High-throughput sequencing revealed that microRNAs were involved in the development of superior and inferior grains in bread wheat

Wang, Yongyan; Shi, Cheng; Yang, Tianxiao; Zhao, Lei; Chen, Jianhui; Zhang, Ning; Ren, Yan; Tang, Guiliang; Cui, Dangqun; Chen, Feng

doi:10.1038/s41598-018-31870-z

Cited by 13 publications

(13 citation statements)

References 57 publications

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“…In wheat, about a dozen studies have been performed on miRNA identification using sRNA sequencing (sRNA-Seq) (Yao et al, 2007; Wei et al, 2009; Li et al, 2013; Meng et al, 2013; De Paola et al, 2016; Fileccia et al, 2017; Wang et al, 2018). miRNAs responding to diverse stresses in wheat have also been reported (Xin et al, 2010; Zhou et al, 2015; Akdogan et al, 2016; Chen et al, 2017; Zuluaga et al, 2017; Han et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…miRNAs responding to diverse stresses in wheat have also been reported (Xin et al, 2010; Zhou et al, 2015; Akdogan et al, 2016; Chen et al, 2017; Zuluaga et al, 2017; Han et al, 2018). miRNAs related to the development and filling of wheat seeds have been studied (Meng et al, 2013; Han et al, 2014; Li et al, 2015; Wang et al, 2018). For example, Meng et al (2013) identified 104 miRNAs associated with grain filling in wheat.…”

Section: Introductionmentioning

confidence: 99%

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Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Wei

Wang

et al. 2019

Front. Genet.

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Cold acclimation and vegetative/reproductive transition are two important evolutionary adaptive mechanisms for winter wheat surviving the freezing temperature in winter and successful seeds setting in the next year. MicroRNA (miRNA) is a class of regulatory small RNAs (sRNAs), which plays critical roles in the growth and development of plants. However, the regulation mechanism of miRNAs during cold acclimation and vegetative/reproductive transition of winter wheat is not much understood. In this study, four sRNA libraries from leaves of winter wheat grown in the field at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage were analyzed to identify known and novel miRNAs and to understand their potential roles in the growth and development of winter wheat. We examined miRNA expression using a high-throughput sequencing technique. A total of 373 known, 55 novel, and 27 putative novel miRNAs were identified. Ninety-one miRNAs were found to be differentially expressed at the four stages. Among them, the expression of six known and eight novel miRNAs was significantly suppressed at the winter dormancy stage, whereas the expression levels of seven known and eight novel miRNAs were induced at this stage; three known miRNAs and three novel miRNAs were significantly induced at the spring green-up stage; six known miRNAs were induced at the spring green-up stage and reached the highest expression level at the jointing stage; and 20 known miRNAs and 10 novel miRNAs were significantly induced at the jointing stage. Expression of a number of representative differentially expressed miRNAs was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Potential target genes for known and novel miRNAs were predicted. Moreover, six novel target genes for four Pooideae species-specific miRNAs and two novel miRNAs were verified using the RNA ligase-mediated 5′-rapid amplification of cDNA ends (RLM-5’RACE) technique. These results indicate that miRNAs are key non-coding regulatory factors modulating the growth and development of wheat. Our study provides valuable information for in-depth understanding of the regulatory mechanism of miRNAs in cold acclimation and vegetative/reproductive transition of winter wheat grown in the field.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Wei

Wang

et al. 2019

Front. Genet.

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“…More recently, a short-tandem target mimic (STTM) method was used to verify if miR166 regulates important agronomic traits in rice . In a study, transgenic STTM165/166 plants showed significantly reduced seed number and sterile siliques in Arabidopsis, suggesting that miR166 plays a vital role in seed development and it might be useful evidence to improve inferior grain size in wheat (Wang et al, 2018). Among the detected and annotated genes in the MQTLs regions in this study, the OsMED9 (TraesCS3B02G077100), which is an orthologous gene of rice, was identified in the MQTL_3B_1 region that was associated with GY and its components.…”

Section: Mqtls and Functional Candidate Genesmentioning

confidence: 63%

Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat (Triticum aestivum L.)

et al. 2021

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Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.

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“…Additionally, novel miRNAs were predicted from unannotated sequences without similarity to known miRNAs (Additional file 2: Table S2, Additional file 3: Table S3). Since many miRNAs have not been deposited into miRBase, the novel miRNAs identified in this study were also compared with previously published wheat miR-NAs [12,[14][15][16][31][32][33][34][35]. In total, the sequences of 39 miRNAs from among the newly identified miRNAs were the same as those of previously found novel miRNAs (Table S2; the miRNAs are labeled in yellow).…”

Section: Identification Of Known Mirnas and Predicted Novel Mirnasmentioning

confidence: 99%

“…In rice, osa-miR167 regulates the auxin-miR167-ARF8-OsGH3.2 pathway, which functions during grain filling [13]. High-throughput sequencing revealed that the differentially expressed miRNAs between superior and inferior wheat grain are likely related to cell division, carbohydrate metabolism and hormone biosynthesis [14]. Han et al [15] demonstrated that miR164, miR160, and miR169 show different expression profiles during grain filling, suggesting that their functions are coordinated during the different stages of wheat seed development.…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

Hou

Gao

et al. 2020

BMC Plant Biol

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Background: MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. Results: A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. Conclusions: The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.

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High-throughput sequencing revealed that microRNAs were involved in the development of superior and inferior grains in bread wheat

Cited by 13 publications

References 57 publications

Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat (Triticum aestivum L.)

Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

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