Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S

Wang, Ying; Zhang, Hongyuan; Li, Qian; Jin, Jing; Chen, Hao; Zeng, Yu; Huang, Xingguo; Ding, Yi

doi:10.3389/fpls.2020.580050

Cited by 15 publications

(15 citation statements)

References 54 publications

(56 reference statements)

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“…Given the current developments in genome-wide sequencing technology, a very large number of microRNAs (miRNAs), lncRNAs and circRNAs involved in fertility transition and abiotic stress responses have been identified in plants. For example, miRNA expression profiles from rice anthers at high and low temperatures were also reported in PTGMS rice, which provides a beneficial pathway for understanding the role of miRNAs in rice anther and PTGMS development [ 25 , 26 ]. One key issue with the two-line system has been revealed as research on this topic has continued: the critical male-sterile temperature changes and shifts slightly with the increase in the number of generations produced, leading to substantial reproductive difficulties and causing uncertainties related to food security [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

Jasmonic Acid Plays a Pivotal Role in Pollen Development and Fertility Regulation in Different Types of P(T)GMS Rice Lines

Liu

Zhu

et al. 2021

IJMS

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Two-line hybrid rice systems represent a new technical approach to utilizing the advantages of rice hybrids. However, the mechanism underlying the male sterile-line fertility transition in rice remains unclear. Peiai 64S (PA64S) is a photoperiod- and thermo-sensitive genic male sterile (PTGMS) line in which male sterility manifests at an average temperature above 23.5 °C under long-day (LD) conditions. Nongken 58S (NK58S) is a LD-sensitive genic male sterile (PGMS) rice that is sterile under LD conditions (above 13.75 h-day). In contrast, D52S is a short-day (SD)-PGMS line that manifests male sterility under SD conditions (below 13.5 h-day). In this study, we obtained fertile and sterile plants from all three lines and performed transcriptome analyses on the anthers of the plants. Gene ontology (GO) analysis suggested that the differentially expressed genes identified were significantly enriched in common terms involved in the response to jasmonic acid (JA) and in JA biosynthesis. On the basis of the biochemical and molecular validation of dynamic, tissue-specific changes in JA, indole-3-acetic acid (IAA) levels, gibberellin (GA) levels, and JA biosynthetic enzyme activities and expression, we proposed that JA could play a pivotal role in viable pollen production through its initial upregulation, constant fluctuation and leaf-spikelet signaling under certain fertility-inducing conditions. Furthermore, we also sprayed methyl jasmonate (MEJA) and salicylhydroxamic acid (SHAM) on the plants, thereby achieving fertility reversal in the PGMS lines NK58S and D52S, with 12.91–63.53% pollen fertility changes. Through qPCR and enzyme activity analyses, we identified two key enzymes—allene oxide synthase (AOS) and allene oxide cyclase (AOC)—that were produced and upregulated by 20–500-fold in PGMS in response to spraying; the activities of these enzymes reversed pollen fertility by influencing the JA biosynthetic pathway. These results provide a new understanding of hormone interactions and networks in male-sterile rice based on the role of JA that will help us to better understand the potential regulatory mechanisms of fertility development in rice in the future.

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Section: Introductionmentioning

confidence: 99%

Jasmonic Acid Plays a Pivotal Role in Pollen Development and Fertility Regulation in Different Types of P(T)GMS Rice Lines

Liu

Zhu

et al. 2021

IJMS

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“…Studies have shown that lncRNAs interact with miRNAs as miRNA precursors, target mimics, or targets to affect plant growth and development or in response to abiotic stress ( Wu et al, 2013 ; Lu et al, 2019 ; Wang et al, 2020b ; Feng et al, 2021 ). Interestingly, we found that the same lncRNA would correspond to multiple miRNA precursors or become an eTM of multiple miRNAs.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, we found that the same lncRNA would correspond to multiple miRNA precursors or become an eTM of multiple miRNAs. Similarly, several lncRNAs may correspond to the same miRNA precursor or eTMs becoming the same miRNA ( Wang et al, 2020b ). This result demonstrated the existence of a complex regulatory interaction between lncRNAs and miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Long Noncoding RNAs in Populus × canescens Roots Treated With Different Nitrogen Fertilizers

et al. 2022

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Nitrate (NO3−) and ammonium (NH4+) are the primary forms of inorganic nitrogen acquired by plant roots. LncRNAs, as key regulators of gene expression, are a class of non-coding RNAs larger than 200 bp. However, knowledge about the regulatory role of lncRNAs in response to different nitrogen forms remains limited, particularly in woody plants. Here, we performed strand-specific RNA-sequencing of P. × canescens roots under three different nitrogen fertilization treatments. In total, 324 lncRNAs and 6,112 mRNAs were identified as showing significantly differential expression between the NO3− and NH4NO3 treatments. Moreover, 333 lncRNAs and 6,007 mRNAs showed significantly differential expression between the NH4+ and NH4NO3 treatments. Further analysis suggested that these lncRNAs and mRNAs have different response mechanisms for different nitrogen forms. In addition, functional annotation of cis and trans target mRNAs of differentially expressed lncRNAs indicated that 60 lncRNAs corresponding to 49 differentially expressed cis and trans target mRNAs were involved in plant nitrogen metabolism and amino acid biosynthesis and metabolism. Furthermore, 42 lncRNAs were identified as putative precursors of 63 miRNAs, and 28 differentially expressed lncRNAs were potential endogenous target mimics targeted by 96 miRNAs. Moreover, ceRNA regulation networks were constructed. MSTRG.6097.1, MSTRG.13550.1, MSTRG.2693.1, and MSTRG.12899.1, as hub lncRNAs in the ceRNA networks, are potential candidate lncRNAs for studying the regulatory mechanism in poplar roots under different nitrogen fertilization treatments. The results provide a basis for obtaining insight into the molecular mechanisms of lncRNA responses to different nitrogen forms in woody plants.

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“…Based on the product length, ncRNAs could be subdivided into two groups: long ncRNAs (lncRNAs, length > 200 nt) and microRNAs (miRNAs) that are about 21 nt [ 10 ]. Recent studies have revealed that plant lncRNAs may regulate gene expression in floral transition [ 11 ], flower development [ 12 ], flowering time regulation [ 13 ] and male sterility [ 14 ]. For example, Huang et al [ 15 ] found 14 lncRNAs that were highly co-expressed with 10 pollen-associated target genes and might participate in pollen development in Brassica rapa .…”

Section: Introductionmentioning

confidence: 99%

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

Kong

Zhuo

et al. 2022

BMC Genomics

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Background Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively. Results These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development. Conclusions This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.

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Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S

Cited by 15 publications

References 54 publications

Jasmonic Acid Plays a Pivotal Role in Pollen Development and Fertility Regulation in Different Types of P(T)GMS Rice Lines

Jasmonic Acid Plays a Pivotal Role in Pollen Development and Fertility Regulation in Different Types of P(T)GMS Rice Lines

Genome-Wide Identification and Characterization of Long Noncoding RNAs in Populus × canescens Roots Treated With Different Nitrogen Fertilizers

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

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