Environment-dependent genetic architecture of seed vigor reveals antagonistic allelic effects under water deficit in rapeseed (Brassica napus)

Abstract Background Seed vigor is the ability of seeds to germinate quickly and uniformly and produce seedlings capable of emerging under a wide range of environmental conditions. It is a key determinant of crop establishment, particularly under water limited conditions. However, the genetic architecture underlying seed vigor and its stability across environment remain poorly understood. This study aims to investigate the genetic basis of seed vigor under water deficit. This was achieved by using a panel of 192 rapeseed accessions encompassing winter, spring, and semi-winter genotypes, and by phenotyping germination capacity and speed under osmotic stress induced by polyethylene glycol (-0.5 MPa) using a high-throughput imaging platform. Results Genetic analyses identified 22 QTL associated with seed vigor related-traits, explaining between 1.2 and 13.1% of phenotypic variance. Germination speed and germination capacity traits were controlled by distinct genomic regions, although several co-localizations suggested shared genetic control of several components of seed germination. Evaluation of QTL stability across water regimes pointed out four significant QTL-by-environment interactions, revealing strong environmental dependency of allelic effects. Notably, favorable alleles under water deficit became unfavorable under optimal conditions, indicating antagonistic genetic effects across environments. Candidate gene analyses within environment-responsive QTL identified nine genes combining coding-sequence polymorphism and germination-associated expression pattern. Conclusion This study reveals a complex and environment-dependent genetic architecture of seed vigor and provides new targets for breeding oilseed rape varieties with improved germination under water-limited conditions.