Tree Genetics & Genomes

, 12:8 | Cite as

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

  • Mingyang Quan
  • Jiaxing Tian
  • Xiaohui Yang
  • Qingzhang Du
  • Yuepeng Song
  • Qingshi Wang
  • Jinhui Chen
  • Deqiang Zhang
Original Article
First Online:
Received:
Revised:
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Part of the following topical collections:
  1. Complex Traits

Abstract

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.

Keywords

Long noncoding RNAs lncRNA-mRNA interaction Multi-SNP association UDP-glucosyltransferases Wood formation Epistasis 
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Notes

Acknowledgments

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.

Supplementary material

11295_2015_967_MOESM1_ESM.doc (29 kb)
Table S1 The real-time PCR primers used in this study.(DOC 29 kb)
11295_2015_967_MOESM2_ESM.doc (42 kb)
Table S2 Significant SNPs associated with all traits calculated by MLM in the association population of Populus tomentosa.(DOC 41 kb)
11295_2015_967_MOESM3_ESM.doc (50 kb)
Table S3 Significant haplotypes from UGTRL and its putative target PtoUGT88A1 associated with growth, wood properties, and photosynthetic traits in the association population of Populus tomentosa.(DOC 50 kb)
11295_2015_967_MOESM4_ESM.doc (142 kb)
Table S4 Additive effect of all significant SNPs from UGTRL and PtoUGT88A1 associated with each trait in the association population of Populus tomentosa.(DOC 142 kb)
11295_2015_967_MOESM5_ESM.doc (114 kb)
Table S5 Dominant effect of all significant SNPs from UGTRL and PtoUGT88A1 associated with each trait in the association population of Populus tomentosa(DOC 113 kb)
11295_2015_967_MOESM6_ESM.doc (158 kb)
Table S6 The additive, dominant and R 2 (phenotypic contributions) of significant SNPs associated with all the traits under both additive and dominant effects in the association population of Populus tomentosa.(DOC 157 kb)
11295_2015_967_MOESM7_ESM.doc (124 kb)
Table S7 The SNP pairs and their main effects detected from UGTRL and PtoUGT88A1 under epistasis model in the association population of Populus tomentosa.(DOC 123 kb)
11295_2015_967_MOESM8_ESM.doc (82 kb)
Fig. S1 Sequence complementarity of UGTRL and its putative target PtoUGT88A1.(DOC 82 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Mingyang Quan
    • 1
  • Jiaxing Tian
    • 1
  • Xiaohui Yang
    • 1
    • 2
  • Qingzhang Du
    • 1
    • 2
  • Yuepeng Song
    • 1
    • 2
  • Qingshi Wang
    • 1
    • 2
  • Jinhui Chen
    • 1
    • 2
  • Deqiang Zhang
    • 1
    • 2
  1. 1.National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingPeople’s Republic of China
  2. 2.Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingPeople’s Republic of China

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