<i>ZmCCT9</i> enhances maize adaptation to higher latitudes.

Abstract

From its tropical origin in southwestern Mexico, maize spread over a wide latitudinal cline in the Americas. This feat defies the rule that crops are inhibited from spreading easily across latitudes. How the widespread latitudinal adaptation of maize was accomplished is largely unknown. Through positional cloning and association mapping, we resolved a flowering-time quantitative trait locus to a Harbinger-like transposable element positioned 57 kb upstream of a CCT transcription factor (<i>ZmCCT9</i>). The Harbinger-like element acts in <i>cis</i> to repress <i>ZmCCT9</i> expression to promote flowering under long days. Knockout of <i>ZmCCT9</i> by CRISPR/Cas9 causes early flowering under long days. <i>ZmCCT9</i> is diurnally regulated and negatively regulates the expression of the florigen <i>ZCN8</i>, thereby resulting in late flowering under long days. Population genetics analyses revealed that the Harbinger-like transposon insertion at <i>ZmCCT9</i> and the CACTA-like transposon insertion at another CCT paralog, <i>ZmCCT10</i>, arose sequentially following domestication and were targeted by selection for maize adaptation to higher latitudes. Our findings help explain how the dynamic maize genome with abundant transposon activity enabled maize to adapt over 90° of latitude during the pre-Columbian era.