Small RNA changes in synthetic Brassica napus

Abstract

Small RNAs and microRNAs were found to vary extensively in synthetic Brassica napus and subsequent generations, accompanied by the activation of transposable elements in response to hybridization and polyploidization. Resynthesizing B. napus by hybridization and chromosome doubling provides an approach to create novel polyploids and increases the usable genetic variability in oilseed rape. Although many studies have shown that small RNAs (sRNAs) act as important factor during hybridization and polyploidization in plants, much less is known on how sRNAs change in synthetic B. napus, particularly in subsequent generations after formation. We performed high-throughput sequencing of sRNAs in S1-S4 generations of synthetic B. napus and in the homozygous B. oleracea and B. rapa parent lines. We found that the number of small RNAs (sRNAs) and microRNAs (miRNAs) doubled in synthetic B. napus relative to the parents. The proportions of common sRNAs detected varied from the S1 to S4 generations, suggesting sRNAs are unstable in synthetic B. napus. The majority of miRNAs (67.2 %) were non-additively expressed in the synthesized Brassica allotetraploid, and 33.3 % of miRNAs were novel in the resynthesized B. napus. The percentage of miRNAs derived from transposable elements (TEs) also increased, indicating transposon activation and increased transposon-associated miRNA production in response to hybridization and polyploidization. The number of target genes for each miRNA in the synthesized Brassica allotetraploid was doubled relative to the parents, enhancing the complexity of gene expression regulation. The potential roles of miRNAs and their targets are discussed. Our data demonstrate generational changes in sRNAs and miRNAs in synthesized B. napus.

Peer Review #3 of "Analysis of small RNA changes in different Brassica napus synthetic allopolyploids (v0.1)"

“…The results indicate that hybridization and polyploidization caused a surge in siRNA. siRNA has the effect of mitigating polyploidy shock, which was consistent with the previous conclusions (Fu et al 2016b). In addition, the number of siRNAs in eight F2 plants was 249275 -516295, which was much higher than the number of parents (1260) (Fig.…”

“…2b). The reads size distribution is not the same with that of previous reports (Fu et al 2016b), which may be due to different materials used in the experiment. Average 93.69% of the total reads in the eight F2 samples, 96% and 70% of two parents samples, could be perfectly mapped to the B. rapa genome and B. olearea genome with no mismatch (Fig.…”

Untitled

“…2b). The reads size distribution is not consistent with that of previous reports (Fu et al 2016b). It may be due to different materials used in the experiment.…”

“…The results indicat that hybridization and polyploidization caused a surge in siRNA. siRNA has the effect of mitigating polyploidy shock, which was consistent with the previous conclusions (Fu et al 2016b). In addition, the number of siRNAs in eight F2 plants was 249275 -516295, which was much higher than the number of parents (1260) (Fig.…”

“…Therefore, it is necessary to explore the molecular mechanism of the distant hybridization between B. rapa and B. oleracea in order to obtain stable synthesis B. napus and to expand the germplasm resources of B. napus. Previous studies have explored sRNA changes and regulatory patterns in different generations of resynthesized B. napus (Fu et al 2016b). However, these patterns in allopolyploids with different traits are not been fully examined.…”