A combined microRNA and transcriptome analyses illuminates the resistance response of rice against brown planthopper

Heat Stress Is More Damaging to Superior Spikelets than Inferiors of Rice (Oryza sativa L.) due to Their Different Organ Temperatures

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