Association studies reveal the effect of genetic variation in lncRNA UGTRL and its putative target PtoUGT88A1 on wood formation in Populus tomentosa

摘要

Long noncoding RNAs (lncRNAs) play significant roles in the growth and development of herbaceous plants by regulating target genes; however, the significance of lncRNA-messenger RNA (mRNA) interactions needs to be investigated in perennial trees. Here, we combined transcript profiling and multi-single-nucleotide polymorphism (SNP) association mapping to analyze the genetic variation and putative interactions of the lncRNA UDP-glucosyltransferase-related lncRNA (UGTRL) and its predicted target PtoUGT88A1 in a natural population of 435 unrelated Populus tomentosa individuals. We detected 41 and 67 common SNPs (minor allele frequency >0.05) in UGTRL and PtoUGT88A1, respectively, in the association population. Using additive and dominant association models, we identified 86 associations with 12 traits measuring tree growth, wood properties, and photosynthetic parameters. These associations represent 36 significant SNPs (P < 0.01) from UGTRL and its putative target and explained 0.06 to 7.28% of the phenotypic variance, indicating that UGTRL and its putative target affect wood formation. An epistasis model uncovered 84 SNP-SNP association pairs representing 38.89 % of the significant SNPs in UGTRL and PtoUGT88A1 with information gain of -8.01 to 5.57 %, revealing the strong interactions between UGTRL and its putative target. Tissue-specific expression analysis in eight tissues, including xylem and cambium, showed that UGTRL and PtoUGT88A1 displayed similar expression patterns (r=0.77), which implied the putative lncRNA-mRNA interaction and the potential roles of the lncRNA and its target in wood formation. Our study provides a novel method integrating association studies and expression profiling for functional annotation of lncRNAs and dissection of lncRNA-mRNA interactions in trees.