Rice Subspecies: Unlocking the Secrets of Reproductive Isolation
Plant Science Research

New Research Unlocks the Mystery of Reproductive Isolation in Rice Subspecies

In a groundbreaking study published in Nature Communications, scientists have unveiled the genetic mechanisms behind the reproductive isolation between two subspecies of rice, indica, and japonica. This discovery could pave the way for new breeding techniques, unlocking the potential to increase rice yield by 15-30%.

The Discovery

The research team identified a presence-absence variation (PAV) at a specific locus, the Se locus, which functions as a reproductive barrier between indica and japonica rice. This PAV contains two adjacent genes that form a “killer-protector” system, inducing hybrid male sterility (HMS) and, thus, reproductive isolation between the two subspecies.

The Killer-Protector System

The two genes at the Se locus work in tandem to create a killer-protector system. One gene, ORF3, acts as a “killer,” causing sterility in hybrid male pollen. The other gene, ORF4, serves as a “protector,” rescuing the pollen from the killer effect of ORF3. This complementary effect of the two genes leads to reproductive isolation between indica and japonica.

The study also revealed that the Se locus is polymorphic in the AA rice species but absent in other Oryza species. The functional form of ORF3 is maintained in the O. sativa indica subspecies, while in japonica, most varieties have both ORF3 and ORF4 deleted. This makes the Se locus an essential isolation barrier between indica and japonica.

Implications for Rice Breeding

The yield potential of India-japonica hybrid rice is estimated to be significantly higher than that of the indicia intraspecific hybrid rice widely cultivated today. Understanding the reproductive isolation between these subspecies is crucial for unlocking their breeding potential.

By identifying the genetic factors responsible for this isolation, the researchers have opened the door to new breeding techniques that could overcome these barriers. This could lead to the development of new rice subspecies varieties with enhanced yield and resilience.


This study significantly advances our understanding of the genetic factors underlying reproductive isolation in rice. By unraveling the killer-protector system at the Se locus, the research team has provided valuable insights that could revolutionize rice breeding.

The discovery of this mechanism not only contributes to our knowledge of plant genomics and evolution and holds practical implications for agriculture. By harnessing the potential of India-japonica hybrids, we may be able to develop new rice varieties that can meet the growing global demand for this staple food.

Photo by Fajruddin Mudzakkir on Unsplash 

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