Abstract
Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0.62), suggesting that the interaction of NERDL with its putative target might be involved in wood formation. We conducted association mapping in a natural population of P. tomentosa (435 unrelated individuals) to evaluate genetic variation and the interaction of the lncRNA NERDL with PtoNERD. Using additive and dominant models, we identified 30 SNPs (P < 0.01) associated with five tree growth and wood property traits. Each SNP explained 3.90–8.57% of phenotypic variance, suggesting that NERDL and its putative target play a common role in wood formation. Epistasis analysis uncovered nine SNP-SNP association pairs between NERDL and PtoNERD, with an information gain of -7.55 to 2.16%, reflecting the strong interactions between NERDL and its putative target. This analysis provides a powerful method for deciphering the genetic interactions of lncRNAs with mRNA and dissecting the complex genetic network of quantitative traits in trees.
Highlights
DNA methylation is a conserved epigenetic silencing mechanism that functions in many crucial plant growth and developmental processes, such as genomic imprinting and abiotic stress responses (Bird, 2002; Song et al, 2016)
To further explore the roles of PtoNERD in plant development, using genome annotation and a genome browser, we identified NERDL, an Long non-coding RNAs (lncRNAs) located in the antisense strand and overlapping with the promoter region of PtoNERD, which acts as a cis-regulator of PtoNERD
We identified 4 significant SNPs in NERDL and 26 in PtoNERD associated with D, FW, AC, HEC, and/or LC, and 15 haplotypebased associations that were strongly supported by single-marker associations (Table 3), leading to the suggestion that NERDL and its potential target might play a role in tree growth and wood formation
Summary
DNA methylation is a conserved epigenetic silencing mechanism that functions in many crucial plant growth and developmental processes, such as genomic imprinting and abiotic stress responses (Bird, 2002; Song et al, 2016). Another siRNA-dependent DNA methylation pathway, the NERD (Needed for RDR2-independent DNA methylation)dependent pathway (Matzke et al, 2015), involves RDR1/RDR6 and AGO2 and is guided by 21-nt siRNAs (Matzke and Mosher, 2014) to mediate gene silencing at the post-transcriptional level in Arabidopsis thaliana. NERD, a key protein in the NERD pathway, plays important roles in plant growth and development. NERD was identified in Populus trichocarpa through database searches (Pontier et al, 2012), but the effect of allelic variations within NERD on tree growth and wood formation, which could be utilized for genetic improvement of important economic traits in forest trees, remains unknown
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