The rapidly evolving genome editing technologies have demonstrated strong application potential in animal and plant breeding, microbial engineering, and basic scientific research. Current genome editing techniques allow for the insertion, deletion, and substitution of single or multiple nucleotides at specific genomic targets across a wide range of species. However, editing types involving large DNA fragment insertion or replacement still face technical bottlenecks, such as low efficiency and fidelity, as well as difficulties in donor delivery. These limitations restrict the application of gene editing in important scenarios, including multigene stacking with genetic linkage, precise replacement of favorable alleles, and targeted integration of DNA fragments at genomic safe harbors. Transposable elements, as mobile genetic elements widely present in biological genomes, offer a novel approach to overcoming these challenges due to their inherent mobility and large DNA cargo capacity. They hold promise for being engineered into key molecular tools for precise large DNA fragment editing. This review summarizes recent advances in targeted large DNA fragment insertion technologies based on transposable elements, focusing on the application status and prospects of prokaryotic-derived CRISPR-associated transposons (CAST) and certain DNA transposons and retrotransposons in eukaryotes. Prokaryotic-derived CAST systems have shown outstanding performance, enabling efficient large fragment integration in prokaryotes and, after optimization, also achieving large fragment insertion in eukaryotic cells. In eukaryotes, engineered DNA transposons such as mPing/Pong and retrotransposon-related tools like R2 and L1 have been utilized for large DNA fragment insertion in animals and plants. At the same time, the field of transposon-based large DNA fragment insertion faces challenges. On the one hand, the cross-species adaptability of transposable elements is limited, making it difficult for some elements to function when transferred to other species. On the other hand, the large size or multiplicity of protein components involved leads to low delivery efficiency in certain types of eukaryotic cells. Additionally, some systems carry safety risks, such as stimulating the mammalian immune system and triggering inflammatory responses. Future research may focus on the discovery of novel transposable elements, engineering of transposases, development of new delivery vectors, and in-depth elucidation of transposition mechanisms, in order to provide key technical support for establishing efficient and safe large fragment editing technologies. This will contribute to foundational innovations in crop genetic improvement, gene therapy, and microbial genome editing.

Heading date (or flowering time), an important agronomic trait in crop species, is closely associated with regional adaptation and yield. Members of the Pseudo-Response Regulator (PRR) family play key roles in regulating flowering. However, their role and molecular mechanism controlling heading date in rice is not very clear. Here, we identified rice OsPRR protein, OsPRR59, which delayed heading under long-day conditions. OsPRR59 positively regulates yield by affecting plant height, secondary branches number per panicle, grain number per panicle, seed setting rate, and grain weight per plant. OsPRR59 is expressed in most tissues and its protein is localized to the nucleus. We also found that OsPRR59 directly binds to the promoter of Ehd3 to inhibit its expression. Compared with the WT, osprr59 ehd3 showed a significantly delayed heading phenotype, as did the ehd3 mutant. This was opposite to the phenotype of the osprr59 mutant, confirming that Ehd3 acted downstream of OsPRR59 in regulating rice flowering. Our results identified a direct regulator of Ehd3, and revealed a novel molecular mechanism of clock component OsPRR proteins in regulating heading date and provide a new genetic resource for fine-tuning heading date in rice.

Endosperm as the storage organ of starch and protein in cereal crops largely determines grain yield and quality. Despite the fact that several pentatricopeptide repeat (PPR) proteins required for endosperm development have been identified in rice, the molecular mechanisms of many P-type PPR proteins in endosperm development remains unclear. Here, we isolated a rice floury endosperm mutant ppr5 that developed small starch grains and an abnormal aleurone layer, accompanied by decreased starch, protein, and amylose contents. Map-based cloning combined with a complementation test demonstrated that PPR5 encodes a P-type PPR protein that is localized to the mitochondria. The mutation in PPR5 caused reduced splicing efficiency of mitochondrial NADH dehydrogenase 4 (nad4) gene intron 3 and reduced complex Ⅰ assembly and activity. Loss of PPR5 function greatly up-regulated expression of alternative oxidases (AOXs), reduced ATP production, and affected mitochondrial morphology. We demonstrate that PPR5, as a P-type PPR protein, is required for mitochondrial function and endosperm development by controlling the cis-splicing of mitochondrial nad4 intron 3.

The International Crop Science Congress (ICSC) is a regularly held event allowing crop scientists to integrate current knowledge into a global context and international applications. The 7th ICSC was held on August 14–19, 2016 in Beijing, China, with the theme “Crop Science: Innovation and Sustainability”. As a companion production for this great congress, the nine papers collected in this special issue feature important fields of crop science in China. This editorial first briefly introduces the 7th ICSC, followed by a brief discussion of the current status of, constraints to, and innovations in Chinese agriculture and crop science. Finally, the main scientific points of the papers published in this special issue are surveyed, covering important advances in hybrid rice breeding, minor cereals, food legumes, rapeseed, crop systems, crop management, cotton, genomics-based germplasm research, and QTL mapping. In a section describing future prospects, it is indicated that China faces a full transition from traditional to modern agriculture and crop science.

Breeding to Optimize Chinese Agriculture (OPTICHINA) was a three-year EU–China project launched in June of 2011. As designed, the project acted as a new strategic model to reinforce systematic cooperation on agricultural research between Europe and China. The OPTICHINA International Conference “Breeding to Optimize Agriculture in a Changing World” was held in Beijing, May 26–29, 2014. The conference included six thematic areas: (1) defining and protecting the yield potential of traits and genes; (2) high-throughput precision phenotyping in the field; (3) molecular technologies in modern breeding; (4) plant ideotype; (5) data analysis, data management, and bioinformatics; and (6) national challenges and opportunities for China. The 10 articles collected in this special issue represent key contributions and topics of this conference. This editorial provides a brief introduction to the OPTICHINA project, followed by the main scientific points of articles published in this special issue. Finally, outcomes from a brainstorming discussion at the end of the conference are summarized, representing the authors' opinions on trends in breeding for a changing world.