## 5 Conclusions  
This study is the first to use a GWAS in faba bean to dissect the genetic architecture of chemical compounds related to seed quality and off-flavours. We provided key breeding insights, including heritability estimates and genetic correlations (type-A and type-B), facilitating efficient multi-trait selection strategies. We identified 148 SNP loci for 14 traits in 2021 and 167 SNP loci for 15 traits in 2022. The detection of intragenic SNPs and short linkage disequilibrium decay (\(\sim\)268 Kbp) revealed promising candidate genes. Notably, we reported missense variants that may be causal polymorphisms affecting phenotypes. This research paves the way for validation studies and applications to improve seed quality and reduce off-flavours in faba bean. **Supplementary Materials:** The following supporting information can be downloaded at: [[https://www.mdpi.com/article/10.3390/plants14020193/s1](https://www.mdpi.com/article/10.3390/plants14020193/s1)]([https://www.mdpi.com/article/10.3390/plants14020193/s1](https://www.mdpi.com/article/10.3390/plants14020193/s1)), Figure S1: Distribution of marker missing data. Figure S2: Quantile-Quantile Plot (QQ) for protein content and off-flavours (2021). Figure S3: Quantile-Quantile Plot (QQ) for protein content and off-flavours (2022). Table S1: SNPs distribution and coverage along the six faba bean chromosomes. Table S2: Type-A additive genetic correlation and their approximated standard error estimated in 2021. Table S3: Type-A additive genetic correlation and their approximated standard error estimated in 2022. Table S4: GWAS-detected SNPs in 2021 and candidate genes. Table S5: GWAS-detected SNPs in 2022 and candidate genes. Table S6: Genomic inflation factors (\(\lambda\)) of the GWAS models. Table S7: Standards used for quantification. Table S8: Retention times and mass traces used for quantification. **Author Contributions:** A.L. : Writing--original draft, Conceptualization, Methodology, Formal analysis, Data curation, Visualization. B.H. : Writing--review and editing, Formal analysis, Data curation. V.A. : Writing--review & editing, Formal analysis, Data curation. C.d.J. : Writing--review and editing. L.P.: Project administration, Funding acquisition. J.P.: Writing--review and editing, Supervision; S.A.G. : Writing--review & editing, Supervision. L.M.T. : Writing--review and editing, Supervision, Project administration, Funding acquisition, Conceptualization. All authors have read and agreed to the published version of the manuscript. **Funding:** This research is part of project \"Pulses optimized for flavour and functionality\" co-financed by the Top Consortium for Knowledge and Innovation Agri & Food by the Dutch Ministry of Economic Affairs under contract number LWV19028. Website: [[https://www.wur.nl/en/research-results/research-funded-by-the-ministry-of-lvru/types-research/soorten-onderzoek/kennisonline/pulses-optimised-for-flavour-and-functionality.htm](https://www.wur.nl/en/research-results/research-funded-by-the-ministry-of-lvru/types-research/soorten-onderzoek/kennisonline/pulses-optimised-for-flavour-and-functionality.htm)]([https://www.wur.nl/en/research-results/research-funded-by-the-ministry-of-lvru/types-research/soorten-onderzoek/kennisonline/pulses-optimised-for-flavour-and-functionality.htm](https://www.wur.nl/en/research-results/research-funded-by-the-ministry-of-lvru/types-research/soorten-onderzoek/kennisonline/pulses-optimised-for-flavour-and-functionality.htm)), accessed on 15 November 2024. **Data Availability Statement:** The datasets containing sequencing data generated and analysed during the current study are available in the Genome Sequence Archive (GCA) repository under the accession number CRA017806, [[https://ngdc.cncb.ac.cn/gsa/browse/CRA017806](https://ngdc.cncb.ac.cn/gsa/browse/CRA017806)]([https://ngdc.cncb.ac.cn/gsa/browse/CRA017806](https://ngdc.cncb.ac.cn/gsa/browse/CRA017806)) (accessed on 15 November 2024). **Acknowledgments:** The authors extend their gratitude to the partners of the TKI Pulses project.