Integrating small RNA sequencing with QTL mapping for identification of miRNAs and their target genes associated with heat tolerance at the flowering stage in rice
Qing
Liu 1, 2†, TifengYang1, 2†, TingYu3 †,
ShaohongZhang1, 2, XingxueMao1, 2,
Junliang
Zhao1, 2, XiaofeiWang1, 2, JingfangDong1, 2 and BinLiu 1, 2*
Frontiers in Plant
Science
doi: org/10.3389/fpls.2017.00043
Abstract
Although,
microRNAs (miRNAs) have been reported to be associated with heat tolerance at
the seedling stage in rice, their involvement in heat tolerance at the
flowering stage is still unknown. In this study, small RNA profiling was
conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive
variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were
differentially expressed (DE) under heat stress. Compared to HJX, GXN had more
DE miRNAs and its DE miRNAs changed earlier under heat stress. Plant Ontology
(PO) analysis of the target genes revealed that many DE miRNAs were involved in
flower development. As a parallel experiment, QTL mapping was also conducted
and four QTLs for heat tolerance at the flowering stage were identified using
chromosome single-segment substitution lines derived from GXN and HJX. Further,
through integrating analysis of DE miRNAs with QTLs, we identified 8 target
genes corresponding to 26 miRNAs within the four QTL regions. Some meaningful
target genes such asLOC_Os12g42400, SGT1, andpectinesterasewere within the QTL
regions. The negative correlation between miR169r-5p and its target
geneLOC_Os12g42400was confirmed under heat stress, and overexpression of
miR169r-5p enhanced heat tolerance at flowering stage in rice. Our results
demonstrate that the integrated analysis of genome-wide miRNA profiling with
QTL mapping can facilitate identification of miRNAs and their target genes
associated with the target traits and the limited candidates identified in this
study offer an important source for further functional analysis and molecular
breeding for heat tolerance in rice.
