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Background Awn of rice is an important domestication trait closely associated with yield traits. Therefore, the identification of genes for awn development is of great significance for the elucidation of molecular mechanism of awn development and the genetic improvement of yield traits in rice. Results In this study, using chromosome segment substitution lines (CSSLs) derived from a long-awned Guangxi common wild rice (GXCWR, Oryza rufipogon Griff.) and a short-awned indica cultivar 9311, we identified An-4, a potential quantitative trait locus (QTL) for awn development. Then, An-4 was fine mapped into a 56-kb region of chromosome 2, which contained four annotated genes. Among these four annotated genes, Os02g0594800 was concluded to be the potential candidate gene for An-4. An-4 exhibited pleiotropic effects on awn development and several yield traits. Scanning electron microscopy (SEM) analysis showed that An-4 significantly promoted awn development at Sp7 and Sp8 stage of spikelet development. Transcriptome analysis suggested that An-4 might influence the development of awn by regulating the expression of genes related to growth, developmental process, channel regulation and extracellular region. By contrast to those of 9311, the expression level of OsRR5 in CSSL128 was significantly down-regulated, whereas the expression levels of OsCKX2 and OsGA2ox5 in CSSL128 were significantly up-regulated. In addition, our study showed that An-4 had additive effects with other genes for awn development, such as An-1, An-2/LABA1 and An-3/GAD1/RAE2. Conclusions The identification of An-4 lays a foundation for cloning of An-4 and further elucidation of the molecular mechanism of awn development. Moreover, the identification of favorable allelic variation of An-4 from 9311 will be useful to improve rice yield traits.

Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403. We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

Background Rice (Oryza sativa L.) is a thermophilic crop vulnerable to chilling stress. However, common wild rice (Oryza rufipogon Griff.) in Guangxi (China) has the ability to tolerate chilling stress. To better understand the molecular mechanisms underlying chilling tolerance in wild rice, iTRAQ-based proteomic analysis was performed to examine CTS-12, a major chilling tolerance QTL derived from common wild rice, mediated chilling and recovery-induced differentially expressed proteins (DEPs) between the chilling-tolerant rice line DC90 and the chilling-sensitive 9311. Results Comparative analysis identified 206 and 155 DEPs in 9311 and DC90, respectively, in response to the whole period of chilling and recovery. These DEPs were clustered into 6 functional groups in 9311 and 4 in DC90. The majority were enriched in the ‘structural constituent of ribosome’, ‘protein-chromophore linkage’, and ‘photosynthesis and light harvesting’ categories. Short Time-series Expression Miner (STEM) analysis revealed distinct dynamic responses of both chloroplast photosynthetic and ribosomal proteins between 9311 and DC90. Conclusion CTS-12 might mediate the dynamic response of chloroplast photosynthetic and ribosomal proteins in DC90 under chilling (cold acclimation) and recovery (de-acclimation) and thereby enhancing the chilling stress tolerance of this rice line. The identified DEPs and the involvement of CTS-12 in mediating the dynamic response of DC90 at the proteomic level illuminate and deepen the understanding of the mechanisms that underlie chilling stress tolerance in wild rice. Electronic supplementary material The online version of this article (10.1186/s12870-018-1381-7) contains supplementary material, which is available to authorized users.