Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus

Abstract

Background Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. napus will enrich the knowledge of genomic imprinting in dicotyledon plants. Results In this study, we performed reciprocal crosses between B. napus L. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted in Arabidopsis, rice, castor bean, maize, B. rapa, and other B. napus lines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud of B. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5 AGLs and 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm. Conclusion This research provided a comprehensive identification of imprinted genes in B. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.

Transgressive and parental dominant gene expression and cytosine methylation during seed development inBrassica napushybrids

“…At the same time, TEs are a source of sRNAs, including siRNAs, that could potentially silence TEs through a post-transcriptional gene silencing (PTGS) process as discussed in Matzke and Mosher (2014) and Gill et al (2021). Similarly to Rong et al (2021) most differentially methylated TEs were found in 5 kbp gene flanking regions, as expected since 78% of TEs are in such loci in the employed Express 617 reference (Lee et al, 2020). Our results also outline that most TEs, DMRs and DE-siRNAS converged in .…”

“…At the same time, TEs are a source of sRNAs, including siRNAs, that could potentially silence TEs through a post-transcriptional gene silencing (PTGS) process as discussed in Matzke and Mosher (2014) and Gill et al (2021). Similarly to Rong et al (2021) most differentially methylated TEs were found in 5 kbp gene flanking regions, as expected since 78% of TEs are in such loci in the employed Express 617 reference (Lee et al, 2020). Our results also outline that most TEs, DMRs and DE-siRNAS converged in 14 5 kbp gene flanking regions rather than in 5 kbp DEG flanking regions (Tables S30); thus, highlighting a putative conservation of most genetic functions by reducing the number of DMRs, DE-siRNAs and differentially methylated TEs in the proximity of DEGs.…”

“…The threshold was selected based on previous work on transposable elements and genomic imprinting in B . napus by Rong et al (2021) and the fact that the average distance between genes in assigned chromosomes of the Express 617 reference is approximately 7.5 kbp. Chi-square tests followed with an FDR post-hoc adjustment (p < 0.05) were carried to find significant associations between differentially methylated and non-methylated features and distance to genes or DEGs across all stages.…”

The evolution of imprinting in plants: beyond the seed

“…There are around one hundred imprinted genes in maize and Arabidopsis, found in roughly equal proportions from both maternal and paternal genomes (Schon and Nodine 2017 ; Wyder et al 2019 ). While some genes have been found to be imprinted across species and have strong effects on endosperm function when their imprinting is perturbed (Grossniklaus et al 1998 ; Ingouff et al 2005 ; Makarevich et al 2008 ), there has been a wide debate regarding the conservation of the imprinted status of genes (Chen et al 2018 ; Hatorangan et al 2016 ; Klosinska et al 2016 ; Lafon-Placette et al 2018 ; Liu et al 2021 ; Pignatta et al 2014 ; Rong et al 2021 ; Roth et al 2018 ; Tuteja et al 2019 ; Waters et al 2013 ; Yang et al 2018 , 2020 ; Yoshida et al 2018 ). Yet, a conservation of imprinting targets may exist for molecular complexes or pathways rather than individual genes.…”

Exploring Breakthroughs in Three Traits Belonging to Seed Life

“…In the present year, a work on the genomic imprinted genes of dicot B. napus endosperm provided 297 imprinted genes, including 283 MEGs and 14 PEGs. More specifically, (i) 36 of 297 imprinted genes were continuously imprinted during endosperm development; (ii) only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in other tissues of B. napus, rather than specifically in endosperm; and (iii) a total of 109 imprinted genes were clustered on rapeseed chromosomes [73]. Recently, imprinting status in two closely related dicot species, Arabidopsis and Capsella rubella, was analyzed, revealing that less than one-third of orthologous genes are imprinted in both species, and that genomic imprinting is a highly dynamic process [74].…”