Genomic analysis of emmer wheat (Triticum dicoccon): insights into domestication, dispersal and adaptation

Abstract

Emmer wheat (Triticum dicoccon), among the earliest plants domesticated in Southwest Asia, is the progenitor of the economically important durum and bread wheat. While it is acknowledged that domesticated emmer emerged from an admixture of wild wheat populations, details behind this process remain obscure. After domestication, emmer spread outside of Southwest Asia, adapting to a multitude of ecosystems. Open questions persist regarding the most likely route of dispersal to Africa and Asia, with various hypotheses being proposed. In this study, I use whole genome sequences from wild and domestic emmer wheat specimens to gain insights into these critical events and understand the role of wild ancestry in domestic populations. I analyze the population structure within the dataset and I delve into the wild ancestry of domestic landraces, estimating for the first time the contribution of each wild population to the domesticated ones. The results obtained, combined with archaeological evidence, provide a deeper and more detailed understanding of the domestication process. Around 9500 years ago, protodomestic emmer from the Southern Levant hybridized with its counterpart from the Northern Levant, giving rise to fully domesticated plants. Notably, I observe a higher proportion of wild ancestry from the Southern Levant in the population that dispersed southward and eastward, as opposed to the one that moved northward and westward. This discrepancy is attributed to post-domestication gene flow during dispersal approximately 6500 years ago, as confirmed by different tests. The inclusion of an ancient sample from Egypt in the analysis proves the antiquity of these events, suggesting that modern emmer from Ethiopia, Oman, and India descends from emmer that reached Egypt prior to 3000 years ago. This finding supports a dispersal route through Africa and the Arabian Peninsula before ultimately reaching India. Moreover, I explore the contribution of the until now unexplored Southern Levant ancestry to the functional fraction of the genome, identifying regions that are related to biotic and abiotic stress resistance. These findings underscore the potential of emmer wheat landraces in wheat improvement efforts and emphasize the vital significance of domestication studies in advancing our understanding of agricultural history and genetic diversity.

Date of Award	18 Dec 2023
Original language	English
Supervisor	Laura Rodríguez Botigué (Director)