Gene Expression Changes In The Full-Sib Allotriploid Population Of Populus Spp. (Section Tacamahaca)

Poplar triploids are derived from the fusion of unreduced gametes between species, the triploids of poplar have manifested significant advantages in growth. In this study, we used the Populus model system to investigate hybridization and polyploidization-induced changes in gene transcription and the differential patterns of gene expression in a newly synthesized diploid F1 and three allotriploid populations driven by 2n female gametes [FDR (First division restitution)、SDR(Second division restitution)、PMR (Postmeiotic restitution)] at the population level. Comparative analyses of allotriploids driven by three types of 2n female gamete may provide insight into the mechanism by which the 2n gametes mediate sexual polyploidization to affect differences of gene expression in allopolyploids. In addition, we also identified the differences in gene expression patterns between high and low growth vigor Populus. Apical buds were sampled from plants from four populations of synthetic Populus hybrids, including three triploids formed by 2n maternal gametes differing in their mechanism of formation, as well as the corresponding diploid F1 hybrid, and their gene expression profiles were compared using high-throughput sequencing (Illumina HiSeq 2000 sequencing platform).According to the different gene expression patterns evaluated in this study, polyploids originating from the three types of 2n female gametes will have applications in polyploidy breeding programs, applied research, and theoretical studies. Collectively, these results provide a novel perspective on allopolyploid gene regulation and hint at the underlying genetic basis of allopolyploid adaptation in forest tree plants. The main research results are as follows:(1) The results indicated that the overall transcriptome of both the diploid F1 and allotriploids displayed transcriptomes that were more similar to the maternal parents Zheyin3# than to BJY. The proportion of differentially expressed genes between the hybrid and three allopolyploids and their maternal parent Zheyin3# was 2.8,2.3,2.0, and 1.9%, respectively, and to its paternal parent BJY was 8.2,10.2,8.4, and 7.4%, respectively. In addition, GO enrichment analysis of maternal dominance genes were enrichment for epigenetic regulation, and the paternal dominance genes were enrichment for energy metabolism and transcriptional regulation. In the triploid-F,7648 (24.3% of 31437 expressed genes) genes displayed nonadditive expression. The percentage in the triploid-S was even lower (6292,20.0%), and the triploid-P was the lowest (4652,14.8%). Interestingly, about twice as many genes were upregulated than downregulated in the diploid F1 (2376 (73.2%) versus 868 (26.8%)), triploid-F (2130 (63.5%) versus 1222 (36.5%)), triploid-S (2110 (72.4%) versus 805 (27.6%)), and triploid-P (1346 (69.8%) versus 581 (30.2%)).(2) The number of DEGs between the triploid-F and diploid included 464 and 676 genes that were up-and down-regulated, respectively. Only 32 (15 up- and 17 down-regulated) and 55 (29 up-and 26 down-regulated) genes differentially expressed between the triploid-S and triploid-P compared with the diploid, respectively. We further investigated the possible functions of genes that were difFerentially expressed between the triploid-F and diploid F1. GO analysis of the 1140 DEGs indicated that they were significantly enriched for the generation of precursor metabolites and energy, protein metabolic processes, positive regulation of translation, response to jasmonic acid, and response to stress and heat shock protein binding (FDR<0.05).(3) We investigated gene expression levels between each of the three allotriploid populations, and we found more DEGs between the triploid-F and the triploid-P than between the triploid-F and triploid-S. There were 2829 DEGs between the triploid-F and triploid-P, including 1027 upregulated and 1802 downregulated genes. In addition, there were 1624 DEGs between the triploid-F and triploid-S, including 606 upregulated and 1018 downregulated genes. In contrast, there were only 30 DEGs between the triploid-S and triploid-P, including 11 upregulated and 19 downregulated genes. We performed GO enrichment analysis on the DEGs in common between the triploid-F/triploid-S and triploid-F/triploid-P comparisons. This indicated the enrichment of these genes for the generation of precursor metabolites and energy, carbon fixation, response to jasmonic acid, and response to stress and heat-shock protein binding(4) There were significant differences in gene expression between high growth vigor plants and their parents. There is a strong relationship between the differently expressed genes and the heterosis. The non-additive and transgressive genes were enriched mainly for cell growth, cell proliferation and DNA methylation.(5) There were significant differences in expression between high and low growth vigor plants. Function analysis revealed that the differentially expressed genes were mainly related to carbohydrate metabolism, auxin and signal transduction. Major changes in gene expression probably provide a driving force for phenotypic variation and adaptation in allopolyploids. The DEGs selected in this study provide important insight to obtain a better understanding of height growth heterosis in Populus allotriploids.