Gene expression profiling reveals subgenome dominance duringBrassica napusseed development

Abstract

One Sentence Summary: 23Global RNA sequencing coupled with laser microdissection provides a critical resource to study 24 subgenome bias in whole seeds and specific tissues of polyploid plants. 25 26 Abstract 27We profiled the gene regulatory landscape of Brassica napus reproductive development using 28 RNA sequencing. Comparative analysis of this nascent amphidiploid across the plant lifecycle 29 revealed the contribution of each subgenome to plant reproduction. Global mRNA profiling 30 revealed lower accumulation of C n subgenome transcripts relative to the A n subgenome. 31Subgenome-specific transcriptional networks identified distinct transcription factor families 32 enriched in each of the A n and C n subgenome early in seed development. Global gene expression 33 profiling of laser-microdissected seed subregions further reveal subgenome expression dynamics 34 in the embryo, endosperm, and seed coat of early stage seeds. Transcription factors predicted to 35 be regulators encoded by the A n subgenome are expressed primarily in the seed coat whereas 36 regulators encoded by the C n subgenome were expressed primarily in the embryo. Data suggest 37 subgenome bias are characteristic features of the B. napus seed throughout development, and that 38 such bias might not be universal across the embryo, endosperm, and seed coat of the developing 39 seed. Whole genome transcription factor networks identified BZIP11 as a transcriptional 40 regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference 41 resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive-lethal 42 phenotype. Taken together, transcriptional networks spanning both the A n and C n genomes of the 43 B. napus seed can identify valuable targets for seed development research and that-omics level 44 approaches to studying gene regulation in B. napus can benefit from both broad and high-45 resolution analyses. 46 3 47 49Brassica napus (canola) is the second most important oilseed crop in the world with 50 global production of 75 million tons in 2017 (FAOSTAT 2017). It is a relatively recent 51 allopolyploid derived from hybridization between B. rapa and B. oleracea (Nagaharu, 1935). 52The resulting plant is an amphidiploid species which has retained its progenitor subgenomes 53 from B. rapa (A r A r ) and B. oleracea (C o C o ) to form B. napus (A n A n C n C n ). Despite its 54 importance to the global economy, B. napus genome dynamics are poorly understood, especially 55 in the context of gene regulation during seed development. The developmental transition from 56 seed morphogenesis to maturation (Figure 1A) requires a re-orchestration of the genes and gene 57 regulatory networks underpinning seed development. Therefore, B. napus represents an 58 appropriate model for research on transcriptomic changes across seed development of 59 economically important polyploid plants. 60Brassica napus is a nascent amphidiploid which has not yet undergone substantial 61 fractionation, and consequently ha...

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

“…A more recent transcriptome study profiled subregions of B. napus seeds at early (globular, heart) and late (mature green, dry seed) stages, revealing that the smaller A n subgenome derived from B. rapa is preferentially expressed, perhaps because the A n subgenome is less densely populated with transposable elements than the C n subgenome ( Khan et al., 2020 ). Homologs of MYB17 , MYB32 , MYB61 , and MYB95 TFs from both A n and C n subgenomes are expressed in early seed development, suggesting that transcriptional regulation of early stages is conserved in Brassica .…”

“…Interestingly, TFs encoded by the A n subgenome were expressed primarily in the seed coat, whereas those encoded by the C n subgenome were expressed primarily in the embryo. Network analysis of late stage-enriched transcripts derived from the A n and C n subgenomes yielded dramatically different predictions of TF regulatory circuits in seed maturation: the A n subgenome network contained numerous MYB and bHLH interactions, while the C n subgenome network involved only FUS3 and WOX12 ( Khan et al., 2020 ).…”

Evolutionary divergence in embryo and seed coat development of U’s Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas

“…To investigate the biological function of endosperm in Brassica species, the development of methods to isolate endosperm will be indispensable (Chao et al, 2020;Siles et al, 2020). The application of laser capture microdissection has partially resolved this issue in B. napus, with endosperm samples from early seed developmental stages isolated for global transcriptome analyses (Ziegler et al, 2019;Khan et al, 2020). The continued growth and application of technologies for the cell-and tissue-specific transcriptome analysis of Brassica endosperm will expand understanding of subcompartment signal crosstalk within the seed.…”

“…Recent studies on subgenome dominance in B. napus revealed that A and C subgenomes experienced different evolutionary processes at the subgenome level (Khan et al, 2020;Zhou et al, 2020). Compared to the A subgenome, the C subgenome possesses more expressed genes (Zhou et al, 2020) with lower mean expression values (Khan et al, 2020), when analyzing B. rapa and B. oleracea gene expressions. In this study, we further analyzed gene expression bias at the subgenome level for all three tetraploid Brassica species (Fig.…”

RNA-Seq Highlights Molecular Events Associated With Impaired Pollen-Pistil Interactions Following Short-Term Heat Stress in Brassica napus

“…Subtle differences in the distribution of DEGs on sub-genome A n and sub-genome C n in both heat-stressed pollen and pistil was observed ( Figure 3A ). Recent reports are suggesting a sub-genome bias in B. napus favoring the expression of A n sub-genome ( Khan et al, 2020 ; Li et al, 2020 ). However, a further detailed investigation is required to improve the understanding of observed sub-genome expression dominance in B. napus .…”