Elucidating the genetic basis of speciation provides crucial insights into evolutionary novelty. Oryza rufipogon and Oryza nivara are closely related wild rice species that diverged due to habitat differentiation and provide a valuable system for studying ecological speciation.

We constructed a recombinant inbred line population from a cross between two Oryza species and performed a quantitative trait locus (QTL) mapping for 17 traits. We identified 133 QTLs and revealed that a few genes of large effect and many genes of small effect were responsible for the divergence of all measured traits as a whole and for each of the two focal traits (flowering time and perenniality) that play critical roles in the formation of O. nivara. Moreover, we showed that the shared genetic bases among traits promoted the ecological origin of O. nivara.

By integrating the QTL mapping and genome scans, we identified the candidate genes associated with photoperiod sensitivity (Hd1 and OsPRR37) and perenniality (OsEMF2a) and demonstrated that the photoperiod sensitivity loss is the main contributor to the origin of O. nivara. 

This study offers new insights into the genetic mechanisms of ecological speciation and facilitates effective manipulation of specific genes in rice breeding.