Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.)

Sun, Fenglong; Guo, Guanghui; Du, Jing; Guo, Weiwei; Peng, Huiru; Ni, Zhongfu; Sun, Qixin; Yao, Yingyin

doi:10.1186/1471-2229-14-142

Cited by 120 publications

(104 citation statements)

References 70 publications

Supporting

Mentioning

100

Contrasting

Order By: Relevance

“…There also are many nonconserved, evolutionarily recent miRNAs and their corresponding targets that are present only within a few closely related species or appear to be unique to specific species (47)(48)(49). Wheat miRNA sequencing, identification, profiling, and characterization have been reported extensively (50)(51)(52)(53)(54)(55)(56). However, neither miRW1 nor its precursor has been reported, possibly because of the atypical characteristics of Iw1 and Iw2.…”

Section: Discussionmentioning

confidence: 99%

Long noncoding miRNA gene represses wheat β-diketone waxes

Huang

Feurtado

Smith

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The cuticle of terrestrial plants functions as a protective barrier against many biotic and abiotic stresses. In wheat and other Triticeae, β-diketone waxes are major components of the epicuticular layer leading to the bluish-white glaucous trait in reproductive-age plants. Glaucousness in durum wheat is controlled by a metabolic gene cluster at the WAX1 (W1) locus and a dominant suppressor INHIBITOR of WAX1 (Iw1) on chromosome 2B. The wheat D subgenome from progenitor Aegilops tauschii contains W2 and Iw2 paralogs on chromosome 2D. Here we identify the Iw1 gene from durum wheat and demonstrate the unique regulatory mechanism by which Iw1 acts to suppress a carboxylesterase-like protein gene, W1-COE, within the W1 multigene locus. Iw1 is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to W1-COE. The Iw1 transcript forms a miRNA precursor-like long hairpin producing a 21-nt predominant miRNA, miRW1, and smaller numbers of related sRNAs associated with the nonglaucous phenotype. When Iw1 was introduced into glaucous bread wheat, miRW1 accumulated, W1-COE and its paralog W2-COE were down-regulated, and the phenotype was nonglaucous and β-diketone-depleted. The IR region of Iw1 has >94% identity to an IR region on chromosome 2 in Ae. tauschii that also produces miRW1 and lies within the marker-based location of Iw2. We propose the Iw loci arose from an inverted duplication of W1-COE and/or W2-COE in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.glaucous | inhibitor of wax | small RNA | long noncoding RNA | WAX1 P lant epicuticular waxes deposited on the outer surface of the plant cuticle produce a water-resistant layer that serves to reduce nonstomatal water loss and mitigate the effects of heat and UV radiation as well as pathogen and insect attacks (1). Grasses in the Triticeae tribe, subfamily Pooideae, which include the cultivated species barley (Hordeum vulgare; 2n = 2x = 14), rye (Secale cereale, 2n = 2x = 14), durum wheat (Triticum durum; 2n = 4x = 28, AABB), and bread wheat (Triticum aestivum; 2n = 6x = 42, AABBDD), have two predominant pathways for wax production: (i) an alcohol-and alkane-rich wax pathway and (ii) a pathway leading to β-diketones and derivatives including hydroxy-β-diketones (2). The alcohol and alkane waxes are prevalent in earlier development and on leaves, whereas β-diketones dominate during the reproductive phase, particularly on leaf sheaths and flower heads (3, 4). β-Diketone wax is predominantly hentriacontane-14, 16-dione, which consists of a 31-carbon chain with carbonyl groups at C 14 and C 16 . In durum wheat, about 20% of the β-diketone is hydroxylated to form 25-hydroxy-β-diketone, whereas in bread wheat hydroxylation is at C 8 or C 9 (5). β-Diketone wax deposition manifests visibly as glaucousness, a bluish-white coloration on stems, leaves, and flower heads. However, the relationship between a glaucous appearance and the total amount of cuticular wax can be inconsistent, especially during t...

show abstract

Section: Discussionmentioning

confidence: 99%

Long noncoding miRNA gene represses wheat β-diketone waxes

Huang

Feurtado

Smith

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The identification of target genes and the functional analysis of wheat miRNAs are also difficult, since the wheat genome has not been assembled and is poorly annotated. Recently, numerous miRNAs have been identified in wheat by deep sequencing of small RNA libraries (Yao et al 2007;Wei et al 2009;Xin et al 2010;Kantar et al 2012;Meng et al 2013;Sun et al 2014;Akdogan et al 2016), however, most of them have not been registered in the available databases. It has been observed that many wheat miRNAs are regulated by stress conditions such as drought (Akdogan et al 2016) or fungal infections (Xin et al 2010).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

