Plant breeders must continuously generate new better yielding varieties more adapted to local conditions and specialized to specific industry needs. In addition, human food demand is starting to require better quality products which must satisfy essential nutritional requirements, new pre and pro-biotic functions, and low level of antinutritional factors. This constant change has transformed modern varieties into modular entities where genome pieces are moved to answer the needs of farmers and industry. Yellow lupin (L. luteus) has been proposed as an alternative source of protein given its high seed protein content and amino acid profiles. However, like several crops, yellow lupin suffers the presence of anti-nutritionals and limited levels of protein digestibility when included in animal diets. The main goal of this study was to identify lupin seed storage proteins with reduced levels of digestibility in rainbow trout (Oncorhynchus mykiss). By coupling 2D-PAGE gels and HPLC-MS/MS we were able to identify 49 and 47 low digestibility proteins in lupin flour and protein isolate, respectively. We have also developed a yellow lupin mutant population with the main aim to identify genotypes with reduced phytic acid content, one of the main anti-nutritionals in grain crops. So far, we have identify 15 independent mutants with low phytic acid content (<5.25mg/g dehulled seed). We are currently targeting and sequencing several genes previously associated with the phytic acid pathway to identify polymorphisms responsible of the seed phytic acid reduction.