Chloroplast genome assemblies and expanded maternal phylogeny for wild Brassica to advance conservation and pre-breeding
Crop wild relatives (CWRs) are vital reservoirs of genetic diversity for crop improvement, offering economically advantageous traits that enhance resilience, productivity, and nutritional value. The genus Brassica, which includes globally important oilseed, mustard, and vegetable crops, has benefited from many CWR introgressions. However, broader utilization of CWRs in breeding remains constrained by limited genomic resources, which are needed to provide taxonomic clarity and help overcome reproductive barriers. To address this limitation, we sequenced, assembled, and annotated the complete chloroplast genomes of 39 Brassica accessions representing 20 currently accepted wild species. The resources enabled us to construct the first Brassica chloroplast pangenome and identify nine informative polymorphisms to validate species id from genebanks or future collections. Additionally, they enabled us to create the most comprehensive molecular phylogeny of Brassica to date, revealing new insights into taxonomic relationships, including identification of B. deflexa as the most probable maternal progenitor of allotetraploid B. balearica, plus phylogenetic relationships of recently discovered (B. tardarae) or still uncharacterized wild Brassica (B. bourgeaui). The phylogeny also provides new perspectives on chromosome number evolution within Brassica and the taxonomic distinction of B. tardarae and B. mollis as autonomous species. Lastly, we characterized the presence of self-incompatibility, vernalization requirements, and annual vs biennial life cycles of the sequenced accessions. Together, these genomic and biological resources provide an integrated framework for accurate species identification, evolutionary inference, and informed crossing strategies in Brassica. This foundation will directly enable more efficient conservation, characterization, and deployment of Brassica CWRs in crop improvement programs.
Crop wild relatives (CWRs) are vital reservoirs of genetic diversity for crop improvement, offering economically advantageous traits that enhance resilience, productivity, and nutritional value. The genus Brassica, which includes globally important oilseed, mustard, and vegetable crops, has benefited from many CWR introgressions. However, broader utilization of CWRs in breeding remains constrained by limited genomic resources, which are needed to provide taxonomic clarity and help overcome reproductive barriers. To address this limitation, we sequenced, assembled, and annotated the complete chloroplast genomes of 39 Brassica accessions representing 20 currently accepted wild species. The resources enabled us to construct the first Brassica chloroplast pangenome and identify nine informative polymorphisms to validate species id from genebanks or future collections. Additionally, they enabled us to create the most comprehensive molecular phylogeny of Brassica to date, revealing new insights into taxonomic relationships, including identification of B. deflexa as the most probable maternal progenitor of allotetraploid B. balearica, plus phylogenetic relationships of recently discovered (B. tardarae) or still uncharacterized wild Brassica (B. bourgeaui). The phylogeny also provides new perspectives on chromosome number evolution within Brassica and the taxonomic distinction of B. tardarae and B. mollis as autonomous species. Lastly, we characterized the presence of self-incompatibility, vernalization requirements, and annual vs biennial life cycles of the sequenced accessions. Together, these genomic and biological resources provide an integrated framework for accurate species identification, evolutionary inference, and informed crossing strategies in Brassica. This foundation will directly enable more efficient conservation, characterization, and deployment of Brassica CWRs in crop improvement programs.
Institut national de recherche pour l'agriculture, l'alimentation et l'environnement