The genomic landscape and the effect of linked selection during the repeated domestication of grain amaranth

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Plant populations constantly adapt to their environment. The sources for adaptation are mutations and recombination. While the adaptive effect of point mutations has been extensively studied, the role of recombination and the genomic landscape have received less attention. Yet, recent examples have shown the importance of recombination and chromatin accessibility for adaptive phenotypes. Chromatin accessibility and recombination rates can be altered during adaptation. Hence these factors not only influence adaptation but might themselves be shaped by selection.On the population genomic level, adaptation shapes the diversity pattern across the genome. As a result of linkage disequilibrium, not only sites directly affected by selection show reduced diversity, but also linked neutral sites. The extend of linked selection is vastly unknown and affects the interpretation of observed genetic diversity.Chromatin accessibility can be employed as proxy for the functional part of the genome, to evaluate the strength of linked selection as a function of the distance from open chromatin. Crop domestication is a well-suited model for plant adaptation, because selected traits are known, and the ancestors of the adapted populations are often known and still available. Grain amaranth has been domesticated three times independently from a single ancestor and provides an ideal study system to study the importance of recombination and chromatin accessibility during crop domestication, and the consequences on linked selection.In this project, we will construct independent genetic maps for each of the three grain amaranth species and their wild ancestor to evaluate the change in recombination rates during domestication and to identify large scale rearrangements. This will yield high quality genetic maps for all four species and allow us to map adaptation related phenotypes. Furthermore, we will construct independent chromatin accessibility maps across species and tissues to gain insights into the stability of open chromatin. It is expected that recombination and chromatin landscapes are altered during domestication and potentially diverged between crop species. Combining the newly generated data of open chromatin as proxy for functional space in the genome and species-specific recombination maps with population scale genetic diversity estimates, we will study the patterns of linked selection in the four amaranth species and their change during domestication. We will study if these patterns evolve convergently or if the signals differ between grain amaranth species, despite their common ancestry. Our results will give new insights into the interplay between the genomic landscape and crop evolution.