Tracing the origin of non-brittle rachis alleles in wheat

Abstract The evolution of non-brittle rachises, controlled by the TtBTR1 genes, was a key step during wheat domestication. Here, using k -mer-based approaches applied to a large diversity panel, we refine previous estimates of the geographical and temporal origins of the three known Ttbtr1 loss-of-function alleles and show that they emerged in distinct wild emmer subpopulations. For this, we generated a chromosome-scale dika wheat assembly carrying the recently discovered Ttbtr1-Ab allele. Our analyses reveal that the Ttbtr1-A alleles reside on an introgression from the southern judaicum wild emmer population into northern wild emmer wheat, providing an explanation for the long-standing debate about the Ttbtr1-A origin. We further demonstrate that the Ttbtr1-Aa and Ttbtr1-B alleles are already present in wild emmer wheat, with evidence indicating that they arose prior to the advent of agriculture. Together, these findings support a model in which key domestication genes in domesticated crops were selected and combined from standing genetic variation in wild relatives.