Plant non-coding RNAs and epigenetics

Wang, Jiawei; Qi, Yijun

doi:10.1007/s11427-017-9244-0

Cited by 6 publications

(2 citation statements)

References 14 publications

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“…Epigenetics plays a crucial role in various aspects of plant biology, including development, silencing of transposable elements and maintenance of genome stability. In plants, epigenetic regulation involves histone and DNA modifications, and ncRNA [58]. Inter-species hybridization in rice has been shown to be associated with changes in the expression levels of genes involved in epigenetic mechanisms [59].…”

Section: Discussionmentioning

confidence: 99%

“…Some studies suggested that siRNAs regulate the genes expression and play a crucial role in male meiosis and pollen development [2,20]. Many ncRNAs are functional and involved in regulating genes expression at the transcriptional and post-transcriptional level [58]. So expression levels of many genes may change under the influence of ncRNA and TEs-siRNAs-triggered methylation, particularly during the crucial stage of meiosis, which lead to high fertility in neo-tetraploid rice.…”

Section: Discussionmentioning

confidence: 99%

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Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neo-tetraploid rice

Bei

Shahid

et al. 2019

PLoS ONE

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Autotetraploid rice is a useful germplasm for polyploid rice breeding, however, low seed setting is the major barrier in commercial utilization of autotetraploid rice. Our research group has developed neo-tetraploid rice lines, which have the characteristics of high fertility and heterosis when crossed with autotetraploid rice. In the present study, re-sequencing and RNA-seq were employed to detect global DNA variations and differentially expressed genes (DEGs) during meiosis stage in three neo-tetraploid rice lines compared to their parents, respectively. Here, a total of 4109881 SNPs and 640592 InDels were detected in neo-tetraploid lines compared to the reference genome, and 1805 specific presence/absence variations (PAVs) were detected in three lines. Approximately 12% and 0.5% of the total SNPs and InDels identified in three lines were located in genic regions, respectively. A total of 28 genes, harboring at least one of the large-effect SNP and/or InDel which affect the integrity of the encoded protein, were identified in the three lines. Together, 324 specific mutation genes, including 52 meiosis-related genes and 8 epigenetics-related genes were detected in neo-tetraploid rice compared to their parents. Of these 324 genes, five meiosis-related and three epigenetics-related genes displayed differential expressions during meiosis stage. Notably, 498 specific transcripts, 48 differentially expressed transposons and 245 differentially expressed ncRNAs were also detected in neo-tetraploid rice. Our results suggested that genomic structural reprogramming, DNA variations and differential expressions of some important meiosis and epigenetics related genes might be associated with high fertility in neo-tetraploid rice.

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Section: Discussionmentioning

confidence: 99%