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Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus.
Jinhui Chen1,2, Jianbo Xie1,2, Beibei Chen1,2
1National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
The New Phytologist
|June 7, 2016
Summary
Genetic variants in microRNAs (miRNAs) and their targets drive plant trait variation. This study links specific miRNA variants to tension wood formation in Populus, revealing key regulatory roles in natural populations.
Area of Science:
- Plant genetics
- Molecular biology
- Evolutionary biology
Background:
- MicroRNAs (miRNAs) are crucial regulators of gene expression influencing phenotypic traits.
- Understanding miRNA variants and their regulatory networks in natural plant populations is limited.
- Tension wood formation in Populus is a complex trait influenced by various genetic factors.
Purpose of the Study:
- To investigate the association and interaction of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypic variation in Populus.
- To identify specific miRNAs and target genes involved in tension wood formation.
- To elucidate the regulatory networks underlying these associations.
Main Methods:
- RNA-sequencing to identify differentially expressed miRNAs and candidate target genes.
- Degradome sequencing to validate miRNA-target interactions.
- Genome resequencing to identify SNPs in miRNAs and target genes.
- Association analyses (single-SNP and multi-SNP) to link genetic variants with wood traits.
- Regulatory network reconstruction.
Main Results:
- Identified 217 differentially expressed miRNAs and 1196 candidate target genes in tension wood.
- Confirmed 60 miRNA-target sites and found 72 significantly co-expressed miRNA-target pairs.
- Detected thousands of SNPs in miRNAs and target genes, with significant associations to wood traits.
- Identified 102 miRNA-target pairs and 102 epistatic pairs associated with traits.
- miR156i, miR156j, miR396a, and miR6445b were implicated in tension wood formation.
Conclusions:
- Variants in miRNAs and their target genes significantly contribute to natural phenotypic variation in Populus.
- Genetic association analysis successfully annotated roles and interactions of miRNAs and target genes.
- Specific miRNAs play critical roles in the regulation of tension wood formation.
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