| Rapeseed(Brassica napus L.) is an important oil crop in the world. Anti-nutrients are abundant in seeds of Brassica napus, mainly including polyphenolics, lignin, fiber, glucosinolates, and phytic acid. The existence of these anti-nutrients greatly affects the quality of rapeseed oil, as well as the nutritional value of rapeseed meal. Comparing with black-seeded rapeseed cultivars, yellow-seeded rapeseed has several advantages, including lower polyphenols, lignin and fiber contents, higher protein and oil contents. Thus, development of rapeseed with yellow seed character, as well as the dissection of yellow-seeded related molecular mechanism, is significant to rapeseed breeding. In this research, we used the yellow seed lines selected from somatic hybrids of B. napus and Sinapis alba as plant material, which were the first reported yellow seed introgression lines from related genus of Brassica. Here, the metabolites of seed were analyzed to look into the molecular mechanism of yellow seed phenotype.To compare the secondary metabolites in yellow-and black-seeded rapeseeds, we applied the most developed facilities to analyze the quality of different B. napus lines. Firstly, we tried to figure out the best extraction methods for polypenols, and found80%acetone combining ultrasonic decomposition in room temperature results the highest extraction efficiency. Secondary, crude phenolic compounds extracted from rapeseed were subjected to column chromatography, alkaline hydrolysis, and HPLC-PDA-ESI(-)/MS"/HRMS analysis. A total of91flavonoids and hydroxycinnamic acid derivatives were detected, including39kaempferol derivatives,11isorhamnetin derivatives,5quercetin derivatives,6flavanols and its oligomers, and30hydroxycinnamic acid derivatives. A total of78of these chemicals were identified tentatively, of which55were first reported in B. napus and24were first detected in Brassica. Thirdly, according to the histochemical studies, chemical analysis and HPLC-PDA-ESI(-)/MSn/HRMS analysis, we divided polyphenols in rapeseed into three categories, flavonols, hydroxycinnamic acids and proanthocyanidins (including monocharged oligomers of epicatechin). And hydroxycinnamic acids were the most abundant polyphenols in rapeseeds, the content of which were similar in yellow-and black-seeded rapeseeds. However, accumulation of proanthocyanidins and flavonols in yellow-seeded rapeseeds was quite different to black-seeded rapeseeds. We also observed significant differences of polyphenol contents in different colored rapeseeds, and some of these discrepancies might be more than ten times (such as epicatechin). We also applied gas chromatography mass spectrometry to analyse fatty acids in developmental seeds of yellow-and black-seeded B. napus. Accumulation of fatty acid during seed development of yellow-and black-seeded B. napus was quite similar, which was increased gradually in the early developmental stages and decreased at5WAF (weeks after flowering), then finally increased during maturation. Besidses, in comparison of fatty acid content in yellow-and black-seeded B. napus, we found the content of each fatty acid component in yellow seed was generally higher than black rapeseeds. Finally, we used ATR-FTIR and NMR analysis to reveal the different lipids, proteins, lignin and fiber contents in different yellow seed lines and the black seed parent line. And we found these quality characters of yellow seed lines were somehow in between B. napus and S. alba.According to the comparison of polyphenols, fatty acids, lipids, proteins, lignin and fiber components in yellow-and black-seeded B. napus, the yellow seed lines applied in this research could be considered as a improved rapeseed material with higher protein and oil content, as well as lower polyphenols. Meanwhile, the expression value of genes functioned in flavonoid biosynthesis pathway greatly correlates with the variation of flavonoid contents in different B. napus lines.
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