CRISPR Primer Designer:Design primers for knockout and chromosome imaging CRISPR-Cas system

The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system.

Cis-12-Oxo-Phytodienoic Acid Stimulates Rice Defense Response to a Piercing-Sucking Insect

The brown planthopper （BPH, Nilaparvata lugens） is a destructive, monophagous, piercing-sucking insect pest of rice. Previous studies indicated that jasmonic acid （JA） positively regulates rice defense against chewing insect pests but negatively regulates it against the piercing-sucking insect of BPH. We here demonstrated that overexpression of allene oxide cyclase （AOC） but not OPR3 （cis-12-oxo-phytodienoic acid （OPDA） reductase 3, an enzyme adjacent to AOC in the JA synthetic pathway） significantly increased rice resistance to BPH, mainly by reducing the feeding activity and survival rate. Further anal- ysis revealed that plant response to BPH under AOC overexpression was independent of the JA pathway and that significantly higher OPDA levels stimulated rice resistance to BPH. Microarray analysis identified multiple candidate resistance-related genes underAOCoverexpression. OPDA treatment stimulated the resistance of radish seedlings to green peach aphid Myzus persicae, another piercing-sucking insect. These results imply that rice resistance to chewing insects and to sucking insects can be enhanced simultaneously through AOC-mediated increases of JA and OPDA and provide direct evidence of the potential application of OPDA in stimulating plant defense responses to piercing-sucking insect pests in agriculture.

The rice PLATZ protein SHORT GRAIN6 determines grain size by regulating spikelet hull cell division

Grain size is a major determinant of cereal grain yields;however,the relevant regulatory mechanisms controlling this trait have not been fully elucidated.The rice(Oryza sativa)mutant short grain6(sg6)was identified based on its reduced grain length and weight.Here,we functionally characterized the role of SG6 in determining grain size through the regulation of spikelet hull cell division.SG6 encodes a previously uncharacterized plant ATrich sequence and zinc-binding(PLATZ)protein that is ubiquitously localized throughout the cell and is preferentially expressed in the early developing panicles but not in the endosperm.The overexpression of SG6 resulted in significantly larger and heavier grains,as well as increased plant heights,which is consistent with its elevated spikelet hull cell division rate.Yeast two-hybrid analyses revealed that SG6 interacts with the core cell cycle machinery DP protein and several other putative cell division regulators,consistent with our transcriptomic analysis,which showed that SG6 activates the expression of many DNA replication and cell-cycle-related genes.These results confirm the crucial role of SG6 in determining grain size by regulating spikelet hull cell division and provide clues for understanding the functions of PLATZ family proteins and the network regulating cereal grain size.