Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions

PLoS One. 2017 Oct 18;12(10):e0186382. doi: 10.1371/journal.pone.0186382. eCollection 2017.

Abstract

A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line. In this study, more drought-responsive microRNAs were identified in the inflorescence tissues of IR64, IR77298-14-1-2-10 and IR87705-7-15-B via next-generation sequencing. Among the 32 families of inflorescence-specific non-conserved microRNAs that were identified, 22 families were up-regulated in IR87705-7-15-B. Overall 9 conserved and 34 non-conserved microRNA families were found as drought-responsive in rice inflorescence with 5 conserved and 30 non-conserved families induced in the IR87705-7-15-B. The observation of more drought-responsive non-conserved microRNAs may imply their prominence over conserved microRNAs in drought response mechanisms of rice inflorescence. Gene Ontology annotation analysis on the target genes of drought-responsive microRNAs identified in IR87705-7-15-B revealed over-representation of biological processes including development, signalling and response to stimulus. Particularly, four inflorescence-specific microRNAs viz. osa-miR5485, osa-miR5487, osa-miR5492 and osa-miR5517, and two non-inflorescence specific microRNAs viz. osa-miR169d and osa-miR169f.2 target genes that are involved in flower or embryonic development. Among them, osa-miR169d, osa-miR5492 and osa-miR5517 are related to flowering time control. It is also worth mentioning that osa-miR2118 and osa-miR2275, which are implicated in the biosynthesis of rice inflorescence-specific small interfering RNAs, were induced in IR87705-7-15-B but repressed in IR77298-14-1-2-10. Further, gene search within qDTY4.1 QTL region had identified multiple copies of NBS-LRR resistance genes (potential target of osa-miR2118), subtilisins and genes implicated in stomatal movement, ABA metabolism and cuticular wax biosynthesis.

MeSH terms

  • Droughts
  • Flowers / genetics
  • Flowers / growth & development
  • Gene Expression Regulation, Plant
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Inflorescence / genetics*
  • MicroRNAs / genetics*
  • MicroRNAs / isolation & purification
  • Molecular Sequence Annotation
  • Oryza / genetics*
  • Oryza / growth & development
  • Plant Leaves / genetics
  • Plant Leaves / growth & development
  • Plant Roots / genetics
  • Plant Roots / growth & development
  • Quantitative Trait Loci / genetics*
  • Transcriptome / genetics

Substances

  • MicroRNAs

Grants and funding

BHC is sponsored by MyBrain 15 (MyPhD) scholarship. The funder provided support in the form of salaries and study allowances for BHC. KN received Research University Grants UKM-GUP-2011-215 and UKM-GUP-2012-075 (http://www.ukm.my/seri/research-university-grant-gup/) from Universiti Kebangsaan Malaysia, which funded this research. Both funders did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors from Bionivid Technology Private Limited are our service providers cum collaborators who are entasked with the role of bioinformatics analyses. They do not provide any financial support in this research. The specific roles of these authors are articulated in the 'author contributions' section.