Identification and expression analysis of microRNAs during ovule development in rice (Oryza sativa) by deep sequencing

Wu, Ya Fang; Yang, Liyu; Yu, Meiling; Wang, Jianbo

doi:10.1007/s00299-017-2196-y

Cited by 18 publications

(23 citation statements)

References 63 publications

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“…All studies revealed a complex picture of the meiotic transcriptome, i.e., a large number of genes are expressed and hundreds to thousands of transcripts are differentially expressed. The picture is even more complex, as a high number of mitochondria-encoded genes possibly constituting a source of energy for meiotic progression ( Dukowic-Schulze et al, 2014 ), transposable elements ( Chen et al, 2010 ; Yang et al, 2011 ), and (long) non-coding RNAs ( Dukowic-Schulze et al, 2016 ; Flórez-Zapata et al, 2016 ; Wu et al, 2017 ) are differentially expressed. Changes in chromatin and chromosome organization may cause a general chromatin de-repression accounting for this complexity including an elevated expression of transposable elements in meiocytes ( Chen et al, 2010 ; Yang et al, 2011 ; Dukowic-Schulze et al, 2014 ).…”

Section: Genomic and Transcriptomic Approachesmentioning

confidence: 99%

“…RNA interference (RNAi) machinery components and miRNAs are differentially expressed during meiosis ( Dukowic-Schulze et al, 2014 , 2016 ; Flórez-Zapata et al, 2016 ; Wu et al, 2017 ) and mutations in RNAi machinery components result in aberrant meiotic progression, chromatin structure or HR ( Nonomura et al, 2007 ; Singh et al, 2011 ; Oliver et al, 2014 , 2017 ), indicating that the RNAi machinery plays a role in meiosis. In male monocot meiotic transcriptomes phasiRNAs are detected that originate from a few hundred dispersed intergenic, non-repetitive regions (phasiRNA loci) and apparently do not target any genes but instead mediate in cis DNA methylation at their loci of origin ( Dukowic-Schulze et al, 2016 ).…”

Section: Genomic and Transcriptomic Approachesmentioning

confidence: 99%

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Tackling Plant Meiosis: From Model Research to Crop Improvement

Lambing

Heckmann

2018

Front. Plant Sci.

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Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.

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Section: Genomic and Transcriptomic Approachesmentioning

confidence: 99%

Section: Genomic and Transcriptomic Approachesmentioning

confidence: 99%

Tackling Plant Meiosis: From Model Research to Crop Improvement

Lambing

Heckmann

2018

Front. Plant Sci.

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“…Gene expression can be controlled at the RNA level, both quantitatively and qualitatively, and at various steps during RNA processing (alternative splicing, RNA editing, RNA silencing and translation regulation among others), with important consequences for the availability of different kinds of transcripts, and ultimately of proteins. The importance of the RNA interference (RNAi) machinery during meiosis has become clear in recent years (Dukowic-Schulze et al, 2014, 2016; Flórez-Zapata et al, 2016; Wu et al, 2017; Oliver et al, 2017), with small RNAs adding additional layers to the regulation of gene expression. A good example of this are phasiRNAs, a type of 21− and 24-nt phased, secondary siRNA from non-repeat regions produced specifically in male monocot meiotic transcriptomes (Johnson et al, 2009; Song et al, 2012), and whose function remains elusive.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and thePh1locus

Martín

Borrill

Higgins

et al. 2018

Preprint

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Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologues and homoeologues at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-Seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologues is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. This suggests that post-transcriptional and post-translational processes are likely to be more important. Thus, further studies will be required to reveal whether these observations are specific to wheat meiosis, and whether there are significant changes in post-transcriptional and post-translational modifications in wheat and other polyploid species associated with their polyploidisation.

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“…FMFs' pistils mainly arrested after ovule inner tegument primordium formed [8,9]. Recently, increasing attention has been paid to the roles of miRNAs in ovule development, including A. thaliana [22], cotton [18], and rice [34]. In this study, a total of 161 miRNAs (including conserved and novel miRNAs) were identified in BFs and FMFs' pistil.…”

Section: Potential Roles Of Mirnas In Pomegranate Female Sterilitymentioning

confidence: 91%

Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility

Chen

Luo

Yang

et al. 2020

IJMS

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Female sterility is a key factor restricting plant reproduction. Our previous studies have revealed that pomegranate female sterility mainly arose from the abnormality of ovule development. MicroRNAs (miRNAs) play important roles in ovule development. However, little is known about the roles of miRNAs in female sterility. In this study, a combined high-throughput sequencing approach was used to investigate the miRNAs and their targeted transcripts involved in female development. A total of 103 conserved and 58 novel miRNAs were identified. Comparative profiling indicated that the expression of 43 known miRNAs and 14 novel miRNAs were differentially expressed between functional male flowers (FMFs) and bisexual flowers (BFs), 30 known miRNAs and nine novel miRNAs showed significant differences among different stages of BFs, and 20 known miRNAs and 18 novel miRNAs exhibited remarkable expression differences among different stages of FMFs. Gene ontology (GO) analyses of 144 predicted targets of differentially expressed miRNAs indicated that the “reproduction process” and “floral whorl development” processes were significantly enriched. The miRNA–mRNA interaction analyses revealed six pairs of candidate miRNAs and their targets associated with female sterility. Interestingly, pg-miR166a-3p was accumulated, whereas its predicted targets (Gglean012177.1 and Gglean013966.1) were repressed in functional male flowers (FMFs), and the interaction between pg-miR166a-3p and its targets (Gglean012177.1 and Gglean013966.1) were confirmed by transient assay. A. thaliana transformed with 35S-pre-pg-miR166a-3p verified the role of pg-miR166a-3p in ovule development, which indicated pg-miR166a-3p’s potential role in pomegranate female sterility. The results provide new insights into molecular mechanisms underlying the female sterility at the miRNA level.

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Identification and expression analysis of microRNAs during ovule development in rice (Oryza sativa) by deep sequencing

Cited by 18 publications

References 63 publications

Tackling Plant Meiosis: From Model Research to Crop Improvement

Tackling Plant Meiosis: From Model Research to Crop Improvement

Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and thePh1locus

Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility

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