Abstract
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.
Highlights
Day length and temperature are two major environmental factors that shape plant growth and development and affect the flowering time and photoperiod sensitivity that determines the seasonal and regional adaptation of crops
Previous studies have shown that several variants occur in the coding region of the transcription factor Ghd[8] that alter the function on flowering time or heading date[8,13,23]
Variations in the expression levels of several flowering time genes due to cis-regulatory polymorphisms have been reported in maize and Arabidopsis[31,32]
Summary
Day length and temperature are two major environmental factors that shape plant growth and development and affect the flowering time and photoperiod sensitivity that determines the seasonal and regional adaptation of crops. Ghd[8] was identified as a transcription factor belonging to NF-YB It was cloned as a major quantitative trait locus (QTL) controlling heading date, plant height and grain productivity in rice. To study whether natural variations of Ghd[8] exhibit an important determinant function in rice adaptation, we conducted sequence analysis of the entire Ghd[8] gene, including the promoter region and coding region, in a panel of 198 rice germplasm accessions. Our results demonstrate that the cis-regulatory variation of the Ghd[8] promoter modulating its transcription level confers a selective advantage and plays a critical role in adapting rice to a wide range of environments
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