PopAmaranth: a population genetic genome browser for grain amaranths and their wild relatives

The combination of genomic, physiological, and population genetic research has accelerated the understanding and improvement of numerous crops. For nonmodel crops, the lack of interdisciplinary research hinders their improvement. Grain amaranth is an ancient nutritious pseudocereal that has been domesticated three times in different regions of the Americas. We present and employ PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three-grain amaranth species (Amaranthus hypochondriacus, Amaranthus cruentus, and Amaranthus caudatus) and two wild relatives (Amaranthus hybridus and Amaranthus quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.html.