By precisely editing the D3 gene, which regulates both plant height and tillering, researchers developed compact, high-tillering rice plants that maintain grain yield while showing enhanced resistance to bacterial blight. The gene-edited plants reached 73%–79% of the original height of the donor variety yet produced more tillers and matured earlier.
Rice (Oryza sativa L.) feeds over half of the global population and is central to food security across Asia, Africa, and the Americas. To meet the world’s growing demand, breeders are pursuing ideal plant architecture that optimizes light interception, resource use, and yield. Strigolactones (SLs), a class of plant hormones, play a critical role in shaping this architecture by regulating shoot branching, tillering, and root development. Among the key genes in this pathway, D3 acts as a positive regulator of height but suppresses tiller growth. However, traditional breeding has struggled to separate these traits efficiently. Due to these challenges, researchers turned to CRISPR/Cas9 genome editing to precisely modify D3 and improve rice performance.
A study (DOI:10.48130/ph-0025-0017 ) published in Plant Hormones on 25 August 2025 by Jing Fan’s & Wen-Ming Wang’s team, Sichuan Agricultural University, highlights the power of gene editing in balancing multiple agronomic traits and sheds new light on the D3 gene’s role in coordinating rice architecture and stress resilience.
Using CRISPR/Cas9 genome editing, researchers designed a gene-specific guide RNA to target the D3 gene in the japonica rice cultivar DS, known for its high grain quality and cold tolerance. The D3 sequence in DS was first verified to match that of Nipponbare, and four distinct mutant lines—d3-DS-1 through d3-DS-4—were generated, each carrying small deletions or substitutions that caused truncated or frameshifted proteins. To ensure that the mutations were stably inherited and transgene-free, T₁ plants were screened using hygromycin selection and PCR identification, producing several homozygous mutants lacking foreign DNA, particularly in the d3-DS-2 line. In the subsequent T₂ generation, these non-transgenic mutants maintained stable genotypes and exhibited distinct morphological changes. Phenotypic assessments revealed that d3-DS-2, d3-DS-3, and d3-DS-4 plants had significantly reduced height—approximately 19 cm shorter than wild-type DS—and increased tiller numbers averaging 20 panicles per plant, compared to about 8 in the wild type. Although panicle length and grains per panicle were slightly reduced, overall yield per plant and 1,000-grain weight remained unchanged, indicating that higher tiller production compensated for smaller panicles. Additionally, D3-edited mutants showed earlier heading, with a developmental deviation of about 1.2 leaves and visibly faster transition to the reproductive phase. Disease resistance assays further demonstrated that lesion lengths caused by Xanthomonas oryzae pv. oryzae (Xoo) were reduced by 22–38% in mutants compared to wild-type plants. Collectively, the CRISPR/Cas9-mediated D3 knockout produced compact, high-tillering, early-heading rice lines with enhanced bacterial blight resistance and stable, non-transgenic inheritance, offering a promising strategy for rice architecture and disease resistance improvement.
This research provides a practical blueprint for developing high-yield, stress-tolerant rice cultivars using precision genome editing. The D3-edited lines combine ideal plant structure—shorter stature, more tillers, and early heading—with strong bacterial blight resistance, reducing the need for chemical inputs. As the edited plants are free of foreign DNA, they align with regulatory frameworks favoring non-transgenic crop development. Beyond rice, this approach may be extended to other cereal crops to achieve balanced gains in yield and resilience. The dual-function nature of D3 highlights how single-gene editing can accelerate breeding efficiency, offering new tools for sustainable agriculture and food security amid changing climates.
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References
DOI
10.48130/ph-0025-0017
Original Source URL
https://doi.org/10.48130/ph-0025-0017
Funding Information
This work was supported by a grant from the National Natural Science Foundation of China to JF (Grant No. 32372490).
About Plant Hormones
Plant Hormones (e-ISSN 3067-221X) is an open access, online-only, academic journal publishing rigorously peer-reviewed original articles, reviews, break-through methods, editorials, and perspectives on broad aspects of plant hormone biosynthesis, signal transduction, and crosstalk. The journal primarily publishes fundamental research that represents significant advances or new insight into specialized areas of plant hormones, and review articles that provide comprehensive and critical review of current research areas and offer directions or perspectives for future research. The journal publishes applied research that has significant implications for the development of agriculture, horticulture, and forestry. Plant Hormones also provides a community forum by publishing editorials and perspective papers for expressing opinions on specific issues or new perspectives about existing research on particular topics. Plant Hormones is hosted by Chongqing University, and published by Maximum Academic Press.