Global identification and analysis revealed differentially expressed lncRNAs associated with meiosis and low fertility in autotetraploid rice

Abstract

Background: Autotetraploid rice is a useful germplasm for polyploid rice breeding. Our previous research showed that non-coding RNAs might be associated with low fertility in autotetraploid rice. However, little information is available on long non-coding RNAs (lncRNAs) involved in the low fertility of autotetraploid rice. In the present study, RNA-seq was employed to detect the differentially expressed meiosis-related lncRNAs in autotetraploid rice, and gene overexpression and knock out experiments were used to validate the potential function of candidate lncRNA. Results: A total of 444 differentially expressed lncRNAs (DEL) were detected during anther and ovary meiosis in autotetraploid rice. Of these, 328 DEL were associated with the transposable elements, which displayed low expression levels during meiosis in autotetraploid rice. We used rapid amplification of cDNA ends (RACE) assay to validate 10 DEL and found that the lncRNAs were not assembly artifacts, and six of them were conserved in tetraploid rice. Moreover, 237 and 20 lncRNAs were associated with pollen mother cell (PMC) and embryo sac mother cell (EMC) meiosis in autotetraploid rice, respectively. The differential expressions of some meiosis-related targets and its DEL regulator, including MEL1 regulated by TCONS_00068868, LOC_Os12g41350 (meiotic asynaptic mutant 1) by TCONS_00057811 in PMC, and LOC_Os12g39420 by TCONS_00144592 in EMC, were confirmed by qRT-PCR. TCONS_00057811, TCONS_00055980 and TCONS_00130461 showed anther specific expression patterns and were found to be highly expressed during meiosis. CRISPR/Cas9 editing of lncRNA57811 displayed similar morphology compared to wild type. The overexpression of lncRNA57811 resulted in low pollen fertility (29.70%) and seed setting (33%) in rice. Conclusion: The differential expression levels of lncRNAs, associated with transposable elements and meiosisregulated targets, might be endogenous noncoding regulators of pollen/embryo sac development that cause low fertility in autotetraploid rice. The results enhance our understanding about rice lncRNAs, and facilitate functional research in autotetraploid rice.

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

“…Here, we found that almost 30% of the triticale lncRNAs possessed exons with similarity to TEs. This is in accordance with previous reports on rice [ 79 ], where 73% lncRNAs were found to overlap with different TEs. Furthermore, 9.18% of sunflower lncRNAs have TE-related exons [ 80 ].…”

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

“…On the other hand, compared to its wild relative, meiotic recombination was shown to be higher in cultivated sunflower and many long non-coding RNAs (lncRNAs) were exclusively up-regulated in its meiocytes ( Flórez-Zapata et al, 2016 ). Similarly, low fertility in autotetraploid rice was attributed to differential expression of lncRNAs during anther and ovule meiosis ( Li et al, 2020 ). LncRNAs are poorly characterized compared to protein-coding genes but these studies highlight their potential importance during development ( Ponting et al, 2009 ; Ariel et al, 2015 ; Shafiq et al, 2016 ) including their regulatory role during sexual reproduction ( Golicz et al, 2018 ).…”

“…The processing of a subset of lncRNAs has been shown to generate small RNAs in animals ( Jalali et al, 2012 ) and plants ( Ma et al, 2014 ). Although the regulation of gene expression by small RNA has been reported in cotton anthers ( Chen et al, 2018 ), Arabidopsis meiocytes ( Huang et al, 2019 ) and rice ovules ( Li et al, 2020 ), the full integration of small RNAs and lncRNAs biogenesis and function remains to be determined.…”

A New Way of Rice Breeding: Polyploid Rice Breeding

“…In autotetraploid rice, 24 nt TEs-siRNAs could cause genome instability and sterility. On the other hand, Li et al pointed out that the differential expression level of lncRNAs was related to transposable factors and meiotic regulatory targets, which may be the endogenous noncoding regulatory factors of pollen/embryo sac development in autotetraploid rice [131,132]. They also found that the low fertility of autotetraploid rice was caused not only by the differential expression of pollen development related genes, but also by sequence variation and differential methylation.…”