*Corresponding author: flu@genetics.ac.cn (F.L.)

Understanding the function of genomes is of paramount importance in biology. Comparative genomics has emerged as an invaluable tool decrypting the code of life, offering potent metrics of evolutionary constraint to pinpoint functional elements in the genome.

The tribe Triticeae encompasses major cereal crops, such as bread wheat, barley, rye, and their wild relatives. Not only being economically important, but also Triticeae exhibits tremendous diversity that facilitates comparative genomic studies for bread wheat.

Here, we sequenced and assembled genomes of 18 Triticeae species using PacBio HiFi sequencing. By integrating 60 genomes of other species across Poaceae, we developed the first generation of evolutionary constraint map of bread wheat (CMap 1.0), which captures the selective footprints shaped over the past 100 million years. Using the genome conservation score, we identified 2.8 million conserved non-coding sequences (CNSs) showing regulatory functions.

Further analyses revealed that CNSs are crucial in wheat adaptation across both micro and macro evolutionary scales. Given the changing climate and the pressing need for crop adaptation, our findings are expected to significantly benefit genetic research and breeding for bread wheat and many other crops.