PopAmaranth is a population genetic genome browser allowing including 5 amaranth species:
Many underutilized crops are characterized by high nutritional quality and resilience to abiotic stress, but their yield and agronomic properties are significantly lower compared to major crops. The last decades of genomic, physiological, and population genetic research provide the opportunity to transfer methods to minor crops to accelerate their improvement if knowledge is effectively shared between disciplines. Grain amaranth is an ancient nutritious pseudocereal from the Americas that is regaining importance due to its high protein content and favorable amino acid and micronutrient composition. To effectively combine genomic and population genetic information with molecular genetics, plant physiology, and use it for interdisciplinary research and crop improvement, an intuitive interaction for scientists across disciplines is essential. Here, we present PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three grain amaranth species (A. hypochondriacus, A. cruentus, and A. caudatus) and two wild relatives (A. hybridus and A. quitensis) along the A. hypochondriacus reference sequence. We provide population scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We incorporate the domestication history of the three grain amaranths to provide an evolutionary perspective for candidate genes. We show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for converged saponin reduction between amaranth and quinoa. These examples show that our tool enables the detailed study of individual genes, provides target regions for breeding efforts, and can enhance the interdisciplinary integration of population genomic findings across species.