Mining genetic changes underlying perennial-to-annual transitions in Oryza with comparative genomics

Perennial rice has shown great potential for alleviating multidimensional sustainability issues that are prevalent in current rice agriculture, prompting widespread interest in its breeding. Currently, one major hurdle for these breeding efforts is our limited knowledge about the evolutionary mechanisms of the perennial-to-annual transition in Oryza . Here, by performing comparative genomics of three annual-perennial pairs of Oryza species ( Oryza rufipogon / O. nivara , O. glumaepatula / O. glaberrima , and O. meyeriana / O. brachyantha ), we identified 91 gene families that are present in all the perennial species but absent from all the annual species. Annotations and functional predictions of these gene families demonstrated that they may be associated with a battery of physiological components of perenniality, such as phenology, energy allocation, and source–sink dynamics. Furthermore, comparative co-expression analysis revealed that many of these families likely also play important regulatory roles in orchestrating diverse processes that differ between perennial and annual Oryza species, including reproduction, root development, and responses to environmental stimuli. These results underscore the potential evolutionary complexity involved in the emergence of annuality in Oryza and imply that a wide range of aspects of perenniality need to be considered in a combinatorial manner for improving the overall agronomic performance of perennial rice.