A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history

Tetraploid emmer wheat (Triticum turgidum subsp. dicoccon) is a progenitor of the world’s most widely grown crop, hexaploid bread wheat (T. aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals domesticated in the old world, cultivated from around 9700 BCE in the Levant(1,2) and subsequently in South-Western Asia, Northern Africa, and Europe with the spread of Neolithic agriculture(3,4). Here we report whole genome sequence from a museum specimen of Egyptian emmer wheat chaff, (14)C-dated to the New Kingdom 1,130 – 1,000 BCE. Its genome shares haplotypes with modern domesticated emmer at shattering, seed size, and germination loci, and within other putative domestication loci, suggesting these traits share a common origin prior to emmer’s introduction to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early South-Eastern dispersals, while inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.