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.

Xingxue Mao,Junliang Zhao,Jingfang Dong,Xiaofei Wang,Ting Yu,Qing Liu,Shaohong Zhang,Bin Liu,Tifeng Yang

doi: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 as LOC_Os12g42400, SGT1, and pectinesterase were within the QTL regions. The negative correlation between miR169r-5p and its target gene LOC_Os12g42400 was 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.

Highlights

Rice is the major food for over half of the world population
Our results showed that GXN, an indica variety from China exhibited strong heat tolerance, whereas HJX, an indica variety from China was sensitive to heat stress (Figure S2)
Recent studies have uncovered the complexity of miRNAs in regulation of plants in responses to heat stress using high-throughput sequencing technology and demonstrated that miRNAs may function as important modulators in heat acclimation (Xin et al, 2010; Jeong et al, 2011; Yu et al, 2011; Chen et al, 2012)

Summary

Introduction

Rice is the major food for over half of the world population. sustainable rice production is very important for the world food security. Heat stress is one of the major abiotic stresses that significantly affect rice growth and development. The previous study showed that a 7 ∼ 8% yield decrease in rice for miRNAs Associated with Heat Tolerance in Rice each 1◦C increase in daytime maximum/nighttime minimum temperature from 28/21 to 34/27◦C (Baker et al, 1992). Flowering (anthesis and fertilization) is the most sensitive stage to temperature in rice (Satake and Yoshida, 1978; Farrell et al, 2006). Rice plants at anthesis that are exposed to temperatures >35◦C for 5 days are sterile and set no seed (Satake and Yoshida, 1978). It is an urgent task to develop rice variety with heat tolerance to cope with the world climate change. Understanding the mechanisms of rice in response to heat stress and identifying the genes associated with heat tolerance are the prerequisite for effective molecular breeding for heat tolerance in rice

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Results

Conclusion