Integrating Small RNA Sequencing with QTL Mapping for Identi?cation of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice
Qing Liu§, Tifeng Yang§,
Ting Yu§, Shaohong Zhang, Xingxue Mao, Junliang Zhao, Xiaofei Wang,
Jingfang Dong, Bin Liu*
Frontiers in Plant Science
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 ?owering stage is still unknown. In this
study, small RNA pro?ling 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 ?ower development. As a parallel experiment, QTL mapping was also conducted
and four QTLs for heat tolerance at the ?owering stage were identi?ed using chromosome
single-segment substitution lines derived from GXN and HJX. Further, through
integrating analysis of DE miRNAs with QTLs, we identi?ed 8 target genes corresponding
to 26 miRNAs within the four QTL regions. Some meaningful target genes such as LOC_Os12g42400, SGT1, and pectinesterase
were within the QTL regions. The negative correlation between miR169r-5p and
its target gene LOC_Os12g42400 was
con?rmed under heat stress, and overexpression of miR169r-5p enhanced heat tolerance
at ?owering stage in rice. Our results demonstrate that the integrated analysis
of genome-wide miRNA pro?ling with QTL mapping can facilitate identi?cation of miRNAs
and their target genes associated with the target traits and the limited
candidates identi?ed in this study offer an important source for further
functional analysis and molecular breeding for heat tolerance in rice.
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