Epigenetic Variation In The Full-sib Allotriploid Population Of Populus Spp. (Section Tacamahaca)

Expression of gene could be regulated by epigenetic modification, as well as the post-transcriptional regulator. Study of epigenetic variation and post-transcriptional regulator expression variation will be valuable in providing insights into the molecular mechanism for growth vigor in Populus allotriploid populations. In the present study, an F1 hybrid diploid population and three full-sib allotriploid populations with different heterozygosity [originating from first-division restitution (FDR), second-division restitution (SDR), and post-meiotic restitution (PMR) 2n eggs of the same female parent], and their common parents (ZY3 and BJY) were used to investigate cytosine methylation inheritance and variation relative to their common parents using methylation-sensitive amplification polymorphism (MSAP). In addition, expression variations of miRNA in the three newly synthesized allotriploid populations and interspecific hybrid population were analyzed by high-throughput sequencing. The effects of hybridization and polyploidization on DNA methylation and miRNA expression were investigated in population samples to eliminate genotypic differences among individuals. Moreover, we also discussed the role of DNA methylation and miRNA expression variations in polyploid advantage. Major results as follows:Both hybridization and polyploidization could induce cytosine methylation variation. The total methylation levels of the three triploid populations were significantly lower than that in the parents and diploid-F1 population, with the lowest in triploid-F population (19.88%) and highest in diploid-Fl population (23.93%). The vast majority of methylated status could be inherited from the parents, but there were still any variation in DNA methylation patterns, and the hyper-methylation was the major variation type in the four hybrid progeny populations. The average percentages of hyper-methylation variation were 2.04,3.60,3.59 and 4.97% in the triploid-F, triploid-S, triploid-P, and diploid-F1 progeny populations, respectively. However, the three allotriploid populations showed higher levels of demethylation variation (with 0.81,1.09, and 0.96% in the triploid-F, triploid-S, and triploid-P populations) than that in diploid-F1 population (0.73%). Due to the lower frequency of hyper-methylation and higher frequency of demethylation in allotriploid populations, the total methylation level in three allotriploid populations were lower than that in diploid-Fl popualtion, which could contribute to the advantages of vegetative growth in Populus allotriploids.251 miRNAs were significantly differentially expressed between the parents (ZY3 and BJY), and the majority of differentially expressed miRNAs were up-regulated in the female parent. We also identified 29 maternal-specific expressed miRNAs. In addition, the expression level of miRNAs in the four hybrid progeny populations showed a strong expression bias toward the female parents, and an unbalanced parental expression level dominance, which may reprogram gene expression networks and contribute to the growth, adaptation, and genome stability of Populus allotriploid. In addition, no significant variation in miRNA expression was observed between each of the allotriploid populations and the full-sib diploid hybrid population, indicating that miRNA expression does not have a dosage effect in plant polyploidization. Therefore, the expression of miRNA in Populus allotriploid does not increase as genomic content added, suggesting that additional genomic content would be expected to result in over-expression of a few target genes, and thus induce changes in physiological pathways, and ultimately in growth and development outcomes. Consequently, it is possible that Populus polyploid populations may gain advantages from the slight decrease in miRNA regulation, leading to increases in growth, vigor, and biomass.There were significant differences in miRNA expression between high growth vigor plants and their parents, and mainly up-regulated in high-growth progenies. MiRNA in high-growth allotriploids and interspecific hybrids showed expression bias toward the female parent, and the character of parental expression level dominance (ELD). Maternal ELD miRNA were mainly related to the lignin biosynthetic and catabolic process, negative regulation of growth, multicellular organismal development. While the paternal ELD miRNA were enriched in the biological process "regulation of vegetative phase change", "floral organ formation " and "response to stress". Moreover, we also found several miRNA were significantly repressed in high-growth Populus allotriploids, which were related to the synthesis and deposition of secondary wall cellulose and cellular macromolecule catabolic process. Collectively, several miRNA may play a vital role in the high growth vigor of Populus allotriploids. Furthermore, no significant variation in miRNA expression was observed between each of the high-growth allotriploids and the full-sib diploid hybrids, which further validated no dosage effect of miRNA expression in Populus allotriploids.