In a study published in Science, the research groups led by HAN Bin and WANG Jiawei from the Center for Excellence in Molecular Plant Sciences (CEMPS) of the Chinese Academy of Sciences (CAS) have cloned Endless Branches and Tillers 1 (EBT1), a key gene that determines whether wild rice grows as a perennial, and revealed that changes in the expression pattern of this gene underlie the transition of rice from perennial to annual during domestication.

The researchers first conducted a systematic phenotypic survey of 446 wild rice accessions. They found that unlike annual cultivated rice, some wild rice plants did not senesce and die after seed maturation; instead, new branches continuously emerged from axillary buds at the nodes. These branches elongated and spread outward. They later produced roots and developed into new plants once they contacted the soil, forming a weedy growth pattern.

This phenotype was found to result from a reversal of developmental programming after flowering—plants return from reproductive growth to vegetative growth, a phenomenon known as “floral reversion.” Through this mechanism, the plants acquire a perennial lifestyle with clonal propagation.

To identify the genetic basis of this perennial trait, the researchers crossed the perennial Dongxiang wild rice (Oryza rufipogon) accession W1943 with the annual indica cultivar Guangluai 4 (GLA4) and developed chromosome segment substitution lines for forward genetic analysis. Using fine map-based cloning, they eventually identified the responsible gene, which they named EBT1. The locus consists of two tandemly arranged microRNA genes, MIR156B and MIR156C.

It has been well established that miR156 functions as a developmental “age switch” in plants, regulating the progression of plant development. According to the classical model, miR156 is highly expressed during the juvenile stage and gradually declines as plants age, promoting the transition from vegetative to reproductive growth.

Surprisingly, the researchers discovered that although MIR156B/C in wild rice followed a similar developmental expression pattern, they were reactivated in axillary buds of tiller nodes after flowering. This resetting of expression enabled axillary buds to undergo developmental reversion, regain vegetative growth capacity, and continuously produce new tillers, generating a clonal growth pattern. This unique expression pattern was revealed to be closely associated with the epigenetic state of the EBT1 locus in wild rice.

The comparison of wild and cultivated rice through population genomic analyses showed that the genomic region harboring EBT1 experienced artificial selection during rice domestication. This finding suggested that while selecting for higher yield and more compact plant architecture, early farmers might have inadvertently eliminated the perennial trait present in wild rice.

Moreover, the researchers combined EBT1 with two identified rice prostrate growth genes, PROG1 and TIG1, and generated wild-rice-like plants that reproduced the weedy growth pattern of wild rice. These plants exhibited strong clonal propagation ability and could survive for at least two years under field conditions in Hainan Province, China.

This study offers novel insights into the evolutionary transition of plant life-history strategies, and provides important genetic resources and theoretical foundations for the development of perennial rice varieties and the improvement of ratoon rice breeding, in which a second crop can be produced from the same plant after the first crop is harvested.