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Association genetics in Populus reveals the interactions between Pto-miR160a and its target Pto-ARF16

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Abstract

MicroRNAs (miRNAs) play important roles in the regulation of gene expression in various biological processes. However, the interactions between miRNAs and their targets are largely unknown in plants. As a powerful tool for identification of variation associated with traits, association genetics provides another strategy for exploration of interactions between miRNAs and their targets. Here, we conducted expression analysis and association mapping to evaluate the interaction between Pto-miR160a and its target Pto-ARF16 in Populus tomentosa. By examining the expression patterns of Pto-MIR160a and Pto-ARF16, we identified a significant, negative correlation between their expression levels, indicating that Pto-miR160a may affect the expression of Pto-ARF16. Among the single nucleotide polymorphisms (SNPs) identified in this study, one common SNP in the pre-miRNA region of Pto-miR160a altered its predicted secondary structure while another common SNP in the predicted miRNA target site changed the binding affinity of Pto-miR160a. Linkage disequilibrium (LD) analysis revealed low LD levels of Pto-MIR160a and Pto-ARF16, indicating that they are suitable for candidate gene-based association analysis. Single SNP-based association analysis identified 19 SNPs (false discovery rate Q < 0.05) in Pto-MIR160a and Pto-ARF16 associated with three phenotypic traits. Epistasis analysis further identified 36 SNP–SNP interactions between SNPs in Pto-MIR160a and SNPs in Pto-ARF16, reflecting the possible genetic interaction of Pto-miR160a and Pto-ARF16. Taking these results together, our study identified SNPs in Pto-MIR160a and Pto-ARF16 associated with tree growth and wood properties, providing SNPs with potential applications in marker-assisted breeding and evidence for the genetic interaction of Pto-miR160a and Pto-ARF16.

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Acknowledgments

This work was supported by the Fundamental Research Funds for the Central Universities (Project No. BLYJ201408), and Shandong Province Agriculture Improved Variety Project (No. 2012213) and the Project of the National Natural Science Foundation of China (No. 31170622).

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Authors and Affiliations

  1. National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Jiaxing Tian, Jinhui Chen, Bailian Li & Deqiang Zhang

  2. Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Jiaxing Tian, Jinhui Chen, Bailian Li & Deqiang Zhang

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  1. Jiaxing Tian
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Communicated by S. Hohmann.

Sequence data from this article have been deposited in the GenBank Data Library under the accession Nos. KT585479-KT585565.

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Tian, J., Chen, J., Li, B. et al. Association genetics in Populus reveals the interactions between Pto-miR160a and its target Pto-ARF16 . Mol Genet Genomics 291, 1069–1082 (2016). https://doi.org/10.1007/s00438-015-1165-9

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