Computational Molecular Biology 2025, Vol.15, No.2, 65-74 http://bioscipublisher.com/index.php/cmb 67 The situation on the carotenoid side is similar. Although BnaA09.ZEP and BnaC09.ZEP have names like structural genes, in fact, they are also silently regulating the proportion of different types of carotenoids. Once lacking, the balance of lutein and zeaxanthin is disrupted, and the flower color changes accordingly. 2.4 Epigenetic and environmental influences In fact, the color formation of B. napus is not entirely determined by genes themselves-epigenetic modifications and environmental factors often play a role. For example, although BnaA07.PAP2 is a crucial regulatory gene, if something is inserted into its promoter region, its expression may be enhanced, ultimately leading to an increase in pigment accumulation. The environment can also be quite "mixed in", as factors such as lighting, temperature, and exposure to drought or pests can all affect the synthesis of pigments. Take drought as an example. Although it may sound like a bad thing, it actually stimulates the accumulation of anthocyanins, helping plants enhance their antioxidant and stress resistance abilities (Chen et al., 2022). So you see, the matter of color is quite complicated. It depends not only on how genes are adjusted themselves, but also on how the external environment changes. The two sides blend together to form the color we see in the end. 3 Molecular Mechanisms in Brassica napus Flower Pigmentation 3.1 Recent advances in genomic studies When it comes to the research on the color formation mechanism of rape flowers in recent years, it is truly thanks to the progress of genomics and various omics methods. The combination of technologies such as metabolomics, BSA-seq and RNA-seq has helped us identify many key genes and metabolites involved in flower color formation. Take the research of Ye et al. (2022) for example. They found that there are both yellow carotenoids and red anthocyanins in apricot petals, while pink petals mainly accumulate colorless carotenoids and red anthocyanins-you see, color is not determined by a single pigment at all, but by the mixture of several components. Behind the scenes, there is a bunch of genes pulling at each other, and only then do the colors we see become visible. 3.2 Identification of candidate genes for pigmentation Now we already know quite a few genes related to the flower color of B. napus, although the mechanisms by which each of them functions are rather complex. For instance, the gene BnaA07.PAP2 is now generally regarded as the key to regulating anthocyanin synthesis-it is particularly active in both apricot and pink flowers. In addition, the formation of orange petals is actually closely related to BnaA09.ZEP and BnaC09.ZEP. If the functions of these two genes are deficient, lutein will increase, while zeaxanthin will decrease, and eventually the color will lean towards orange. Another point that cannot be overlooked is BnaA03.ANS, which is almost irreplaceable in red petals. Without it, red pigment could not accumulate at all. 3.3 Functional characterization using CRISPR-Cas9 and RNA interference Nowadays, technologies like CRISPR-Cas9 and RNA interference (RNAi) have really helped us a lot, allowing us to see more clearly how various genes in B. napus affect flower color. For example, someone used CRISPR to knock out the carotenoid isomerase gene BnaCRTTISO, and surprisingly, the petals turned creamy white and even the leaves appeared yellow-which effectively confirmed its role in carotenoid synthesis. Similarly, after silencing the BnaA03.ANS gene using RNAi, the original raspberry red petals became noticeably lighter in color, turning into rice red or even zinc yellow. This once again demonstrates how crucial this gene is for anthocyanin synthesis. To be honest, without these technologies, we might still be guessing what role these genes play. 3.4 Gene expression patterns across developmental stages In fact, to understand how a flower gradually shows its color, one really needs to look at how its genes work at different stages of development. The transcriptome data tells us that many genes related to the synthesis of carotenoids and flavonoids are not expressed from beginning to end-some are active in the early stage, while others come into play later. Jia et al. (2021) found that compared with white flowers, the total amount of carotenoids in yellow flowers was much higher throughout the development process, indicating that the color was not formed all at once but accumulated gradually. Genes like BnaPSY and BnaC4H are also quite interesting.
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