Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)

Li, Ming; Liang, Zhaoxu; He, Shikun; Zeng, Yuan; Ji, Yan; Wei, Fang; Wu, Kai–Chao; Wang, Guanyu; Xia, Ning; LunWang, Wang; Li, Song; Tan, Huachun; Tan, Feiquan

doi:10.1186/s12864-017-4053-3

Cited by 33 publications

(27 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It has been proven for sugarcane that miR156, miR319-3p, miR396 and miR408 take part in leaf abscission [160]. In their study, both mature (5p) and passenger (3p) miRNAs from MIR167 family were up-regulated in leaf abscission sugarcane plants (LASP), comparing to leaf packaging sugarcane plants (LPSP) (which corresponds to the FPAB vs. FPNAB comparison in our study).…”

Section: Srnas Are Involved In Flower Abscission In L Luteussupporting

confidence: 46%

“…Apart from the above-mentioned sugarcane miRNAs, miR396, miR395 and miR171 were up-regulated in this library comparison, as well. Four miRNAs, namely miR164, 166, 159, 319-3, showed an opposite trend [160]. In our study, both mature and passenger members of the MIR167 family were leaders among DEMs, too, (Table 6) pointing to their crucial role in both vegetative and generative organ abscission.…”

Section: Srnas Are Involved In Flower Abscission In L Luteusmentioning

confidence: 49%

“…In their study, both mature (5p) and passenger (3p) miRNAs from MIR167 family were up-regulated in leaf abscission sugarcane plants (LASP), comparing to leaf packaging sugarcane plants (LPSP) (which corresponds to the FPAB vs. FPNAB comparison in our study). A total of four pairs of mature and passenger miRNAs were differentially expressed in this comparison, and they were members of the MIR156, MIR167 and MIR393 families [160]. Apart from the above-mentioned sugarcane miRNAs, miR396, miR395 and miR171 were up-regulated in this library comparison, as well.…”

Section: Srnas Are Involved In Flower Abscission In L Luteusmentioning

confidence: 82%

“…Little is known about sRNA engagement in flower abscission. Research into the involvement of miRNAs in this process has been already carried out in cotton [158], tomato [152,159], and sugarcane [160]. Our investigation provided a more comprehensive view of this process and allowed us to explore cues for abscission present long before AZ formation.…”

Section: Srnas Are Involved In Flower Abscission In L Luteusmentioning

confidence: 91%

See 3 more Smart Citations

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Glazińska

Kulasek

Glinkowski

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

show abstract

Section: Srnas Are Involved In Flower Abscission In L Luteussupporting

confidence: 46%

Section: Srnas Are Involved In Flower Abscission In L Luteusmentioning

confidence: 49%

Section: Srnas Are Involved In Flower Abscission In L Luteusmentioning

confidence: 82%

Section: Srnas Are Involved In Flower Abscission In L Luteusmentioning

confidence: 91%

See 2 more Smart Citations

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Glazińska

Kulasek

Glinkowski

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Several publications reported the identification of miRNAs in biofuel crops such as Miscanthus giganteus (Jha & Shankar, ), Setaria italica (Yadav, Muthamilarasan, Pandey, Khan, & Prasad, ; Yi, Xie, Liu, Qi, & Yu, ), Sorghum bicolor (Calviño, Bruggmann, & Messing, ), Z. mays (Aravind et al, ; Liu et al, ), and Saccharum sp. (Gentile, Dias, Mattos, Ferreira, & Menossi, and references therein; Li et al, ; Thiebaut et al, ; Su et al, ; Yang et al, ). However, only a few of them addressed specific miRNAs predicted to be involved in cell wall construction or remodeling.…”

Section: Discussionmentioning

confidence: 99%

Newly identified miRNAs may contribute to aerenchyma formation in sugarcane roots

et al. 2020

View full text Add to dashboard Cite

Small RNAs comprise three families of noncoding regulatory RNAs that control gene expression by blocking mRNA translation or leading to mRNA cleavage. Such post‐transcriptional negative regulation is relevant for both plant development and environmental adaptations. An important biotechnological application of miRNA identification is the discovery of regulators and effectors of cell wall degradation, which can improve/facilitate hydrolysis of cell wall polymers for second‐generation bioethanol production. The recent characterization of plant innate cell wall modifications occurring during root aerenchyma development triggered by ethylene led to the possibility of prospection for mechanisms of cell wall disassembly in sugarcane. By using next‐generation sequencing, 39 miRNAs were identified in root segments along the process of aerenchyma development. Among them, 31 miRNAs were unknown to the sugarcane miRBase repository but previously identified as produced by its relative Sorghum bicolor. Key putative targets related to signal transduction, carbohydrate metabolic process, and cell wall organization or biogenesis were among the most representative gene categories targeted by miRNA. They belong to the subclasses of genes associated with the four modules of cell wall modification in sugarcane roots: cell expansion, cell separation, hemicellulose, and cellulose hydrolysis. Thirteen miRNAs possibly related to ethylene perception and signaling were also identified. Our findings suggest that miRNAs may be involved in the regulation of cell wall degradation during aerenchyma formation. This work also points out to potential molecular tools for sugarcane improvement in the context of second‐generation biofuels.

show abstract

Comparative Transcriptome Analysis Reveals Potential Gene Modules Associated with Cold Tolerance in Sugarcane (Saccharum officinarum L.)

Huang

Liang

Zhang

et al. 2021

J Plant Growth Regul

View full text Add to dashboard Cite

Sugarcane is an important crop worldwide, and most sugar is derived directly from sugarcane. Due to its thermophilic nature, the yield of sugarcane is largely influenced by extreme climate conditions, especially cold stress. Therefore, the development of sugarcane with improved cold tolerance is an important goal. However, little is known about the multiple mechanisms underlying cold acclimation at the bud stage in sugarcane. In this study, we emphasized that sensitivity to cold stress was higher for the sugarcane variety ROC22 than for GT42, as determined by physical signs, including bud growth capacity, relative conductivity, malonaldehyde contents, and soluble sugar contents. To understand the factors contributing to the difference in cold tolerance between ROC22 and GT42, comparative transcriptome analyses were performed. We found that genes involved in the regulation of the stability of the membrane system were the relative determinants of difference in cold tolerance. Additionally, genes related to protein kinase activity, starch metabolism, and calcium signal transduction were associated with cold tolerance. Finally, 25 candidate genes, including 23 variety-specific and 2 common genes, and 7 transcription factors were screened out for understanding the possible cold resistance mechanism. The findings of this study provide candidate gene resources for cold resistance and will improve our understanding of the regulation of cold tolerance at the bud stage in sugarcane.

show abstract

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)

Cited by 33 publications

References 77 publications

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Newly identified miRNAs may contribute to aerenchyma formation in sugarcane roots

Comparative Transcriptome Analysis Reveals Potential Gene Modules Associated with Cold Tolerance in Sugarcane (Saccharum officinarum L.)

Contact Info

Product

Resources

About