Elucidating the molecular basis of natural variation in complex traits is the key for their effective management in crops or natural systems. This review focuses on plant variation. It will first, show that genetic modifications causing major alterations in polygenic phenotypes often hit targets within an array of 'candidate genes', second, present new methods that include mutations of all effect sizes, and help exhaustively describe the molecular systems underlying complex traits, and third, discuss recent findings regarding the role of epigenetic variants, which in plants are often maintained through both mitosis and meiosis. Exploring the whole spectrum of mutations controlling complex traits is made possible by the combination of genetic, genomic and epigenomic approaches.
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