BackgroundUnderstanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development.ResultsWe performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer.ConclusionThrough the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0219-0) contains supplementary material, which is available to authorized users.

Promoters can direct gene expression specifically to targeted tissues or cells. Effective with both crop species and model plant systems, these tools can help researchers overcome the practical obstacles associated with transgenic protocols. Here, we identified promoters that allow one to target the manipulation of gene expression during pollen development. Utilizing published transcriptomic databases for rice, we investigated the promoter activity of selected genes in Arabidopsis. From various microarray datasets, including those for anthers and pollen grains at different developmental stages, we selected nine candidate genes that showed high levels of expression in the late stages of rice pollen development. We named these Oryza sativa late pollen-specific genes. Their promoter regions contained various cis-acting elements that could be responsible for anther-/pollen-specific expression. Promoter::GUS-GFP reporters were constructed and introduced into Arabidopsis plants. Histochemical GUS staining revealed that six of the nine rice promoters conferred strong GUS expression that was restricted to the anthers in Arabidopsis. Further analysis showed that although the GUS signals were not detected at the unicellular stage, they strengthened in the bicellular or tricellular stages, peaking at the mature pollen stage. This paralleled their transcriptomic profiles in rice. Based on our results, we proposed that these six rice promoters, which are active in the late stages of pollen formation in the dicot Arabidopsis, can aid molecular breeders in generating new varieties of a monocot plant, rice.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Gene flow events from genetically modified (GM) rice to adjacent non-GM rice lines naturally happen in the field. GM rice lines containing desirable agronomic traits such as tolerance to abiotic stresses and resistance to biotic stresses can be used to cross with non-GM cultivated rice and also to wild species of rice. This event can eventually lead to offspring which possess traits that allows a better chance of survival in the field. However this phenomenon has the possibility to produce undesirable effect in the environment surrounding the rice field. The objective of this study was to determine the out-crossing rate of GM rice to cultivated rice. Transgenic rice, Hwangkembyeo (containing beta-carotene enhancing gene and bar gene) and cultivated rice, Nakdongbyeo (mother plant of Hwangkembyeo) were used in this study. Results showed that most gene flow events occurred within 1 m range. In particular, gene flow events mostly happened within 30 cm, while it was rarely observed beyond 90 cm range. The maximum distance for gene flow event was observed at 6 m range however the sharp cut point distance was observed at 60-90 cm range. The prevailing gene flow direction was Northwest (NW) which coincided with the prevailing wind of Southeastern (SE) direction. Wind direction and distance were found to be the most important factors for determining rice out-crossing rate. But for more accurate prevention of GM gene flow, many factors should be considered like the local weather condition, wind direction, wind speed and flowering time.

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Male sterility is an important trait for crop breeding program based on heterosis. Recent advances in molecular researches have led to the identification of genes involved in plant reproductive development and understanding the molecular functions of rice male gametophyte including roles of phytohormones in reproduction process. Here, we review the genes required for key aspects of anther/pollen development and conventional methods for the production of hybrid seeds in rice. Finally, we discuss the molecular approaches for the generation of male-sterile lines through the regulation of phytohormonal biosynthesis in reproductive organs.