Association studies reveal the effect of genetic variation in lncRNA UGTRL and its putative target PtoUGT88A1 on wood formation in Populus tomentosa
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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.
KeywordsLong noncoding RNAs lncRNA-mRNA interaction Multi-SNP association UDP-glucosyltransferases Wood formation Epistasis
This work was supported by the National “863” Plan Project (No. 2013AA102702), the State Key Basic Research Program of China (No. 2012CB114506), and the Fundamental Research Funds for the Central Universities (No. BLYJ201408).
Data archiving statement
Sequence data from this article have been deposited with the GenBank Data Library under the accession nos. KR492527–KR492612.
- Aspeborg H, Schrader J, Coutinho PM, Stam M, Kallas A, Djerbi S, Nilsson P, Denman S, Amini B, Sterky F, Master E, Sandberg G, Mellerowicz E, Sundberg B, Henrissat B, Teeri TT (2005) Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiol 137:983–997PubMedCentralCrossRefPubMedGoogle Scholar
- Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St LGR, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14:723–730PubMedCentralCrossRefPubMedGoogle Scholar
- Hardy O, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes: 618-620Google Scholar
- Li J, Ma W, Zeng P, Wang J, Geng B, Yang J, Cui Q (2014a) LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Brief BioinformGoogle Scholar
- Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ (2014b) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 15:R40PubMedCentralCrossRefPubMedGoogle Scholar
- Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
- Zhang D, Zhang Z, Yang K (2007) Identification of AFLP markers associated with embryonic root development in Populus tomentosa Carr. Silvae Genet: 27-32Google Scholar