Key message Heterosis QTLs, including qSS7 and qHD8, with dominance effects were identified through GBS and large-scale phenotyping of CSSLs and hybrid F 1 populations in a paddy field. Abstract Heterosis has contributed immensely to agricultural production, but its genetic basis is unclear. We evaluated dominance effects by creating two hybrid populations: a B-homo set with a homozygous background and heterozygous chromosomal...