“…It has been observed that many wheat miRNAs are regulated by stress conditions such as drought (Akdogan et al 2016) or fungal infections (Xin et al 2010). Some of them are also associated with morphology and developmental processes including plant height and flowering (Kantar et al 2012) or grain development (Meng et al 2013;Sun et al 2014).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

2017

View full text Add to dashboard Cite

As an essential regulatory component in plants, microRNAs (miRNAs) have been intensively studied over the past decade. Although hundreds of miRNAs have been identified and analyzed in many important crops and model plants, very little is known about the function of common wheat (Triticum aestivum L.) miRNAs. In this study, we performed computational prediction of novel wheat miRNAs based on BLAST searches of the expressed sequence tag database. The expression profiles of all miRNAs were performed for both vegetative and reproductive tissues to identify developmentally regulated miRNAs. A total of 19 new miRNAs belonging to 12 MIR families were identified using stringent criteria for miRNA annotation. For all of the miRNAs, the secondary structures of their precursor sequences were predicted. Two pairs of distinct miRNAs were found to be located on the same precursor. The predicted miRNAs were experimentally verified by a stemloop qRT-PCR-based assay. The expression profiles were performed in both vegetative and reproductive tissues to find the potential correlations between the developmental phase and miRNA activity. Thirteen out of 19 miRNAs were upregulated at certain phases of plant development, and three of them (miR319, miR395, and miR171) showed the greatest expression in young spikes during microsporogenesis. Our results provide useful information for future studies of miRNA-mediated regulation of flower and grain development in wheat.

show abstract

“…A number of miRNA families have now been identified in wheat, and about twenty miRNA families are conserved in diverse plant species (Yao et al, 2007;Feng et al, 2014;Han et al, 2014;Kumar et al, 2014;Sun et al, 2014). Of these, miR408 contains 21 nucleotides and has been annotated in more than 30 plant species to date, indicating a high level of conservation in different plant species (Axtell and Bowman, 2008;Kozomara and Griffiths-Jones, 2011).…”

mentioning

confidence: 99%

The tae-miR408-Mediated Control of TaTOC1 Genes Transcription Is Required for the Regulation of Heading Time in Wheat

Zhao

Hong

et al. 2016

Plant Physiol.

View full text Add to dashboard Cite

ORCID IDs: 0000-0002-1560-7935 (J.Y.W.); 0000-0002-3129-5206 (X.S.Z.).Timing of flowering is not only an interesting topic in developmental biology, but it also plays a significant role in agriculture for its effects on the maturation time of seed. The hexaploid wheat (Triticum aestivum) is one of the most important crop species whose flowering time, i.e. heading time, greatly influences yield. However, it remains unclear whether and how microRNAs regulate heading time in it. In our current study, we identified the tae-miR408 in wheat and its targets in vivo, including Triticum aestivum TIMING OF CAB EXPRESSION-A1 (TaTOC-A1), TaTOC-B1, and TaTOC-D1. The tae-miR408 levels were reciprocal to those of TaTOC1s under long-day and short-day conditions. Wheat plants with a knockdown of TaTOC1s via RNA interference and overexpression of tae-miR408 showed early-heading phenotype. Furthermore, TaTOC1s expression was down-regulated by the tae-miR408 in the hexaploid wheat. In addition, other important agronomic traits in wheat, such as plant height and flag leaf angle, were regulated by both tae-miR408 and TaTOC1s. Thus, our results suggested that the tae-miR408 functions in the wheat heading time by mediating TaTOC1s expression, and the study provides important new information on the mechanism underlying heading time regulation in wheat.

show abstract

Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.)

Cited by 120 publications

References 70 publications

Long noncoding miRNA gene represses wheat β-diketone waxes

Long noncoding miRNA gene represses wheat β-diketone waxes

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

The tae-miR408-Mediated Control of TaTOC1 Genes Transcription Is Required for the Regulation of Heading Time in Wheat

Contact Info

Product

Resources

About