White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.

We report the first transcript profiling of a high-alkaloid lupin variety and identify a new alkaloid biosynthetic gene, thus accelerating the efforts to develop alkaloid-free lupin crops.

This review summarizes the different hypotheses surrounding the biosynthesis of quinolizidine alkaloids in lupins and discusses strategies for gene discovery and pathway elucidation.

Faba bean ( Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds ( 1 ). However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause hemolytic anemia (favism) in 400 million genetically predisposed individuals ( 2 ). Here, we use gene-to-metabolite correlations, gene mapping, and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1 . Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.