Unearthing old rice germplasm, illuminating a new way to improvement

 Xiaoming Zheng, Ramaiah Venuprasad, and Ajay Kohli   |  

Scientists are delving into molecular genetics to enhance crop yield per unit. This approach hinges on unlocking the potential of favorable gene resources, which lie dormant within the vast collections of germplasms stored in worldwide germplasm banks, akin to a treasure trove awaiting discovery. That being said, only a small fraction of germplasms have been thoroughly examined thus far. This study highlights the effectiveness of mining gene resources from germplasm to overcome current yield limitations in crops. 


We are on the cusp of a new era, with the global population surpassing 8 billion, and over half relying on rice as their staple food. Despite this growing demand, rice yield per unit has seemingly plateaued for many years. This stagnation raises serious concerns about future global food security, especially considering the shrinking arable land in many countries.

To tackle this challenge, scientists are delving into molecular genetics to enhance crop yield per unit. This approach hinges on unlocking the potential of favorable gene resources, which lie dormant within the vast collections of germplasms stored in worldwide germplasm banks, akin to a treasure trove awaiting discovery.

That being said, only a small fraction of germplasms have been thoroughly examined thus far. Insights into this issue can be gleaned from the study of a particular rice germplasm known as clustered-spikelet rice (CL). CL, with its distinctive clustered growth of multiple grains, played a significant role in constructing the rice chromosome linkage map when genome sequence information was lacking.

Despite being recognized for its linkage with the Wx gene on chromosome 6 for approximately 84 years, the specific causal gene underlying CL remained elusive, even after 22 years since the release of the first rice genome sequence. Notably, a recent study shed light on the mechanism behind CL formation in rice.

The study identified the gene responsible for CL formation, BRD3, which encodes a catabolic enzyme of the plant hormone brassinosteroid (BR). Due to the significant structural variations preceding the gene in CL, BRD3 is activated specifically during rice panicle branching development. As a result, a series of molecular events triggered by changes in BR levels promote rice panicle branching and grain number, ultimately leading to a substantial increase in yield.

The exceptional phenotype of CL was regarded as a qualitative trait. Theoretically, it should have been readily cloned using traditional positional cloning strategies. However, the repeated failures of previous attempts suggest the presence of additional underlying mysteries.

In response to this challenge, the research team employed chemical mutagenesis against a backdrop of CL. From a population of 10,000 mutagenized strains were screened out two non-clustered mutant strains. Furthermore, utilizing bulked-segregant analysis, the team pinpointed the gene BRD3 on chromosome 6.

Further genome-resembling efforts uncovered that the CL locus spans the entire chromosomal region with intricate structural variations that activate BRD3 expression. This partially elucidates the difficulties encountered in its traditional cloning methods, while offering a methodological framework for cloning genes governing other complex traits in crops.

The researchers further elucidated the molecular pathway through which BR regulates grain number in rice panicles. It was revealed that BRD3 is activated specifically in the secondary branch meristem of the rice panicle, leading to a decrease in BR content in this region.

This reduction in BR levels promotes the accumulation of the hormone signal inhibitor kinase GSK2, which, in turn, phosphorylates and stabilizes the OsMADS1 protein. Consequently, OsMADS1 upregulates the expression of the meristem transition regulator RCN2, thereby delaying the transformation of secondary branch meristems into spikelet meristems.

As a result, more secondary branches are produced, ultimately leading to an increase in grain number. This study represents the first discovery of the inhibitory role of BR in rice panicle branching and grain formation.

A negative correlation exists between grain number and grain size, presenting a challenge in breeding and restraining further enhancements in rice yield potential.  While a decrease in BR content typically results in smaller grains, this effect is mitigated by the specific activation of BRD3 in certain tissues of CL.

The reduction in BR content within CL contributes to an increase in grain number without altering other agronomic traits such as grain size. Upon introducing CL into multiple varieties, researchers observed a significant increase in grain number due to the augmented number of secondary panicle branches in CL compared to non-clustered controls.

Notably, other yield traits showed no significant differences. Consequently, yield improved by 11.27%–20.96%, with no adverse effects on grain quality. These findings imply that spatially specific control of hormone levels can effectively decouple the interdependence between traits, offering a novel avenue for achieving breakthroughs in rice yield for future varieties.

Clustered growth is widely observed across various species in nature, and the research team has also validated the mechanism of cluster formation in other species. By comparing the levels of BR in clustered and non-clustered peppers, as well as in roses with clustered flowers and non-clustered roses, similar fluctuations in BR content were observed between clustered and non-clustered varieties, similar to what was observed in rice. This result suggests that the mechanism by which BR content regulates cluster formation may be universal in nature.

In summary, this study highlights the effectiveness of mining gene resources from germplasm to overcome current yield limitations in crops. The comprehensive scope of this research, ranging from genetic analysis to cytological observations, chemical mutagenesis, gene cloning, genome assembly, molecular mechanism analysis, breeding evaluations, and even extending to other species, serves as a roadmap for future germplasm exploration.

While it was exhilarating to unravel the mystery of CL, we anticipate greater utilization of crop germplasms to discover additional valuable gene resources. These efforts are not only instrumental in enhancing crop improvement, but also contribute to a deeper understanding of fundamental biological processes, as exemplified in this study.

Read the study:
Zheng X, Venuprasad R, & Kohli A. (2024) Unearthing old rice germplasm, illuminating a new way to improvement. Journal of Integrative Plant Biology.

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