Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids

Abstract

Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

“…CHH methylation of both BnA and BnC genes and LTR retrotransposons showed transgressive hypermethylation patterns, first matching parental methylation levels in the 1 st generation, and then surpassing parental methylation levels in 5 th and 10 th generations. This increase in LTR methylation over parental and mid‐parent value in later generations matched previous observations in resynthesised B. napus that LTR‐derived 21 and 24 nucleotide (nt) siRNAs are transgressively expressed in later generations (Martinez Palacios et al ., 2019). Additionally, for the BnC subgenome, CG methylation also appeared to be transgressively hypermethylated in the later generations.…”

Genomics of Evolutionary Novelty in Hybrids and Polyploids

“…As such, the combination of two populations of diverged sRNAs has the potential to change patterns of gene expression, TE activity, and all of the developmental programs and phenotypes that might result from this altered regulatory environment. Micro RNAs, for example, are known to be important players in stress responses and other forms of ecological adaptation (Song et al, 2019;Yu et al, 2019), which raises the possibility that these small regulatory molecules might facilitate neofunctionalization of duplicated stress-related and other signaling genes (Palacios et al, 2019).…”

“…A growing literature attests to the effects of polyploidy on expression of small RNAs (reviewed in Ng et al, 2012;Wendel et al, 2016). As with protein-coding genes, in most studies at least some sRNAs are non-additively expressed (e.g., Li et al, 2014;Xie and Zhang, 2015;Cavé-Radet et al, 2019;Palacios et al, 2019;Wei et al, 2019), being subject to novel trans regulation. sRNA non-additivity in polyploids may be unsurprising in that this also has been observed within species as well, as in maize hybrids (Crisp et al, 2020).…”

Exploring the gene pool ofBrassica napusby genomics‐based approaches

“…Synthetic B. napus (A r A r C o C o ) is known to be meiotically unstable with frequent chromosomal exchanges between the A and C subgenomes, which can result in genomic rearrangements and structural variants (Song et al ., 1995 ; Szadkowski et al ., 2010 ; Xiong et al ., 2011 ). Other changes may involve gene expression and epigenetic modifications (Chen and Pikaard, 1997 ; Gaeta et al ., 2007 ; Lukens et al ., 2006 ; Ran et al ., 2016 ; Xu et al ., 2009 ), transposable element activation and small RNA changes (Albertin et al ., 2006 ; Fu et al ., 2016 ; Hurgobin et al ., 2018 ; Palacios et al ., 2019 ), changes in tRNA (Wei et al ., 2014 ), and the rapid mutation of repetitive sequences (Gao et al ., 2014 ). Synthetic B. napus (A r A r C c C c ), whose genome was mostly replaced by B. rapa and B. carinata , showed a stable genome after generations of self‐pollination and recurrent selection but still contained numerous structural variation that was significantly different from that of traditional B. napus (Hu et al ., 2019 ; Zou et al ., 2018 ).…”