Whole genome sequence from 3,000-year-old Egyptian emmer wheat reveals dispersal and domestication history

Tetraploid emmer wheat was among the first domesticated cereals and is a progenitor of modern durum and bread wheat. Here we report the first whole genome sequence from an ancient wheat; a 3000-year-old museum specimen of Egyptian emmer chaff, containing 66% endogenous DNA. It shares haplotypes with modern domesticated emmer at shattering, seed size, and germination loci, and within other putative domestication loci, suggesting fixation of these traits preceded emmer's introduction to Egypt. Genetic similarity with modern Arabian and Indian landraces connects this Egyptian emmer with early South-Eastern dispersals while introgressions from Southern Levant wild emmer signpost its route into Egypt. Despite carrying modern domestication haplotypes, its genotype is unusual, indicating extinct or unsampled modern alleles. Our results show the importance of museum collections as sources of genetic data that can inform on the history and diversity of ancient cereals.