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.
Highlights
Rice (Oryza sativa) together with wheat and maize provides half of the total calories consumed by the entire world population
The classification of conserved miRNA families based on their relative expression levels in rice inflorescence is comparable to that in the vegetative tissues of leaf and stem found in our previous study, majority of the conserved miRNAs are expressed at lower levels in rice inflorescence than in leaf and stem tissues. 32 families of non-conserved miRNAs were observed to be expressed in rice inflorescence of which 22 families were up-regulated in the drought-tolerant IR87705-7-15-B
The higher number of identified drought-responsive non-conserved miRNAs may imply that non-conserved miRNAs has a more prominent role to play than conserved miRNAs in drought response of rice inflorescence
Summary
Rice (Oryza sativa) together with wheat and maize provides half of the total calories consumed by the entire world population. 23% is provided by rice, 17% by wheat and 9% by maize [1]. The 158 million hectares of annual harvested rice area is made up of various agricultural systems, including irrigated (50%), rainfed lowland (34%), rainfed upland (9%) and deepwater (7%) [4]. Rice agriculture requires 2–3 times more water than wheat or maize owing to well-puddled and irrigated conditions required for cultivation [4,5]. One of the most critical challenges facing rice agriculture nowadays, with a total of 23 million hectares of rice fields affected by drought at variable intensities [12]. Breeding rice varieties with increased yield under drought could be the answer to this challenge.
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