Brassica napus is an important cash crop broadly grown for the vegetable and oil values.  Yellow-seeded B. napus is preferred by breeders due to its improved oil and protein quality, less pigments and lignin compared with the black-seeded counterpart.  This study compared the differences in flavonoid and fatty acid contents between yellow rapeseed from the progenies of B. napus–Sinapis alba somatic hybrids and the black-seeded counterpart using RNA-seq analysis.  Through HPLC-PDA-ESI(−)/MS² analysis, it was found that phenylpropanoids and flavonoids (i.e., isorhamnetin, epicatechin, kaempferol, and other derivatives) in yellow seed were significantly lower than those in black seed.  The fatty acid (FA) content in yellow rapeseed was higher than that in black rapeseed due to the variation of C16:0, C18:0, C18:1, C18:2, and C18:3 contents.  RNA-seq analysis of seeds at four and five weeks after flowering (WAF) indicated that differentially expressed genes (DEGs) between black and yellow rapeseeds were enriched in flavonoid and FA biosynthesis, including BnTT3, BnTT4, BnTT18, and BnFAD2.  Also, genes related to FA biosynthesis, desaturation and elongation (FAD3, LEC1, FUS3, and LPAT2) in yellow seed were up-regulated compared to those in black seed, while genes involved in beta-oxidation cycle (AIM1 and KAT2) of yellow seed were down-regulated compared to those in black seed.  The DEGs related to the variation of flavonoids, phenylpropanoids, and FAs would help improve the knowledge of yellow seed character in B. napus and promote rapeseed improvement.

    DNA methylation, an important epigenetic modification, serves as a key function in the polyploidization of numerous crops. In this study, early generations of resynthesized Brassica napus (F₁, S₁–S₃), ancestral parents B. rapa and B. oleracea were analyzed to characterize their DNA methylation status during polyploidization, applying DNA methylation-sensitive amplification polymorphism (MSAP) and high-performance liquid chromatography methods. In F₁, 53.4% fragments were inherited from both A- and C-genomes. Besides, 5.04 and 8.87% fragments in F₁ were inherited from A- and C- genome, respectively. 5.85 and 0.8% fragments were newly appeared and disappeared in resynthesized B. napus, respectively. 13.1% of these gene sites were identified with methylation changes in F₁, namely, hypermethylation (7.86%) and hypomethylation (5.24%). The lowest methylation status was detected in F₁ (38.7%) compared with in S₁–S₃. In S₃, 40.32% genes were methylated according to MSAP analysis. Sequencing of methylated fragments indicated that genes involved in multiple biological processes were modified, including transcription factors, protein modification, and transporters. Expression ananlysis of DNA methyltransferase 1 and DNA methyltransferase chromomethylase 3 in different materials was consistent to the DNA methylation status. These results can generally facilitate dissection of how DNA methylation contributes to genetic stability and improvement of B. napus during polyploidization.

 Drought is one of the major environmental constraints that significantly affects seedling emergence, yield, and quality of Tartary buckwheat, thereby hindering the development of its industry.  However, the molecular mechanisms underlying drought tolerance genes in Tartary buckwheat remain largely unexplored.  Alcohol dehydrogenase (ADH), one of the essential plant proteins, plays a crucial role in growth, development, and stress responses, but its specific role in drought resistance is still unclear.  In this study, we identified an ADH gene FtADH1, using a membership function value of drought tolerance (MFVD) combined with a genome-wide association study (GWAS) and transcriptomic profiles that confers drought tolerance in Tartary buckwheat. Our findings demonstrated that the overexpression of FtADH1 in Arabidopsis and Tartary buckwheat hairy roots enhances drought tolerance by promoting root elongation and mitigating elevated levels of reactive oxygen species (ROS).  Our findings demonstrated that FtADH1 can enhanced tolerance to drought stresses in both Tartary buckwheat and Arabidopsis.  This study identifies the FtADH1 as a new player in affecting ROS level and the stress response of Tartary buckwheat by regulating protective enzyme activities at a high level to scavenge ROS and modulating root growth under drought stress.  Further, we identified proteins interacting with FtADH1 through a prokaryotic expression pull-down assay combined with mass spectrometry, revealing that FtADH1 specifically interacts with the S-adenosyl-L-methionine (SAM) synthetase protein, FtSAMS1.  Overexpression of FtSAMS1 was found to enhance ADH enzymatic activity, leading to increased SAM content in overexpressing Tartary buckwheat hairy roots under water-deficit conditions.  Additionally, FtSAMS1 overexpression induced a drought-resistant phenotype in Arabidopsis and Tartary buckwheat hairy roots under drought stress, revealing the biological function of FtADH1. Evolutionary analysis indicates that ADH1 in Fagopyrum species has undergone significant evolutionary events, including duplication and purifying selection, which may contribute to functional diversification and adaptive advantages such as drought resistance in cultivated buckwheat.  In summary, this study proposes that FtADH1 is a key contributor to drought tolerance, and its interaction with FtSAMS1 holds potential for the development of drought-resistant varieties in Tartary buckwheat and its relative species.