Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility

Common buckwheat (Fagopyrum esculentum) is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F. esculentum var.homotropicum, a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (F.esculentum) and Tartary buckwheat (F.tataricum), underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat, including FhFAR genes, is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation