Abstract
BackgroundGenomic 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.ResultsIn 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.ConclusionThis 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.
Highlights
Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring
This research provided a more 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
Transcriptome sequencing and parental specific Single nucleotide polymorphism (SNP) calling To distinguish the parental-derived allelic expression in hybrids, we performed the deep high-throughput RNA sequencing on the 20 days after pollination (DAP) and 25 DAP endosperm of Zhongshuang 11 (ZS11) and Yangyou 6 (Y6) to discover the SNPs between two parents
Summary
Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Until 1999, imprinted genes in plants have been gradually identified by the analysis of transcript expressional level, reporter gene activity, or DNA methylation level on alleles that inherited from one specific parent following reciprocal crosses. These genes include MEA, FIS2, MPC, HDG3/8/9, FH5 in Arabidopsis, and FIE1, FIE2, PEG1, MEG1 in maize [9, 15,16,17,18,19,20,21]. It has been proved that imprinted genes primarily influence the nutrient requirements and distribution during endosperm development through dosage effects, which are critical for seed development and vigor [30, 31]
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