Since the highest phenotypic variation in the Z114 × M305 mapping population was found for ADF/NDF and SCC, the strongest emphasis on the identification of candidate genes was made for genes known to be involved in carbohydrate metabolism and flavonoid biosynthesis. In the
qGLS-A02 region, one of the identified genes, Korrigan2 (
KOR2), encodes endo-1,4-β-d-glucanase, known to be involved in cellulose synthesis
[18,43][32][33]. Interestingly, the same region of chromosome A02 was found to be correlated with seed fibre in a study performed by Miao
[11]. The interesting candidate genes underlying QTL regions on chromosome A04 include pectin methylesterase (
BnaA04g27070D) and pectin lyase-like protein (
BnaA04g25420D). The presence of SNP variation in these genes and their relatively close physical locations from the QTL (100–500 kbp) indicates that they are very likely regulators of fibre composition in
B. napus seeds. Another gene,
BnaA04g03060D, located 10 kbp from
qGLS-A04, encodes β-1,3-glucanase 3, glycoside hydrolase, which functions in cell wall degradation
[19][34]. Other interesting genes underlying QTL on chromosome C08 include cellulase, glycosyl hydrolase family 5
GH5, and UDP-glycosyl transferase
UGT73C7, which are known to be involved in carbohydrate metabolic process and cell wall lignification
[27,30][35][36]. Another strong candidate is peroxidase 64 (
PRX64) (
BnaC07g05860D), located 173 kbp from the
qSCC/ADF-C07, the major oxidase enzyme known to play a role in proanthocyanidins and lignin biosynthesis
[9,25,28,43][9][29][30][33]. RING-type E3 ubiquitin transferase (
CMPG1) (
BnaC07g05860D) with two SNPs located 16,6 kbp from the QTL. These genes are known to play a role in lignin biosynthesis and response to chitin
[21,29,44][37][38][39]. A key gene found to be correlated with seed colour in previous studies, namely transparent testa 12 (
TT12), was not identified in this study.
TT12 encodes a multidrug and toxic compound extrusion (MATE) secondary transporter that is specifically expressed in the developing seed coat and is involved in the transportation of proanthocyanidin precursors into the vacuole
[45][40]. It was found that the
BnaC06g17050D gene, which is orthologous to Arabidopsis
TT12, is associated with seed coat colour in oilseed rape
[4]. However, we could not find any association between this gene and SCC in the present study.
3. Conclusions
In conclusion, a QTL genetic mapping study using an NGS SkimGBS approach allowed us to identify several promising genes, including PE, PLL, TT10/LAC15, SUS2, and GH5, which provides insight into the complex genetic architecture of seed fibre and colour biosynthesis in B. napus. Understanding the mechanism of action and causal polymorphisms of these genes will provide a better understanding of the role of those genes in the regulation of complex traits affecting RSM quality.