Solanum pan-genetics reveals paralogues as contingencies in crop engineering

Abstract Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops 1,2 . A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area) 3–5 to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops 6,7 . Here, by establishing a pan-genome of the crop-rich genus Solanum 8 and integrating functional genomics and pan-genetics, we show that gene duplication and…