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Variations in the gene promoter play critical roles in the evolution of important adaptive traits in crops, but direct links of the regulatory mutation to the adaptive change are not well understood. Here, we examine the nucleotide variations in the promoter region of a transcription factor ( Ghd8 ) that control grain number, plant height and heading date in rice. We find that a dominant promoter type of subspecies  japonica  displayed a high activity for  Ghd8  expression in comparison with the one in  indica . Transgenic analyses revealed that higher expression levels of  Ghd8  delayed heading date and enhanced cold tolerance in rice. Furthermore, a single-nucleotide polymorphism (T1279G) at the position −1279 bp that locates on the potential GA-responsive motif in the  Ghd8  promoter affected the expression of this gene. The 1279 T variant has elevated expression of  Ghd8 , thus conferring increased cold tolerance of rice seedlings. Nucleotide diversity analysis revealed that the approximately 25-kb genomic region surrounding  Ghd8  in the subspecies  japonica  was under significant selection pressure. Our findings demonstrate that the join effects of the regulatory and coding variants largely contribute to the divergence of  japonica  and  indica  and increase the adaptability of  japonica  to the cold environment.

A key variant in the cis-regulatory element of flowering gene Ghd8 associated with cold tolerance in rice