Genetic Subtraction Profiling Identifies Candidate miRNAs Involved in Rice Female Gametophyte Abortion

Yang, Liyu; Wu, Ya Fang; Wang, Wenliang; Mao, Bigang; Zhao, Baisuo; Wang, Jianbo

doi:10.1534/g3.117.040808

Cited by 14 publications

(22 citation statements)

References 59 publications

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“…In rice HEI10, MSH5, ZIP4, and PSS1 while in maize SMC3, ATR, ATM, RMI1, and MPA1 were identified among thousands of differentially expressed genes as meiotic candidates, suggesting that AM1 plays a role in modulating the expression of many critical meiotic genes in a species-specific dependent manner. Rice ovule transcriptomes from different wild-type genotypes and various female-sterile lines revealed a high number of differentially expressed genes and miRNAs ( Yang et al, 2016 , 2017 ; Zhu et al, 2017 ). Even by performing comparative meiotic transcriptomics in various plants, the complexity of meiotic transcriptomes is astonishing.…”

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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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%

Tackling Plant Meiosis: From Model Research to Crop Improvement

Lambing

Heckmann

2018

Front. Plant Sci.

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“…Based on our results, 84 differentially methylated miRNA gene promoters were detected in fsv1 and Gui99 ovules ( Table 5 ), of which 37 were hyper-methylated (for example, miR156i, miR166b-3p, miR166b-5p, miR166e-3p, miR166e-5p, miR169o, miR169g, miR169r-3p, miR169r-5p, miR172a, miR1432-3p, miR1432-5p, miR5535, among others), and 47 were hypo-methylated (miR160c-5p, miR166c-3p, miR166d-3p, miR166d-5p, miR167b, miR167f, miR171d-5p, miR171d-3p, miR1425-3p, miR1425-5p, miR5339, miR5491, miR5810, among others) in fsv1 ovules. Combined with miRNA and RNA-Seq analyses ( Yang et al 2016 , 2017 ), we found that abnormal methylation of these miRNA gene promoters could lead to transcriptional abnormalities in miRNAs, and the abnormal expression of miRNA affected the expression of their coherent target genes ( Figure 5 ). For example, the miR5504 gene promoter was hypo-methylated in fsv1 , then we found that the expression level of miR5504 was up-regulated in miRNA analyze and the expression level of its coherent target gene LOC_Os03g48970 was down-regulated in fsv1 of RNA-Seq.…”

Section: Resultsmentioning

confidence: 97%

“…The GO enrichment analysis of the functional significance applies a hyper-geometric test to map all of the DMGs to terms in the GO database, searching for significantly enriched GO terms in the differentially methylated genes compared with the complete genome. The formula used in this analysis has been described by Yang et al (2017) .…”

Section: Methodsmentioning

confidence: 99%

“… Yang et al (2016) have found that the high-frequency female gametophyte abortion in fsv1 is caused by the abnormal functional megaspore. Furthermore, many differentially expressed genes and miRNAs involved in ovule development and female gametophyte abortion between fsv1 and Gui99 have been identified by high-throughput sequencing ( Yang et al 2016 , 2017 ). These findings provided important clues for revealing the molecular mechanism of female gametophyte abortion and guided the direction of our research.…”

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Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1

Liu

Cao

et al. 2017

G3 Genes|Genomes|Genetics

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The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wildtype rice line (Gui99) using whole-genome bisulfite sequencing (WGBS). Profiling of the global DNA methylation revealed hypo-methylation, and 3471 significantly differentially methylated regions (DMRs) were observed in fsv1 ovules compared with Gui99. Based on functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis of differentially methylated genes (DMGs), we observed more DMGs enriched in cellular component, reproduction regulation, metabolic pathway, and other pathways. In particular, many ovule development genes and plant hormone-related genes showed significantly different methylation patterns in the two rice lines, and these differences may provide important clues for revealing the mechanism of female gametophyte abortion. Rice (Oryza sativa L.) not only feeds half of the global population, but it is also useful for basic molecular and genetic studies because of its relatively small genome size and complete genome information (Goff 1999;Delseny et al. 2001). As an important participant in the sexual reproduction of rice, the fertility of male and female gametes is directly related to rice yield. In recent years, attention has been focused on the mechanism of male fertility regulation, while few studies have been conducted to elucidate the mechanism of female fertility in rice. The rice ovule is an important sexual reproductive organ, and previous studies have demonstrated the inseparability of ovule development and female gametophyte formation (Reiser and Fischer 1993). Generally, the process of female gametophyte formation is mainly divided into three stages: meiotic division of the megaspore mother cell (MMC), mitotic stage of functional megaspore cells, and mature stage of embryo sac. In detail, the MMC originating from a sporogenous cell derives from below the epidermis of the nucellus and divides into the linear tetrad type after meiosis. Subsequently, the megaspore near the chalaza becomes the functional megaspore, and the remaining three megaspores die during ovule development. The functional megaspore undergoes three rounds of mitotic division and finally forms the female gametophyte with eight nuclei (Yadegari and Drews 2004;Pagnussat et al. 2005). The ovule sporophyte tissue provides the necessary nutritional and mechanical support for the formation of the female gametophyte, and communication between the ovule sporophyte and the female gametophyte has bee...

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“…Illumina sequencing, data processing and RNA sequencing generated read mapping to the reference genome (the Rice Genome Annotation Project, http://rice.plantbiology.msu.edu ) were performed as previously described [ 29 ]. The Illumina HiSeq2000 sequencing, data processing and small RNA sequencing generated read mapping to the same reference genome were followed as previously described [ 30 ].…”

Section: Methodsmentioning

confidence: 99%

Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height

Cao

Jin

et al. 2017

PLoS ONE

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Inter-specific hybridization and backcrossing commonly occur in plants. The use of progeny generated from inter-specific hybridization and backcrossing has been developed as a novel model system to explore gene expression divergence. The present study investigated the analysis of gene expression and miRNA regulation in backcrossed introgression lines constructed from cultivated and wild rice. High-throughput sequencing was used to compare gene and miRNA expression profiles in three progeny lines (L1710, L1817 and L1730), with different plant heights resulting from the backcrossing of introgression lines (BC2F12) and their parents (O. sativa and O. longistaminata). A total of 25,387 to 26,139 mRNAs and 379 to 419 miRNAs were obtained in these rice lines. More differentially expressed genes and miRNAs were detected in progeny/O. longistaminata comparison groups than in progeny/O. sativa comparison groups. Approximately 80% of the genes and miRNAs showed expression level dominance to O. sativa, indicating that three progeny lines were closer to the recurrent parent, which might be influenced by their parental genome dosage. Approximately 16% to 64% of the differentially expressed miRNAs possessing coherent target genes were predicted, and many of these miRNAs regulated multiple target genes. Most genes were up-regulated in progeny lines compared with their parents, but down-regulated in the higher plant height line in the comparison groups among the three progeny lines. Moreover, certain genes related to cell walls and plant hormones might play crucial roles in the plant height variations of the three progeny lines. Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines.

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Genetic Subtraction Profiling Identifies Candidate miRNAs Involved in Rice Female Gametophyte Abortion

Cited by 14 publications

References 59 publications

Tackling Plant Meiosis: From Model Research to Crop Improvement

Tackling Plant Meiosis: From Model Research to Crop Improvement

Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1

Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height

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