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MicroRNA expression changes following synthesis of three full-sib Populus triploid populations with different heterozygosities

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Abstract

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Through high-throughput sequencing, we compared the relative expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one diploid hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. In addition, unbalanced parental expression level dominance of miRNAs were found in the three allotriploid and interspecific hybrid populations, which may reprogram gene expression networks and contribute to the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among one diploid and three triploid hybrid populations, hinting that miRNA abundances do not increase with the genome content. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the slight decrease in miRNA regulation, suggesting an important molecular mechanism of polyploid advantage.

Abstract

Hybridization with three types of induced 2n gametes transmitted different parental heterozygosities has been proven as an efficient method for Populus triploid production. Several researches have shown that miRNA could be non-additively expressed in allopolyploids. However, it is still unclear whether the non-additively expressed miRNAs result from the effect of hybridization or polyploidization, and whether a dose response to the additional genomic content exists for the expression of miRNA. Toward this end, through high-throughput sequencing, we compared the expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one interspecific hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. Unbalanced parental expression level dominance of miRNAs were found in the three triploid and diploid hybrid populations, which may reprogram gene expression networks and affect the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among the three triploid populations and the diploid hybrid population. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the decrease in miRNA negative regulation, suggesting an important molecular mechanism of polyploid advantage.

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Acknowledgements

This work was financially supported by National Natural Science Foundation of China (31530012), Special Fund for Forest Scientific Research in the Public Welfare (201404113), National Natural Science Foundation of China (31470667). We thank Dr. Hui Duan for assistance with technical advice, Dai Chen, Bo Zhang and Yang Yang (Novel Bioinformatics Ltd., Co, Shanghai, China) for assistance in bioinformatics analysis.

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Authors and Affiliations

  1. National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People’s Republic of China

    Yujing Suo, Yu Min, Chunbo Dong, Yi Wang, Shiping Cheng & Xiangyang Kang

  2. Key Laboratory of Genetics and Breeding in Forest Tree and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People’s Republic of China

    Yujing Suo, Yu Min, Chunbo Dong, Yi Wang, Shiping Cheng & Xiangyang Kang

  3. China Paulownia Research Center, Zhengzhou, 450003, Henan, People’s Republic of China

    Yujing Suo

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  1. Yujing Suo
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Contributions

YS and XK conceived the project; YS and SC designed experiments; YS, YM and YW performed most of the experiments; YS and CD analysed data; YS wrote the paper; CD reviewed the manuscript; all authors commented on the manuscript.

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Correspondence to Xiangyang Kang.

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Electronic supplementary material

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11103_2017_627_MOESM1_ESM.tif

The developmental processes of Populus triploid resulting from the inhibition of first division restitution, second division restitution, and post-meiotic restitution (TIF 2133 KB)

11103_2017_627_MOESM2_ESM.tif

GO term enrichment analysis of maternal-specific miRNAs (FDR <0.05). BP, biological process; MF, molecular function; CC, cellular component (TIF 1420 KB)

11103_2017_627_MOESM3_ESM.tif

Venn diagram of ELD miRNAs in three allotriploid populations and one diploid F1 population. a, maternal ELD miRNAs; b, paternal ELD miRNAs (TIF 1546 KB)

Supplementary material 4 (XLSX 10 KB)

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Supplementary material 8 (XLSX 11 KB)

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Suo, Y., Min, Y., Dong, C. et al. MicroRNA expression changes following synthesis of three full-sib Populus triploid populations with different heterozygosities. Plant Mol Biol 95, 215–225 (2017). https://doi.org/10.1007/s11103-017-0627-3

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  • DOI: https://doi.org/10.1007/s11103-017-0627-3

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