Precise and efficient genome editing is very important for gene functional characterization. In recent years, sequence-specific DNA nucleases have been developed to increase the efficiency of gene targeting or genome editing in animals and plants. Among them, Zinc-Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs) are two most commonly used sequencespecific chimeric proteins (Gaj et al., 2013). Recently, a breakthrough gene-targeting tool based on RNA-guided Cas9 nuclease from type II prokaryotic Cluster Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated system has been developed (Jinek et al., 2012). CRISPR/Cas system is an adaptive defense system in prokaryotes to fight against alien nucleic acids (Horvath and Barrangou, 2010). The CRISPR loci are variable short spacers separated by short repeats, which are transcribed into synthetic single-guide RNA (sgRNA). The sgRNA forms a functional complex with CRISPR-associated nuclease (Cas9) and guide the nuclease to genomic loci matching a 20-bp complementary invading DNA, cleaving it immediately upstream of a required 5'-NGG Protospacer Adjacent Motif (PAM). A chimeric sgRNA that mimics the natural synthetic sgRNA can be used to target Cas9 for genome editing in eukaryotic cells.Until now, the CRISPR/Cas system has been successfully applied to efficient genome editing in bacteria, animals and plants (Jiang et al., 2013; Mali et al., 2013; Xie and Yang, 2013). To inform the selection of target sites and avoid off-target effects, Hsu and colleagues characterized Cas9 targeting specificity in human cells by a volume of experiments, and built a computational tool for optimized sgRNA selection in human and animal genomes (Hsu et al., 2013). However, with the wide application of CRISPR-system in plant genome editing, tools for optimized sgRNA selection in plants are highly needed. In the current analysis, we present a web application tool-CRISPR-P, for CRISPR sgRNA design in more than 20 plant species. CRISPR-P allows users to search for highly specific Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for further analysis and marks restriction enzyme cutting sites for convenience. CRISPR-P is freely available at http://cbi.hzau.edu.cn/crispr/.Genomic data and annotation of the analyzed plant genomes are obtained from public databases. The genome and annotation of Arabidopsis lyrata (v.1.0), Arabidopsis thaliana (TAIR10), Brachypodium distachyon (v1.0), Brassica

Rice cultivars have been adapted to favorable ecological regions and cropping seasons. Although several heading date genes have separately made contributions to this adaptation, the roles of gene combinations are still unclear. We employed a map-based cloning approach to isolate a heading date gene, which coordinated the interaction between Ghd7 and Ghd8 to greatly delay rice heading. We resequenced these three genes in a germplasm collection to analyze natural variation. Map-based cloning demonstrated that the gene largely affecting the interaction between Ghd7 and Ghd8 was Hd1. Natural variation analysis showed that a combination of loss-of-function alleles of Ghd7, Ghd8 and Hd1 contributes to the expansion of rice cultivars to higher latitudes; by contrast, a combination of pre-existing strong alleles of Ghd7, Ghd8 and functional Hd1 (referred as SSF) is exclusively found where ancestral Asian cultivars originated. Other combinations have comparatively larger favorable ecological scopes and acceptable grain yield. Our results indicate that the combinations of Ghd7, Ghd8 and Hd1 largely define the ecogeographical adaptation and yield potential in rice cultivars. Breeding varieties with the SSF combination are recommended for tropical regions to fully utilize available energy and light resources and thus produce greater yields.

Targeted changes in chromatin state at thousands of genes are central to eukaryotic development. RELATIVE OF EARLY FLOWERING 6 (REF6) is a Jumonji-type histone demethylase that counteracts Polycomb repressive complex 2 (PRC2)-mediated gene silencing in plants and was reported to select its binding sites in a direct, sequence-specific manner. Here we show that REF6 and its two close paralogues determine spatial 'boundaries' of the repressive histone H3K27me3 mark in the genome and control the tissue-specific release from PRC2-mediated gene repression. Targeted mutagenesis revealed that these histone demethylases display pleiotropic, redundant functions in plant development, several of which depend on trans factor-mediated recruitment. Thus, Jumonji-type histone demethylases restrict repressive chromatin domains and contribute to tissue-specific gene activation via complementary targeting mechanisms.

Transcriptional silencer and copy number variants (CNVs) are associated with gene expression. However, their roles in generating phenotypes have not been well studied. Here we identified a rice quantitative trait locus, SGDP7 (Small Grain and Dense Panicle 7). SGDP7 is identical to FZP (FRIZZY PANICLE), which represses the formation of axillary meristems. The causal mutation of SGDP7 is an 18-bp fragment, named CNV-18bp, which was inserted ~5.3 kb upstream of FZP and resulted in a tandem duplication in the cultivar Chuan 7. The CNV-18bp duplication repressed FZP expression, prolonged the panicle branching period and increased grain yield by more than 15% through substantially increasing the number of spikelets per panicle (SPP) and slightly decreasing the 1,000-grain weight (TGW). The transcription repressor OsBZR1 binds the CGTG motifs in CNV-18bp and thereby represses FZP expression, indicating that CNV-18bp is the upstream silencer of FZP. These findings showed that the silencer CNVs coordinate a trade-off between SPP and TGW by fine-tuning FZP expression, and balancing the trade-off could enhance yield potential.

Background Heading date is crucial for rice reproduction and geographic expansion. Many heading date genes are sensitive to photoperiod and jointly regulate flowering time in rice. However, it is not clear how these genes coordinate rice heading. Results Here, we performed a genetic interaction analysis among four major rice heading date genes Ghd7 , Ghd8 , OsPRR37/Ghd7.1 (hereafter PRR37 ) and Hd1 in the near-isogenic background under both natural long-day (NLD) and natural short-day (NSD) conditions. The 4-gene segregating population exhibited a large heading date variation with more than 95 days under NLD and 42 days under NSD conditions. Tetragenic, trigenic and digenic interactions among these four genes were observed under both conditions but more significant under NLD conditions. In the functional Hd1 backgrounds, the strongest digenic interaction was Ghd7 by Ghd8 under NLD but was Ghd7 by PRR37 under NSD conditions. Interestingly, PRR37 acted as a flowering suppressor under NLD conditions, while it functioned alternatively as an activator or a suppressor under NSD conditions depending on the status of the other three genes. Based on the performances of 16 homozygous four-gene combinations, a positive correlation between heading date and spikelets per panicle (SPP) was found under NSD conditions, but changed to a negative correlation when heading date was over 90 days under NLD conditions. Conclusions These results demonstrate the importance of genetic interactions in the rice flowering regulatory network and will help breeders to select favorable combinations to maximize rice yield potential for different ecological areas. Electronic supplementary material The online version of this article (10.1186/s12284-019-0314-x) contains supplementary material, which is available to authorized users.