Unraveling the impact of plant-density genetic architecture on agronomic traits in canola.

Plant density defines vegetative architecture and competition for light between individuals. Brassica napus (canola), as a model system of indeterminate growth, presents a radically different plant architecture compared to traditional crops commonly cultivated at high density. Using a panel of 152 spring-type canola accessions and a double haploid (DH) population of 99 lines from a cross between Lynx and Monty, we performed Genome-Wide-Analysis-Studies (GWAS) and Quantitative Trait Locus (QTL) mapping for 12 growth and yield traits at two contrasting plant densities (15 and 60 plants m -2). We revealed mostly novel associations by GWAS (19) and QTLs (11) for growth and yield traits being the most significant for flowering, biomass, rosette height, silique and seed number, and grain yield; often representing density-independent signals although we also uncovered some density-dependent associations typically mapping at low density. Further RNA-seq transcriptomics revealed distinctive latent gene regulatory responses to simulated shade between Lynx and Monty. Given the phylogenetic relatedness, we additionally used Arabidopsis thaliana aiming at testing genes to validate density effects of homologous counterparts mapping into relevant rapeseed QTLs. Our results suggest that TCP1 may promote the growth independently of plant neighbors, while HY5 could increase biomass and seed yield specifically at high plant density. For flowering time, the observations in tested mutants suggested that the corresponding genes may plausibly contribute to promote flowering in plant-density dependent (i.e., PIN) and independent (i.e., FT, HY5 and TCP1) manner. This work underscores the advantages of using agronomic field experiments together with genetic and transcriptomic approaches to decipher quantitative complex traits that potentially mediate superior crop productivity.