*2.4. Identification of Candidate Genes*

The LD blocks harboring the peak SNPs were mined for genes relevant to MC and HC using the *L. usitatissimum* v.1.0 reference genome. A total of 204 and 118 candidate genes were identified for MC and HC, respectively (Table 2 and Table S2). Several genes ascribed to carbohydrate metabolism, seed mucilage synthesis, modification, and release, and cell wall synthesis and modification were identified at the MC QTL loci (Table 2). Five particularly promising candidate genes were identified. The SNP marker Lu3-26033342 was located 58.92 and 49.60 kb from Lus1007101 and Lus10007083 that encode the ortholog of *A. thaliana*'s *TRANSPARENT TESTA 8* (*TT8*) and *SUBTILISIN-LIKE SERINE PROTEASE* (*SBT1.7*) (Figure S5a, Table 2). In another independent QTL on chromosome 3, the SNP marker Lu3-25559600 was located 64.41 and 67.02 kb from Lus10009311 and Lus10009288 that encode the ortholog of *A. thaliana*'s *GALACTUROSYL TRANSFERASE-LIKE 5* (*GATL5*) and *MUCILAGE-MODIFIED 4* (*MUM4*). On chromosome 5, Lu5-3508878 is located 100.78 kb from Lus10008285, an ortholog of another *A. thaliana* gene implicated in mucilage transcriptional regulation, *NAC-REGULATED SEED MORPHOLOGY 1* (*NARS1*) (Figure S5a, Table 2).



Genes related to embryo, endosperm, and seed coat development, cell wall biogenesis/degradation, anthocyanin biosynthesis, and seed dormancy, were found at QTL loci associated with HC (Table 2 and Table S2). Among the relevant candidate genes, Lus10035456 encodes the ortholog of *A. thaliana*'s *AGAMOUS-LIKE MADS-BOX PROTEIN AGL62* (*AGL62*) and is located 11.40 kb from the SNP marker Lu7-6577527 (Figure S5b, Table 2). On chromosome 12, Lu12-5267706 was situated 39.93 kb from Lus10018306 that encodes the ortholog of *A. thaliana*'s *GLYCOSYL HYDROLASE FAMILY 17* (*GH17*). Two other interesting candidate genes, Lus10026902 and Lus10026926, were situated 96.87 and 238.19 k, respectively, from the SNP marker Lu13-2803224. Lus10026902 and Lus10026926 encode the ortholog of *A. thaliana*'s *LARIAT DEBRANCHING ENZYME* (*DBR1*) and *UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE* (*UGT79B1*), respectively.
