A Comprehensive CRISPR-Based Genome Editing Analysis System And Database For Modifying Rice Seed-Related Genes

As one of the world’s important staple crops,rice plays a vital role as a primary food source for over half of the global population.Although the genome sequences of many rice varieties have been fully sequenced,and numerous genes related to important agronomic traits and stress tolerance have been identified and studied,these achievements have propelled significant advancements in rice functional genomics research.However,due to the complex quantitative nature of yield traits controlled by multiple genes and their susceptibility to environmental changes,the discovery of more genes related to rice yield traits is of paramount importance for high-yield rice breeding.Gene editing holds significant significance in the development of crop improvement and new breeding methods.However,for researchers not involved in bioinformatics,analyzing the efficiency and outcomes of gene editing can be a cumbersome task.To address this issue,this study employed TypeScript scripting and designed a cross-platform software aimed at establishing a simple and efficient system for analyzing high-throughput genome editing sequencing data.The software allows researchers to quickly analyze gene editing efficiency and outcomes.The software primarily encompasses the following important features and functionalities:1.Automatic merging of paired-end sequencing files.2.Batch data splitting based on sequencing sequences.3.Alignment of sequencing sequences to target sites for analysis and statistical evaluation of gene editing mutations.The development goal of the software is to provide a user-friendly interface,simplify the process of gene editing data analysis,and offer researchers accurate and reliable results.The application of this software can assist researchers in the field of gene editing to analyze genome editing sequencing data quickly and accurately,thereby providing support for evaluating gene editing efficiency and outcomes.In rice,the growth and development of seeds are critical,and numerous genes related to quality and yield are involved in the seed development process.In order to explore the functional genes associated with rice yield and provide a reference basis for subsequent high-yield rice breeding,310 seed-specific or preferentially expressed genes were selected from the rice gene expression database.A total of 375 editing sites were designed for CRISPR genome editing,followed by analysis of the editing outcomes of these 310 genes using the previously developed cross-platform software.This culminated in the establishment of the rice seed editing database.The database includes functions such as querying the expression of seed-related genes in different tissues and stages,querying mutant genotypes and corresponding phenotypes,as well as comparing phenotypes with parental controls.It provides researchers with a platform to facilitate further exploration of the mechanisms underlying rice seed development.This has the potential value in promoting increased rice yield and studying high-yield rice breeding patterns.Through the cross-platform gene editing analysis software and rice seed editing database developed in this study,researchers can more efficiently analyze gene editing outcomes and gain in-depth understanding of key genes and regulatory mechanisms in rice seed development.This will contribute to uncovering the molecular mechanisms underlying rice seed formation and development,providing valuable insights for further improvement of rice varieties.It holds potential applications in optimizing crop improvement and new breeding methods,thereby offering references for advancing rice breeding.