Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice

The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci ( , , , , and ) in ten diverse genomes of , additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed and less transcribed flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed . Compared to relatively balanced mutations at oscillator loci of , 5' mutations of (and to a less degree) were under negative selection while those of alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on alleles via local flowering time-yield relationships.