Discovery of a 3D Genomic Loop Boosts Yield and Sustainability in Rice Cultivation

A team of Chinese scientists has uncovered a hidden 3D structure in rice DNA that allows the crop to grow more grain while using less nitrogen fertilizer. The finding, published in Nature Genetics by researchers from the Chinese Academy of Sciences (CAS) on Oct. 29, could guide the next "green revolution" toward higher yields and more sustainable farming.

The study reveals that a looping section of DNA-a "chromatin loop"-controls the activity of a gene called RCN2, which governs how rice plants form their grain-bearing branches. Adjusting this loop boosted both yield and nitrogen use efficiency (NUE), two traits that normally conflict with each other.

According to Prof. FU Xiangdong from the Institute of Genetics and Developmental Biology of CAS, who led the team, boosting crop yields depends on strengthening both the "source" and the "sink" within a plant. The source refers to tissues such as leaves that produce and release sugars through photosynthesis, while the sink includes the growing parts-grains, panicles, young leaves, stems, roots, and fruits-that store or consume those sugars. Improving both sides of this system simultaneously is essential for increasing yield and NUE.

To uncover how this coordination occurs, the researchers identified a major genetic region, or quantitative trait locus, called qINCA2. This locus influences photosynthesis, nitrogen assimilation, and grain number-three core traits for productivity. Within this region, the researchers pinpointed a single nucleotide polymorphism (SNP) located 8,765 base pairs upstream of a gene known as RCN2, which plays a key role in how rice forms its grain-bearing branches, or inflorescences.

That tiny DNA change dramatically increased RCN2 activity. The RCN2 protein then altered how two other molecules-OsSPL14 and DELLA-interact. By loosening their bond, RCN2 effectively freed the OsSPL14 transcription factor to switch on genes responsible for carbon–nitrogen metabolism and panicle development. This chain reaction allowed rice plants to produce more grains and use nitrogen more efficiently-two goals that typically trade off against each other.

The team then turned to a deeper question: How does the SNP trigger such a strong effect on gene expression? Their investigation revealed that the region containing the SNP also carries a series of tandem DNA repeats-CCCTC motifs-known in animals to anchor 3D loops in chromatin, the tightly packed form of DNA. In mammals, such loops are controlled by a protein called CTCF, but no plant equivalent had ever been confirmed.

FU's group identified OsYY1 as the first plant protein to act in this way. OsYY1 binds to the CCCTC-rich DNA sequences near RCN2 and promotes the extrusion of chromatin loops, reshaping the three-dimensional architecture of the genome. This looping mechanism determines whether RCN2 is turned on or off by bringing distant control elements into contact with its promoter region.

By precisely editing these regulatory DNA sequences, the researchers were able to fine-tune chromatin looping at the RCN2 site. The result was enhanced flow of carbon compounds from source tissues to developing grains-the sink-leading to higher harvest index (HI), greater yield, and stronger NUE, even under low-nitrogen conditions.

This discovery introduces chromatin loop extrusion as a new mechanism for crop improvement. Beyond its immediate implications for rice, it opens the door to next-generation breeding strategies that could help feed a growing global population with fewer environmental costs.