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.
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.
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Qing
Q
Liu
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Tifeng
T
Yang
Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences Guangzhou, China.
Ting
T
Yu
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Shaohong
S
Zhang
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Xingxue
X
Mao
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Junliang
J
Zhao
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Xiaofei
X
Wang
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Jingfang
J
Dong
Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China; Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China.
Bin
B
Liu
QTL mapping; RNA Sequencing; heat stress; miRNA; rice