Integrated transcriptome, small RNA, and degradome analysis to elucidate the regulation of rice seedling mesocotyl development during the passage from darkness to light

Lyu, Yusong; Wei, Xiangjin; Zhong, Min; Niu, Shipeng; Ahmad, Shakeel; Shao, Gaoneng; Jiao, Guiai; Sheng, Zhonghua; Xie, Lihong; Hu, Shikai; Wu, Yanjun; Tang, Shaoqing

doi:10.1016/j.cj.2020.05.002

Cited by 7 publications

(6 citation statements)

References 41 publications

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“…The region of interest was annotated according to the MSU Rice Genome Annotation Project Database, which revealed that it harbors five open reading frames (ORFs; Figure S2A). Of these, ORF1 encodes the GA20‐oxidase for GA biosynthesis and is much expressed in the etiolated mesocotyl from our previous transcriptome (Lyu et al, 2020); More importantly, the ORF1 is the famous Green Revolution gene SD1 that led to rice dwarf variety breeding in the 1960s (Monna et al, 2002; Sasaki et al, 2002). Collectively, SD1 is the potential target gene of ME1 .…”

Section: Resultsmentioning

confidence: 99%

“…Previous studies implied that the expansion family genes play important roles in ME and the emergence of etiolated rice seedlings (Choi et al, 2003; Xiong et al, 2017; Lyu et al, 2020). Here, we used reverse transcription quantitative polymerase chain reaction (RT‐qPCR) and revealed that the expansion gene OsEXPA4 is significantly up‐regulated in deep soil cover (Figure 4D).…”

Section: Resultsmentioning

confidence: 99%

“…Mesocotyl elongation of rice is controlled by developmental and environmental signals, such as light and phytohormones (Lyu et al, 2020;Zhan et al, 2020). For example, ethylene, gibberellin (GA), brassinosteroids, jasmonic acid (JA), and strigolactones have been shown to be involved in the regulation of rice ME and seedling emergence from the soil (Xiong et al, 2017;Sun et al, 2018;Zheng et al, 2020;Lv et al, 2021;Wang et al, 2021a;Qiao et al, 2023); however, the mechanisms underlying the ways in which these signaling pathways are orchestrated and regulated in the ME of rice seedlings under soil remain poorly understood.…”

Section: Introductionmentioning

confidence: 99%

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An orchestrated ethylene–gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

Lyu,

Dong,

Niu

et al. 2024

JIPB

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A mechanized direct seeding of rice with less labor and water usage, has been widely adopted. However, this approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME) offers the main drive of fast emergence of rice seedlings from soils; nevertheless, its genetic basis remains unknown. Here, we identify a major rice quantitative trait locus Mesocotyl Elongation1 (qME1), an allele of the Green Revolution gene Semi‐Dwarf1 (SD1), encoding GA20‐oxidase for gibberellin (GA) biosynthesis. ME1 expression is strongly induced by soil depth and ethylene. When rice grains are direct‐seeded in soils, the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription, accelerating bioactive GA biosynthesis. The GAs further degrade the DELLA protein SLENDER RICE 1 (SLR1), alleviating its inhibition of rice PHYTOCHROME‐INTERACTING FACTOR‐LIKE13 (OsPIL13) to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence. The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process, and an elite ME1‐R allele (D349H) is found in some modern Geng varieties (long mesocotyl lengths) in northern China, which can be used in the direct seeding and dwarf breeding of Geng varieties. Furthermore, the ectopic and high expression of ME1 driven by mesocotyl‐specific promoters resulted in rice plants that could be direct‐seeded without obvious plant architecture or yield penalties. Collectively, we reveal the molecular mechanism of rice ME, and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct‐seeding practice.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

An orchestrated ethylene–gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

Lyu,

Dong,

Niu

et al. 2024

JIPB

Self Cite

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“…Then, all transcriptomes were generated using StringTie to examine the expression level for FPKM after the final transcriptome was constructed. Here, the differentially expressed genes (DEGs) and mRNAs with p value of less than 0.05 and a log 2 | fold change| of more than 1 were screened with the R package ( Lyu et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Zhang

Thakur

et al. 2021

Front. Plant Sci.

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Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.

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“…Reads that mapped to the predicted IAA30 target sites were utilized to determine the positions of the 5′transcript ends using an in-house Perl script. A couple of sets publicly available of degradome sequencing data from wild-type seedlings (PRJNA118841, PRJNA123507, PRJNA120547, PRJNA263869, PRJNA170713, PRJNA263450, PRJNA596446, PRJNA627552, PRJNA594662, PRJNA630172, PRJNA561367, PRJNA486509, PRJNA480216, PRJNA388531, PRJNA182050, PRJNA277443 and PRJNA263869) were used as control samples of rice plants without auxin treatments [58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74] .…”

Section: Degradome Sequencing and Analysismentioning

confidence: 99%

Switching action modes of miR408-5p mediates auxin signaling in rice

Rong,

Lv,

Deng

et al. 2024

Nat Commun

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MicroRNAs (miRNAs) play fundamental roles in many developmental and physiological processes in eukaryotes. MiRNAs in plants generally regulate their targets via either mRNA cleavage or translation repression; however, which approach plays a major role and whether these two function modes can shift remains elusive. Here, we identify a miRNA, miR408-5p that regulates AUXIN/INDOLE ACETIC ACID 30 (IAA30), a critical repressor in the auxin pathway via switching action modes in rice. We find that miR408-5p usually inhibits IAA30 protein translation, but in a high auxin environment, it promotes the decay of IAA30 mRNA when it is overproduced. We further demonstrate that IDEAL PLANT ARCHITECTURE1 (IPA1), an SPL transcription factor regulated by miR156, mediates leaf inclination through association with miR408-5p precursor promoter. We finally show that the miR156-IPA1-miR408-5p-IAA30 module could be controlled by miR393, which silences auxin receptors. Together, our results define an alternative auxin transduction signaling pathway in rice that involves the switching of function modes by miR408-5p, which contributes to a better understanding of the action machinery as well as the cooperative network of miRNAs in plants.

show abstract

Integrated transcriptome, small RNA, and degradome analysis to elucidate the regulation of rice seedling mesocotyl development during the passage from darkness to light

Cited by 7 publications

References 41 publications

An orchestrated ethylene–gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

An orchestrated ethylene–gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Switching action modes of miR408-5p mediates auxin signaling in rice

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